From Postmaster at conviron.com Mon Mar 1 06:12:12 2004 From: Postmaster at conviron.com (Postmaster@conviron.com) Date: Mon Mar 1 06:21:14 2004 Subject: [Bioperl-l] MDaemon Notification -- Attachment Removed Message-ID: The following message contained restricted attachment(s) which have been removed: >From : bioperl-l@bioperl.org To : backup@conviron.com Subject : Re: Hello Message-ID: Attachment(s) removed: ----------------------------------------- your_picture.pif From Postmaster at conviron.com Mon Mar 1 06:12:12 2004 From: Postmaster at conviron.com (Postmaster@conviron.com) Date: Mon Mar 1 06:21:15 2004 Subject: [Bioperl-l] MDaemon Notification -- Attachment Removed Message-ID: The following message contained restricted attachment(s) which have been removed: >From : bioperl-l@bioperl.org To : ed@conviron.com Subject : Re: Hello Message-ID: Attachment(s) removed: ----------------------------------------- your_picture.pif From avilella at ebi.ac.uk Mon Mar 1 07:53:55 2004 From: avilella at ebi.ac.uk (avilella) Date: Mon Mar 1 08:00:16 2004 Subject: [Bioperl-l] Bio::PopGen::Statistics discrete calculations Message-ID: <1078145634.5352.29.camel@localhost.localdomain> Hi, I'm interested in calculating some of the statistics in Bio::PopGen::Statistics in a discrete, position-wise, way. For example, I've done a quick implementation of the method "pi" that returns the value of the statistic for each polymorphic positions instead of the mean of all of them. It's "pi_discrete" method: http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-live/Bio/PopGen/Statistics.pm?rev=1.4&content-type=text/x-cvsweb-markup I would also like to have methods to do Sliding Window calculations for these statistics. Something like: "Calculate tajima_D for windows of 100 polymorphisms that slide 10 positions" Any comments about the logic, naming, interest of this methods? Thanks, Albert. -- Albert Vilella Bertran avilella_at_ebi_ac_uk EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom Phone: +44 (0)1223 494 448 FAX: +44 (0)1223 494 468 From bazin at univ-montp2.fr Mon Mar 1 07:57:06 2004 From: bazin at univ-montp2.fr (Eric Bazin) Date: Mon Mar 1 08:02:01 2004 Subject: [Bioperl-l] load_seqdatabase.pl problem References: <403B9762.1060007@univ-montp2.fr> Message-ID: <40433322.2080403@univ-montp2.fr> Hi. I try to import embl sequence datas in a biosql schema using the perl script "load_seqdatabase.pl". Previously I loaded without any problem the taxon schema from the NCBI with load_ncbi_taxonomy.pl. Can anybody give me a help for this? This is what I received: bash#./load_seqdatabase.pl --dbname polymorphix --format embl /home/eric/polybase.dat Could not store AB022832: ------------- EXCEPTION ------------- MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 3 rows instead of 1. Query was [name_class="scie ntific name",binomial="Aspergillus oryzae"] STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Ba sePersistenceAdaptor.pm:960 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Bas ePersistenceAdaptor.pm:856 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence Adaptor.pm:183 STACK Bio::DB::Persistent::PersistentObject::create /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj ect.pm:243 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence Adaptor.pm:170 [root@thaler biosql]# :BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceA daptor.pm:253 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObje ct.pm:270 STACK (eval) ./load_seqdatabase.pl:517 STACK toplevel ./load_seqdatabase.pl:500 -------------------------------------- Thanks a lot Eric bazin From avilella at ebi.ac.uk Mon Mar 1 08:33:33 2004 From: avilella at ebi.ac.uk (avilella) Date: Mon Mar 1 08:39:58 2004 Subject: [Bioperl-l] new Bio::Installer modules in bioperl-run Message-ID: <1078148013.5352.42.camel@localhost.localdomain> Hi, I've been playing with a set of modules to make the installation of bioperl external programes easier. These are modules with methods to basically download, decompress, compile and install the program that is meant to be called by bioperl. For example, for TCoffee, there would be a script in bioperl-run/scripts like: install_tcoffee.PLS ------------------- use strict; use Bio::Installer::TCoffee; # Install in the directory where the script is called use Cwd; my $destination_install_dir = getcwd; my $installer = new Bio::Installer::TCoffee( -destination_install_dir => $destination_install_dir); $installer->download(); $installer->install(); 1; -------------------- that would download, decompress and compile TCoffee to the preferred directory. Feedback is welcomed, Thanks, Albert. From todd.harris at cshl.edu Mon Mar 1 08:56:00 2004 From: todd.harris at cshl.edu (Todd Harris) Date: Mon Mar 1 09:01:55 2004 Subject: [Bioperl-l] new Bio::Installer modules in bioperl-run In-Reply-To: <1078148013.5352.42.camel@localhost.localdomain> Message-ID: Hi Albert - This would be a nice convenience. Do these handle the (potentially) many system-dependent issues as well? Or can you just generically pass configure/make/test/install paramaters to the installer object? Also, a superclass would be nice that creates an installer factory for those wishing to build lots of things from a single script. todd > On 3/1/04 7:33 AM, avilella wrote: > Hi, > > I've been playing with a set of modules to make the installation of > bioperl external programes easier. > > These are modules with methods to basically download, decompress, > compile and install the program that is meant to be called by bioperl. > > For example, for TCoffee, there would be a script in bioperl-run/scripts > like: > > install_tcoffee.PLS > ------------------- > use strict; > use Bio::Installer::TCoffee; > > # Install in the directory where the script is called > use Cwd; > my $destination_install_dir = getcwd; > my $installer = new Bio::Installer::TCoffee( > -destination_install_dir => > $destination_install_dir); > $installer->download(); > $installer->install(); > > 1; > -------------------- > > that would download, decompress and compile TCoffee to the preferred > directory. > > Feedback is welcomed, > > Thanks, > > Albert. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From avilella at ebi.ac.uk Mon Mar 1 09:14:53 2004 From: avilella at ebi.ac.uk (avilella) Date: Mon Mar 1 09:21:22 2004 Subject: [Bioperl-l] new Bio::Installer modules in bioperl-run In-Reply-To: References: Message-ID: <1078150493.5352.88.camel@localhost.localdomain> On Mon, 2004-03-01 at 13:56, Todd Harris wrote: > Hi Albert - > > This would be a nice convenience. > > Do these handle the (potentially) many system-dependent issues as well? Nope. It only checks for: ($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i) or strictly: /linux/ at the points where it does system-dependent calls... for the moment. Has bioperl an estimate of XX% of OSes where is mostly installed/used? > Or > can yo > u just generically pass configure/make/test/install paramaters to the > installer object? Also, a superclass would be nice that creates an installer > factory for those wishing to build lots of things from a single script. There is a Bio::Installer::Generic for the common calls, like ("tar xzf package.tar.gz")... But very "simplistic" right now... http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-run/Bio/Installer/ Still tweaking and adding some bits, Albert. > > todd > > > On 3/1/04 7:33 AM, avilella wrote: > > > Hi, > > > > I've been playing with a set of modules to make the installation of > > bioperl external programes easier. > > > > These are modules with methods to basically download, decompress, > > compile and install the program that is meant to be called by bioperl. > > > > For example, for TCoffee, there would be a script in bioperl-run/scripts > > like: > > > > install_tcoffee.PLS > > ------------------- > > use strict; > > use Bio::Installer::TCoffee; > > > > # Install in the directory where the script is called > > use Cwd; > > my $destination_install_dir = getcwd; > > my $installer = new Bio::Installer::TCoffee( > > -destination_install_dir => > > $destination_install_dir); > > $installer->download(); > > $installer->install(); > > > > 1; > > -------------------- > > > > that would download, decompress and compile TCoffee to the preferred > > directory. > > > > Feedback is welcomed, > > > > Thanks, > > > > Albert. > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > From crabtree at tigr.org Mon Mar 1 10:02:10 2004 From: crabtree at tigr.org (Jonathan Crabtree) Date: Mon Mar 1 10:08:53 2004 Subject: [Bioperl-l] bioperl graphics In-Reply-To: <200402271638.37134.lstein@cshl.edu> References: <1077720594.403cb61235be7@webmail.njit.edu> <403CD165.4090309@tigr.org> <200402271638.37134.lstein@cshl.edu> Message-ID: <40435072.8050206@tigr.org> Hi Lincoln- Thanks for the quick response. I thought there must have been a good reason for using colorAllocate(), but now I'm not sure that this is true. I've been able to generate valid SVG documents using GD::SVG and a copy of Bio::Graphics::Panel modified in the way that I described to Haibo, so I don't think that my proposed change breaks SVG output outright. I've been using GD-SVG-0.25, which already supports colorResolve(). Here are lines 292-297 of SVG.pm: sub GD::SVG::Image::colorResolve { my ($self,$r,$g,$b) = @_; ###GD###my $index = $self->{gd}->colorResolve($r,$g,$b); my $index = $self->colorAllocate($r,$g,$b); return $index; } I haven't looked at any past versions of GD::SVG, however, so perhaps this is a recent change. I do like your suggestion about using multiple GD::Image objects and then copying the various Panel GD::Images into a single target GD::Image. However, this approach definitely won't work with GD::SVG, which does not yet support any of the GD image copying methods (AFAIK, again based on the GD-SVG-0.25 code that I grabbed from CPAN.) I'm not crazy about my current method, which involves manipulating pad_left, pad_top, etc., to arrange the various Bio::Graphics::Panels in their appropriate locations. On the other hand, the API for Bio::Graphics::Panel does explicitly support the use of an externally-supplied GD::Image object when calling gd(), so I don't feel as though I'm abusing the module too much. Using a single GD::Image (or SVG::GD::Image) also makes for a (marginally!) faster and more space-efficient solution. Regards, Jonathan Lincoln Stein wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >Sorry, but if you change colorAllocate() to colorResolve(), you will >break the ability to generate publication-quality images with >GD::SVG. Perhaps Todd Harris will add colorResolve() to a future >version of GD::SVG, in which case I will make the suggested change to >Bio::Graphics. > >I would recommend instead making two Bio::Graphics::Panel objects, and >generating a pair of GD objects (using the Panel->gd() method). Then >you can combine them onto a third GD object in whatever geometry you >want by using GD->copy() > >Lincoln > >On Wednesday 25 February 2004 06:46 pm, Jonathan Crabtree wrote: > > >>Haibo- >> >>hz5@njit.edu wrote: >> >> >>>Is there any way to render 2 Bio::Graphics::Panel into one png >>>image? because I want 2 different arrows with different labeled >>>coordinates on the same image and align to the left, but one >>>Panel can only have one coordinates system. >>> >>> >>The answer is yes, with a couple of caveats. The first is that you >>will have to take care of the layout of the individual >>Panel-generated images. If you're left-justifying everything then >>this should be easy enough. The second is that I would recommend >>making a one-line change to Bio/Graphics/Panel.pm, to prevent the >>package from trying to allocate the same set of colors twice (when >>you reuse the same GD object to draw the two different parts of the >>image.) Search for the following piece of code in Panel.pm (at >>line 411 in bioperl-1.4, I think): >> >> for my $name ('white','black',keys %COLORS) { >> my $idx = $gd->colorAllocate(@{$COLORS{$name}}); >> $translation_table{$name} = $idx; >> } >> >>Change "colorAllocate" to "colorResolve"; this should have no >>effect on any existing Bio::Graphics code (AFAIK) and will allow >>you to do your two (or three or four)-Panel trick. (As an aside, >>I'd like to lobby for this one-line change to be made in a future >>version of >>Bio::Graphics::Panel, for precisely this reason.) In any case, >>once you've made that change and reinstalled your copy of Bioperl, >>here is a rough outline of what you need to do: >> >>1. Set up your individual Bio::Graphics::Panel objects (e.g. $p1, >>$p2, $p3, etc.) as desired to draw your images, but do *not* call >>the gd method on any of them yet. >> >>2. Create a GD::Image object big enough to hold the images that >>will be drawn by $p1, $p2, $p3, etc.: >> my $gdImg = GD::Image->new($fullWidth, $fullHeight); >>(Note: use $p1->width(), $p1->height(), etc., to determine what >>$fullWidth and $fullHeight should be, based on your desired Panel >>layout algorithm.) >> >>4. Use a "dummy" Bio::Graphics::Panel object to allocate all your >>colors (this is an optional step; I do this because my code does >>some drawing that isn't handled by Bio::Graphics::Panel, and want >>to make sure that the palette has been allocated before I start): >> >> my $dummyPanel = Bio::Graphics::Panel->new(-length => 100, >>-offset => 0, -width => $fullWidth); >> $dummyPanel->gd($gdImg); # forces color allocation >> >>5. Draw the individual panels and generate your png image: >> >> $p1->gd($gdImg); >> $p2->gd($gdImg); >> my $pngData = $gdImg->png(); >> >>I've glossed over some of the details here, for example the fact >>that you may need to know the value of $p1->height() before you can >>initialize $p2, but that's the basic idea. I've been using this >>method to generate some comparative sequence displays and while >>it's definitely a bit of a hack, it works well in practice. You >>can also do the same thing with a GD::SVG::Image if you'd like to >>generate SVG output. Good luck, >> >>Jonathan >> >> >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > >- -- >Lincoln D. Stein >Cold Spring Harbor Laboratory >1 Bungtown Road >Cold Spring Harbor, NY 11724 >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.2.1 (GNU/Linux) > >iD8DBQFAP1Zt0CIvUP7P+AkRAreyAJ0XIcjMDeT/Bw69OBOEhD8tsznP+QCfVLWo >+RnQaijXxPlVWTbmjTkbHYw= >=lN1U >-----END PGP SIGNATURE----- > > From jegreenwood25 at hotmail.com Mon Mar 1 10:28:13 2004 From: jegreenwood25 at hotmail.com (Jonathan Greenwood) Date: Mon Mar 1 10:34:07 2004 Subject: [Bioperl-l] Question Message-ID: Hi there, I made a png file with clickable glyphs, now instead of having the description of the feature underneath the glyph, I would like to make it appear as those pop-up boxes that appear when you place the cursor over the glyph. So far the code works but it only takes the first assigned value and ignores the rest(which is a problem if there is more than one of the same feature). Please help!! Sincerely, Jonathan Greenwood email: jegreenwood25@hotmail.com Code: #! /usr/local/bin/perl -w use strict; use Bio::Graphics; use Bio::SeqIO; use Bio::SeqFeature::Generic; use CGI qw / :standard /; use CGI::Pretty; my $io = Bio::SeqIO->new(-file => 'x65306.gb', -format => 'Genbank'); my $seq = $io->next_seq; my $wholeseq = Bio::SeqFeature::Generic->new(-start=>1, -end=>$seq->length); my @features = $seq->all_SeqFeatures; # sort features by their primary tags my %sorted_features; for my $f (@features) { my $tag = $f->primary_tag; push @{$sorted_features{$tag}},$f; } my $panel = Bio::Graphics::Panel->new(-length => $seq->length, -width => 1000, -pad_left => 10, -pad_right => 10, -key_style => 'none', -spacing => -0.25, -box_subparts => 'true' ); $panel->add_track($wholeseq, -glyph => 'arrow', -bump => +1, -double => 1, -tick => 2 ); # special feature if ($sorted_features{CDS}) { $panel->add_track($sorted_features{CDS}, -glyph => 'transcript2', -bgcolor => 'orange', -bump => 0, -height => 12, -title => cds_parsing(), -link => 'http://mgcheo.med.uottawa.ca/cgi-bin/feature.pl#CDS/', ); delete $sorted_features{'CDS'}; } # general case my @colors = qw(wheat blue yellow green cyan purple chartreuse magenta gray); my $idx = 0; for my $tag (sort keys %sorted_features) { my $features = $sorted_features{$tag}; delete $sorted_features{source}; $panel->add_track($features, -glyph => 'generic', -bgcolor => $colors[$idx++ % @colors], -fgcolor => 'black', -bump => 0, -height => 12, -title => other_parsing(), -link => '/cgi-bin/feature.pl', ); } my ($url,$map,$mapname) = $panel->image_and_map(-url => 'tmpfiles'); print "Content-type: text/html\n\n"; print <

These links don't function in the way they are supposed to...

$map END_OF_SCRIPT exit 0; sub cds_parsing { my $seqio_object = Bio::SeqIO->new(-file => 'x65306.gb'); my $seq_object = $seqio_object->next_seq; foreach my $feat_object ($seq_object->get_SeqFeatures) { if ($feat_object->primary_tag eq "CDS") { foreach my $val ($feat_object->get_tag_values('product')){ if ($feat_object->has_tag('product')) { return $val; } } } } } sub other_parsing { return "Still needs some work"; } _________________________________________________________________ Protect your PC - get McAfee.com VirusScan Online http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963 From todd.harris at cshl.edu Mon Mar 1 10:43:37 2004 From: todd.harris at cshl.edu (Todd Harris) Date: Mon Mar 1 10:49:44 2004 Subject: [Bioperl-l] bioperl graphics In-Reply-To: <40435072.8050206@tigr.org> Message-ID: > On 3/1/04 9:02 AM, Jonathan Crabtree wrote: Hi Jason - Well, that's great news! I couldn't remember if I had added colorResolve to GD::SVG. Whoops! As you can see, it's something of a kludge, but I'm glad to hear that it works for you. Regarding Lincoln's suggestion of copying images, correct me if I'm wrong, but I interpreted that to mean copying the images OUTSIDE of Bio::Graphics::Panel. That is, create your Panel, fetch it, then paste it where appropriate into a new GD::Image with the appropriate dimensions. To avoid the method-overriding aspects of GD::SVG, this might need to be done within a separate package or eval block. I'm planning a significant upgrade to GD::SVG over the next few weeks that should 1) enable parallel creation of a GD object; 2) make it compatible with more current GD methods, and 3) make it more robust for future methods. t > > Hi Lincoln- > > Thanks for the quick response. I thought there must have been a good > reason for using colorAllocate(), but now I'm not sure that this is > true. I've been able to generate valid SVG documents using GD::SVG and > a copy of Bio::Graphics::Panel modified in the way that I described to > Haibo, so I don't think that my proposed change breaks SVG output > outright. I've been using GD-SVG-0.25, which already supports > colorResolve(). Here are lines 292-297 of SVG.pm: > > sub GD::SVG::Image::colorResolve { > my ($self,$r,$g,$b) = @_; > ###GD###my $index = $self->{gd}->colorResolve($r,$g,$b); > my $index = $self->colorAllocate($r,$g,$b); > return $index; > } > > I haven't looked at any past versions of GD::SVG, however, so perhaps > this is a recent change. > > I do like your suggestion about using multiple GD::Image objects and > then copying the various Panel GD::Images into a single target > GD::Image. However, this approach definitely won't work with GD::SVG, > which does not yet support any of the GD image copying methods (AFAIK, > again based on the GD-SVG-0.25 code that I grabbed from CPAN.) I'm not > crazy about my current method, which involves manipulating pad_left, > pad_top, etc., to arrange the various Bio::Graphics::Panels in their > appropriate locations. On the other hand, the API for > Bio::Graphics::Panel does explicitly support the use of an > externally-supplied GD::Image object when calling gd(), so I don't feel > as though I'm abusing the module too much. Using a single GD::Image (or > SVG::GD::Image) also makes for a (marginally!) faster and more > space-efficient solution. Regards, > > Jonathan > > > Lincoln Stein wrote: > >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> Sorry, but if you change colorAllocate() to colorResolve(), you will >> break the ability to generate publication-quality images with >> GD::SVG. Perhaps Todd Harris will add colorResolve() to a future >> version of GD::SVG, in which case I will make the suggested change to >> Bio::Graphics. >> >> I would recommend instead making two Bio::Graphics::Panel objects, and >> generating a pair of GD objects (using the Panel->gd() method). Then >> you can combine them onto a third GD object in whatever geometry you >> want by using GD->copy() >> >> Lincoln >> >> On Wednesday 25 February 2004 06:46 pm, Jonathan Crabtree wrote: >> >> >>> Haibo- >>> >>> hz5@njit.edu wrote: >>> >>> >>>> Is there any way to render 2 Bio::Graphics::Panel into one png >>>> image? because I want 2 different arrows with different labeled >>>> coordinates on the same image and align to the left, but one >>>> Panel can only have one coordinates system. >>>> >>>> >>> The answer is yes, with a couple of caveats. The first is that you >>> will have to take care of the layout of the individual >>> Panel-generated images. If you're left-justifying everything then >>> this should be easy enough. The second is that I would recommend >>> making a one-line change to Bio/Graphics/Panel.pm, to prevent the >>> package from trying to allocate the same set of colors twice (when >>> you reuse the same GD object to draw the two different parts of the >>> image.) Search for the following piece of code in Panel.pm (at >>> line 411 in bioperl-1.4, I think): >>> >>> for my $name ('white','black',keys %COLORS) { >>> my $idx = $gd->colorAllocate(@{$COLORS{$name}}); >>> $translation_table{$name} = $idx; >>> } >>> >>> Change "colorAllocate" to "colorResolve"; this should have no >>> effect on any existing Bio::Graphics code (AFAIK) and will allow >>> you to do your two (or three or four)-Panel trick. (As an aside, >>> I'd like to lobby for this one-line change to be made in a future >>> version of >>> Bio::Graphics::Panel, for precisely this reason.) In any case, >>> once you've made that change and reinstalled your copy of Bioperl, >>> here is a rough outline of what you need to do: >>> >>> 1. Set up your individual Bio::Graphics::Panel objects (e.g. $p1, >>> $p2, $p3, etc.) as desired to draw your images, but do *not* call >>> the gd method on any of them yet. >>> >>> 2. Create a GD::Image object big enough to hold the images that >>> will be drawn by $p1, $p2, $p3, etc.: >>> my $gdImg = GD::Image->new($fullWidth, $fullHeight); >>> (Note: use $p1->width(), $p1->height(), etc., to determine what >>> $fullWidth and $fullHeight should be, based on your desired Panel >>> layout algorithm.) >>> >>> 4. Use a "dummy" Bio::Graphics::Panel object to allocate all your >>> colors (this is an optional step; I do this because my code does >>> some drawing that isn't handled by Bio::Graphics::Panel, and want >>> to make sure that the palette has been allocated before I start): >>> >>> my $dummyPanel = Bio::Graphics::Panel->new(-length => 100, >>> -offset => 0, -width => $fullWidth); >>> $dummyPanel->gd($gdImg); # forces color allocation >>> >>> 5. Draw the individual panels and generate your png image: >>> >>> $p1->gd($gdImg); >>> $p2->gd($gdImg); >>> my $pngData = $gdImg->png(); >>> >>> I've glossed over some of the details here, for example the fact >>> that you may need to know the value of $p1->height() before you can >>> initialize $p2, but that's the basic idea. I've been using this >>> method to generate some comparative sequence displays and while >>> it's definitely a bit of a hack, it works well in practice. You >>> can also do the same thing with a GD::SVG::Image if you'd like to >>> generate SVG output. Good luck, >>> >>> Jonathan >>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> - -- >> Lincoln D. Stein >> Cold Spring Harbor Laboratory >> 1 Bungtown Road >> Cold Spring Harbor, NY 11724 >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.2.1 (GNU/Linux) >> >> iD8DBQFAP1Zt0CIvUP7P+AkRAreyAJ0XIcjMDeT/Bw69OBOEhD8tsznP+QCfVLWo >> +RnQaijXxPlVWTbmjTkbHYw= >> =lN1U >> -----END PGP SIGNATURE----- >> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From crabtree at tigr.org Mon Mar 1 11:55:02 2004 From: crabtree at tigr.org (Jonathan Crabtree) Date: Mon Mar 1 12:01:49 2004 Subject: [Bioperl-l] bioperl graphics In-Reply-To: References: Message-ID: <40436AE6.7000303@tigr.org> Hi Todd- Todd Harris wrote: >>On 3/1/04 9:02 AM, Jonathan Crabtree wrote: >> >> > >Hi Jason - > >Well, that's great news! I couldn't remember if I had added colorResolve to >GD::SVG. Whoops! As you can see, it's something of a kludge, but I'm glad >to hear that it works for you. > > Not at all; it works just fine, and I think GD::SVG is a great way to generate SVG documents from GD-aware code. The only problem I see with the current implementation of colorResolve() is that it doesn't try to determine whether the requested color has already been "allocated". This breaks the documented API, although in a rather minor way; it's unlikely that anyone would write code that relies on subsequent identical calls to colorResolve() returning the same color index. It also means that the 'colors_added' array will be larger than it needs to, and that colorsTotal() will return a misleading result, though again these are both very minor issues. I just noticed that the man page does state that colorResolve is unimplemented, so perhaps this is what caused the confusion about the method's disposition: $index = $image->colorResolve(red,green,blue) NOT IMPLEMENTED >Regarding Lincoln's suggestion of copying images, correct me if I'm wrong, >but I interpreted that to mean copying the images OUTSIDE of >Bio::Graphics::Panel. That is, create your Panel, fetch it, then paste it >where appropriate into a new GD::Image with the appropriate dimensions. To >avoid the method-overriding aspects of GD::SVG, this might need to be done >within a separate package or eval block. > Yes, I think my understanding of Lincoln's suggestion is the same as yours. I'm not too familiar with SVG, but it seems as though it might be possible to do a pure SVG implementation of copy() using nothing more than a clipping path (if only a portion of the source image is to be copied), a transform, and an appropriate grouping of the source elements. However, even if GD::SVG::Image supported copy(), I still think I'd lean towards keeping my current multi-Panel implementation, using only a single GD::Image or GD::SVG::Image, and relying on passing the same image object to the gd() method of multiple panels. The copying seems like an unnecessary step when the current Bio::Graphics::Panel API supports reusing a single image object (and the corresponding code can be made to support it with a 1-line change.) >I'm planning a significant upgrade to GD::SVG over the next few weeks that >should 1) enable parallel creation of a GD object; 2) make it compatible >with more current GD methods, and 3) make it more robust for future methods. > > That sounds great. Thanks for the feedback, Jonathan From Anthony.Underwood at hpa.org.uk Mon Mar 1 13:27:06 2004 From: Anthony.Underwood at hpa.org.uk (SRMD, Col - Underwood, Anthony) Date: Mon Mar 1 13:20:18 2004 Subject: [Bioperl-l] Traces as X, Y coordinates Message-ID: <427DA33A6101484BA7A72934AF90DF73051AA816@exchange1.phls.org.uk> Hi there, Please does anyone have experience with using the Bio::Seq::SequenceTrace and Bio::SeqIO::scf modules to extract peak values for the different traces (G,A,T and C) which can then be plotted using a graphics module along with the bases themselves at the appropriate positions. I'm a little unclear as to how the trace, peak indices, peak_index_at, base_at etc methods work. If someone has exprience in how to go from an scf file to arrays of values which represent x, y coords and bases, quality at each x coord then I'd really appreciate your advice and insight. Many thanks, Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 f: 0208 3583138 e: anthony.underwood@hpa.org.uk From rnilsson at clarku.edu Mon Mar 1 14:27:35 2004 From: rnilsson at clarku.edu (henrik nilsson) Date: Mon Mar 1 14:34:04 2004 Subject: [Bioperl-l] Fetching > 500 sequences Message-ID: <200403011427.35507.rnilsson@clarku.edu> Hi, It seems that I have problems with fetching more than 500 sequences from Genbank using Bioperl. It looks like the script (attached below) fetches all the 7000+ sequences, but only 500 make it to the output file. Is there any way to get all these 7000+ sequences written to the file - that is, is it possible to sidestep the 500 seq. limit? Thanks for your time, Rolf Please find the script below. When I run it, I get Writing accession number AJ406491 ... etc ... Writing accession number AJ406489 Writing accession number AJ406471 Writing accession number AJ406465 Writing accession number AJ406461 Total number of records found = 7053 but when I type [rolf@localhost dir]$ cat data.gb | grep 'BASE COUNT' | wc -l 500 [rolf@localhost dir]$ It is clear that only 500 seq. were written to the file. #!/usr/bin/perl -w use strict; use Bio::DB::GenBank; use Bio::DB::Query::GenBank; use IO::String; use Bio::SeqIO; use Bio::Seq::RichSeq; my $query_string = 'Boletales'; my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', -query=>$query_string); my $out = Bio::SeqIO->new(-file=>">data.gb", -format=>'genbank'); my $count = $query->count; my $gb = new Bio::DB::GenBank(); my $stream = $gb->get_Stream_by_query($query); while (my $seq = $stream->next_seq) { print "Writing accession number ", $seq->accession_number,"\n"; $out->write_seq($seq); } print "Total number of records found = $count\n"; exit; From hlapp at gnf.org Mon Mar 1 14:57:51 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Mar 1 15:03:45 2004 Subject: [Bioperl-l] Re: undef strand and biosql In-Reply-To: Message-ID: Hm. Strand being undef is a soft violation, in the sense that there is a value defined for 'unknown strand' (namely 0). Bottom line is that an undef strand should not lead to failure. I'll either fix bioperl-db to automatically substitute 0 for undef, or we could fix bioperl to return 0 if the strand hasn't been set yet. The latter is risky because then it is difficult to impossible to ask whether the strand has already been set but is unknown, or whether it's never been set and therefore you want to set a default. Any votes from the bioperl'ers out there on this question? I'm afraid my vote would go for not returning 0 by default in the location object. Actually, we could also put a DEFAULT 0 in the column definition in the schema DDL. That doesn't necessarily fix it in all RDBMSs though if you directly assign NULL to the column (e.g., in Oracle). Any votes on that from the biosql community? -hilmar On Monday, March 1, 2004, at 09:21 AM, matthieu CONTE wrote: > I solve the problem of 'source_term_id' by create -source_tag => > 'tigr'...and it seems to be ok...... > > "$seq->add_SeqFeature(new Bio::SeqFeature::Generic( > -primary => 'RIGHT_UTR', > -source_tag => 'tigr', > -start .......... > " > But it still have a problem of undef column 'strand' > Maybe in : > $loc->add_sub_Location(new Bio::Location::Simple( > -start => $e->{'start'}, > -end => $e->{'end'}, > -strand => ???? > )); > but I?m also confuse with the tag: ?strand? of Bio::SeqFeature::Generic > > I have this warning: > -------------------- WARNING --------------------- > MSG: insert in Bio::DB::BioSQL::LocationAdaptor (driver) failed, > values were ("1","318","","1") FKs (16957,) > Column 'strand' cannot be null > --------------------------------------------------- > Could not store 8356.t04040: > ------------- EXCEPTION ------------- > MSG: create: object (Bio::Location::Simple) failed to insert or to be > found by unique key > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:207 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK Bio::DB::BioSQL::SeqFeatureAdaptor::store_children > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > SeqFeatureAdaptor.pm:278 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:215 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK Bio::DB::BioSQL::SeqAdaptor::store_children > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > SeqAdaptor.pm:246 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:215 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/BioSQL/ > BasePersistenceAdaptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/DB/Persistent/ > PersistentObject.pm:270 > STACK (eval) load_seqdatabase.pl:517 > STACK toplevel load_seqdatabase.pl:500 > > > > > ----------------------------------------------------------- > Matthieu CONTE > M. Sc. in Bioinformatics from SIB > > CIRAD-Biotrop TA40/03 > Avenue Agropolis > 34398 Montpellier Cedex 5 > FRANCE > > m_conte@hotmail.com > tel: (33)04 67 61 60 21 > fax :(33) 4 67 61 56 05 > > ----------------------------------------------------------- > > > > > >> From: Hilmar Lapp >> To: Josh Lauricha >> CC: "matthieu CONTE" , bioperl-l@bioperl.org >> Subject: Re: [Bioperl-l] Re: Bio ::seqIO ::tigr >> Date: Fri, 27 Feb 2004 16:45:13 -0800 >> >> >> On Thursday, February 26, 2004, at 09:45 AM, Josh Lauricha wrote: >> >>> Does the source_term_id refer to the source_tag()? >> >> Yes. >> >>> >>> On Feb 26, 2004, at 9:08 AM, matthieu CONTE wrote: >>> >>>> [conte@bearn biosql]$ perl load_seqdatabase.pl --dbuser biosql >>>> --dbpass biosql --namespace orysa_tigr --format tigr >>>> /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml >>>> Loading /home/conte/pipeline_orthologues/data/orysa_tigr/chr07.xml >>>> ... >>>> >>>> -------------------- WARNING --------------------- >>>> MSG: insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed, >>>> values were ("","1") FKs (26216,37,) >>>> Column 'source_term_id' cannot be null >>>> --------------------------------------------------- >>>> >> >> What this means is that there was no $feat->source_tag set, and >> looking up undef resulted in undef for the foreign key :-) >> >> While bioperl doesn't enforce it, for biosql the source_tag() as well >> as the primary_tag() of a feature are mandatory and cannot be undef. >> Most SeqIO parsers set source_tag() to a static default if there is >> no value, e.g. 'EMBL/GenBank/SwissProt' if you're using FTHelper.pm. >> >> -hilmar >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> > > _________________________________________________________________ > MSN Messenger : discutez en direct avec vos amis ! > http://www.msn.fr/msger/default.asp > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From thies at itg.fzk.de Mon Mar 1 11:40:29 2004 From: thies at itg.fzk.de (Wolf-Gerolf Thies) Date: Mon Mar 1 15:18:13 2004 Subject: [Bioperl-l] Problems with BioPerl-1.4 Message-ID: <3.0.5.32.20040301174029.00926430@pop3.fzk.de> Dear BioPerl experts, I have tried to install BioPerl-1.4 on on True64UNIX (OSF-1) Version 5.1. The standard make fails with the error: Make: line too long. Stop. Then I have tested the gnu make, but it also fails: # /usr/local/bin/make mkdir blib mkdir blib/lib mkdir blib/arch mkdir blib/arch/auto mkdir blib/arch/auto/Bio mkdir blib/lib/auto mkdir blib/lib/auto/Bio mkdir blib/man1 mkdir blib/man3 make: execvp: /bin/sh: Arg list too long make: *** [pm_to_blib] Error 127 Do you have any idea what might be my problem ? I join the makefile to this mail. With kind regards Wolf-Gerolf Thies -------------- next part -------------- # This Makefile is for the Bio extension to perl. # # It was generated automatically by MakeMaker version # 5.45 (Revision: 1.222) from the contents of # Makefile.PL. Don't edit this file, edit Makefile.PL instead. # # ANY CHANGES MADE HERE WILL BE LOST! # # MakeMaker ARGV: () # # MakeMaker Parameters: # ABSTRACT => q[Bioinformatics Toolkit] # AUTHOR => q[Bioperl Team (bioperl-l@bioperl.org)] # DIR => [] # DISTNAME => q[bioperl] # EXE_FILES => [q[./scripts_temp/bp_load_gff.pl], q[./scripts_temp/bp_genbank2gff.pl], q[./scripts_temp/bp_bulk_load_gff.pl], q[./scripts_temp/bp_fast_load_gff.pl], q[./scripts_temp/bp_generate_histogram.pl], q[./scripts_temp/bp_pg_bulk_load_gff.pl], q[./scripts_temp/bp_process_gadfly.pl], q[./scripts_temp/bp_process_ncbi_human.pl], q[./scripts_temp/bp_process_sgd.pl], q[./scripts_temp/bp_process_wormbase.pl], q[./scripts_temp/bp_biofetch_genbank_proxy.pl], q[./scripts_temp/bp_bioflat_index.pl], q[./scripts_temp/bp_biogetseq.pl], q[./scripts_temp/bp_flanks.pl], q[./scripts_temp/bp_biblio.pl], q[./scripts_temp/bp_frend.pl], q[./scripts_temp/bp_feature_draw.pl], q[./scripts_temp/bp_search_overview.pl], q[./scripts_temp/bp_fetch.pl], q[./scripts_temp/bp_index.pl], q[./scripts_temp/bp_composite_LD.pl], q[./scripts_temp/bp_heterogeneity_test.pl], q[./scripts_temp/bp_filter_search.pl], q[./scripts_temp/bp_extract_feature_seq.pl], q[./scripts_temp/bp_seqconvert.pl], q[./scripts_temp/bp_split_seq.pl], q[./scripts_temp/bp_translate_seq.pl], q[./scripts_temp/bp_aacomp.pl], q[./scripts_temp/bp_chaos_plot.pl], q[./scripts_temp/bp_gccalc.pl], q[./scripts_temp/bp_oligo_count.pl], q[./scripts_temp/bp_local_taxonomydb_query.pl], q[./scripts_temp/bp_taxid4species.pl], q[./scripts_temp/bp_blast2tree.pl], q[./scripts_temp/bp_nrdb.pl], q[./scripts_temp/bp_mrtrans.pl], q[./scripts_temp/bp_sreformat.pl], q[./scripts_temp/bp_dbsplit.pl], q[./scripts_temp/bp_mask_by_search.pl], q[./scripts_temp/bp_mutate.pl], q[./scripts_temp/bp_pairwise_kaks.pl], q[./scripts_temp/bp_remote_blast.pl], q[./scripts_temp/bp_search2BSML.pl], q[./scripts_temp/bp_search2alnblocks.pl], q[./scripts_temp/bp_search2gff.pl], q[./scripts_temp/bp_search2tribe.pl], q[./scripts_temp/bp_seq_length.pl]] # NAME => q[Bio] # PL_FILES => { doc/makedoc.PL=>[q[bioscripts.pod], q[biodatabases.pod], q[biodesign.pod], q[bioperl.pod]] } # PREREQ_PM => { HTML::Entities=>q[0], File::Spec=>q[0], File::Temp=>q[0], DB_File=>q[0], IO::Scalar=>q[0], IO::String=>q[0] } # VERSION_FROM => q[Bio/Root/Version.pm] # dist => { DIST_DEFAULT=>q[all tardist], COMPRESS=>q[gzip -9f], SUFFIX=>q[.gz] } # realclean => { FILES=>q[./Seq.pm.bak] } # --- MakeMaker post_initialize section: # --- MakeMaker const_config section: # These definitions are from config.sh (via /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/Config.pm) # They may have been overridden via Makefile.PL or on the command line AR = ar CC = cc CCCDLFLAGS = CCDLFLAGS = -Wl,-rpath,/usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE DLEXT = so DLSRC = dl_dlopen.xs LD = ld LDDLFLAGS = -shared -expect_unresolved "*" -O4 -msym -std -s LDFLAGS = LIBC = /usr/shlib/libc.so LIB_EXT = .a OBJ_EXT = .o OSNAME = dec_osf OSVERS = 5.1 RANLIB = : SO = so EXE_EXT = FULL_AR = /usr/bin/ar # --- MakeMaker constants section: AR_STATIC_ARGS = cr NAME = Bio DISTNAME = bioperl NAME_SYM = Bio VERSION = 1.4 VERSION_SYM = 1_4 XS_VERSION = 1.4 INST_BIN = blib/bin INST_EXE = blib/script INST_LIB = blib/lib INST_ARCHLIB = blib/arch INST_SCRIPT = blib/script PREFIX = /usr/lib/perl-5.6.0 INSTALLDIRS = site INSTALLPRIVLIB = $(PREFIX)/lib/5.6.0 INSTALLARCHLIB = $(PREFIX)/lib/5.6.0/alpha-dec_osf INSTALLSITELIB = $(PREFIX)/lib/site_perl/5.6.0 INSTALLSITEARCH = $(PREFIX)/lib/site_perl/5.6.0/alpha-dec_osf INSTALLBIN = $(PREFIX)/bin INSTALLSCRIPT = $(PREFIX)/bin PERL_LIB = /usr/lib/perl-5.6.0/lib/5.6.0 PERL_ARCHLIB = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf SITELIBEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0 SITEARCHEXP = /usr/lib/perl-5.6.0/lib/site_perl/5.6.0/alpha-dec_osf LIBPERL_A = libperl.a FIRST_MAKEFILE = Makefile MAKE_APERL_FILE = Makefile.aperl PERLMAINCC = $(CC) PERL_INC = /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE PERL = /usr/bin/perl FULLPERL = /usr/bin/perl FULL_AR = /usr/bin/ar VERSION_MACRO = VERSION DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\" XS_VERSION_MACRO = XS_VERSION XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\" PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc MAKEMAKER = /usr/lib/perl-5.6.0/lib/5.6.0/ExtUtils/MakeMaker.pm MM_VERSION = 5.45 # FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle). # BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle) # ROOTEXT = Directory part of FULLEXT with leading slash (eg /DBD) !!! Deprecated from MM 5.32 !!! # PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar) # DLBASE = Basename part of dynamic library. May be just equal BASEEXT. FULLEXT = Bio BASEEXT = Bio DLBASE = $(BASEEXT) VERSION_FROM = Bio/Root/Version.pm OBJECT = LDFROM = $(OBJECT) LINKTYPE = dynamic # Handy lists of source code files: XS_FILES= C_FILES = O_FILES = H_FILES = HTMLLIBPODS = HTMLSCRIPTPODS = MAN1PODS = ./scripts_temp/bp_aacomp.pl \ ./scripts_temp/bp_biblio.pl \ ./scripts_temp/bp_biofetch_genbank_proxy.pl \ ./scripts_temp/bp_biogetseq.pl \ ./scripts_temp/bp_blast2tree.pl \ ./scripts_temp/bp_bulk_load_gff.pl \ ./scripts_temp/bp_chaos_plot.pl \ ./scripts_temp/bp_composite_LD.pl \ ./scripts_temp/bp_dbsplit.pl \ ./scripts_temp/bp_extract_feature_seq.pl \ ./scripts_temp/bp_fast_load_gff.pl \ ./scripts_temp/bp_feature_draw.pl \ ./scripts_temp/bp_fetch.pl \ ./scripts_temp/bp_filter_search.pl \ ./scripts_temp/bp_flanks.pl \ ./scripts_temp/bp_frend.pl \ ./scripts_temp/bp_gccalc.pl \ ./scripts_temp/bp_genbank2gff.pl \ ./scripts_temp/bp_generate_histogram.pl \ ./scripts_temp/bp_heterogeneity_test.pl \ ./scripts_temp/bp_index.pl \ ./scripts_temp/bp_load_gff.pl \ ./scripts_temp/bp_local_taxonomydb_query.pl \ ./scripts_temp/bp_mask_by_search.pl \ ./scripts_temp/bp_mrtrans.pl \ ./scripts_temp/bp_mutate.pl \ ./scripts_temp/bp_nrdb.pl \ ./scripts_temp/bp_oligo_count.pl \ ./scripts_temp/bp_pairwise_kaks.pl \ ./scripts_temp/bp_pg_bulk_load_gff.pl \ ./scripts_temp/bp_process_gadfly.pl \ ./scripts_temp/bp_process_ncbi_human.pl \ ./scripts_temp/bp_process_sgd.pl \ ./scripts_temp/bp_process_wormbase.pl \ ./scripts_temp/bp_remote_blast.pl \ ./scripts_temp/bp_search2BSML.pl \ ./scripts_temp/bp_search2alnblocks.pl \ ./scripts_temp/bp_search2gff.pl \ ./scripts_temp/bp_search2tribe.pl \ ./scripts_temp/bp_search_overview.pl \ ./scripts_temp/bp_seq_length.pl \ ./scripts_temp/bp_seqconvert.pl \ ./scripts_temp/bp_split_seq.pl \ ./scripts_temp/bp_sreformat.pl \ ./scripts_temp/bp_taxid4species.pl \ ./scripts_temp/bp_translate_seq.pl MAN3PODS = Bio/Align/AlignI.pm \ Bio/Align/DNAStatistics.pm \ Bio/Align/PairwiseStatistics.pm \ Bio/Align/StatisticsI.pm \ Bio/Align/Utilities.pm \ Bio/AlignIO.pm \ Bio/AlignIO/bl2seq.pm \ Bio/AlignIO/clustalw.pm \ Bio/AlignIO/emboss.pm \ Bio/AlignIO/fasta.pm \ Bio/AlignIO/maf.pm \ Bio/AlignIO/mase.pm \ Bio/AlignIO/mega.pm \ Bio/AlignIO/meme.pm \ Bio/AlignIO/metafasta.pm \ Bio/AlignIO/msf.pm \ Bio/AlignIO/nexus.pm \ Bio/AlignIO/pfam.pm \ Bio/AlignIO/phylip.pm \ Bio/AlignIO/prodom.pm \ Bio/AlignIO/psi.pm \ Bio/AlignIO/selex.pm \ Bio/AlignIO/stockholm.pm \ Bio/AnalysisI.pm \ Bio/AnalysisParserI.pm \ Bio/AnalysisResultI.pm \ Bio/AnnotatableI.pm \ Bio/Annotation/AnnotationFactory.pm \ Bio/Annotation/Collection.pm \ Bio/Annotation/Comment.pm \ Bio/Annotation/DBLink.pm \ Bio/Annotation/OntologyTerm.pm \ Bio/Annotation/Reference.pm \ Bio/Annotation/SimpleValue.pm \ Bio/Annotation/StructuredValue.pm \ Bio/Annotation/TypeManager.pm \ Bio/AnnotationCollectionI.pm \ Bio/AnnotationI.pm \ Bio/Assembly/Contig.pm \ Bio/Assembly/ContigAnalysis.pm \ Bio/Assembly/IO.pm \ Bio/Assembly/IO/ace.pm \ Bio/Assembly/IO/phrap.pm \ Bio/Assembly/Scaffold.pm \ Bio/Assembly/ScaffoldI.pm \ Bio/Biblio.pm \ Bio/Biblio/Article.pm \ Bio/Biblio/BiblioBase.pm \ Bio/Biblio/Book.pm \ Bio/Biblio/BookArticle.pm \ Bio/Biblio/IO.pm \ Bio/Biblio/IO/medline2ref.pm \ Bio/Biblio/IO/medlinexml.pm \ Bio/Biblio/IO/pubmed2ref.pm \ Bio/Biblio/IO/pubmedxml.pm \ Bio/Biblio/Journal.pm \ Bio/Biblio/JournalArticle.pm \ Bio/Biblio/MedlineArticle.pm \ Bio/Biblio/MedlineBook.pm \ Bio/Biblio/MedlineBookArticle.pm \ Bio/Biblio/MedlineJournal.pm \ Bio/Biblio/MedlineJournalArticle.pm \ Bio/Biblio/Organisation.pm \ Bio/Biblio/Patent.pm \ Bio/Biblio/Person.pm \ Bio/Biblio/Proceeding.pm \ Bio/Biblio/Provider.pm \ Bio/Biblio/PubmedArticle.pm \ Bio/Biblio/PubmedBookArticle.pm \ Bio/Biblio/PubmedJournalArticle.pm \ Bio/Biblio/Ref.pm \ Bio/Biblio/Service.pm \ Bio/Biblio/TechReport.pm \ Bio/Biblio/Thesis.pm \ Bio/Biblio/WebResource.pm \ Bio/Cluster/ClusterFactory.pm \ Bio/Cluster/FamilyI.pm \ Bio/Cluster/SequenceFamily.pm \ Bio/Cluster/UniGene.pm \ Bio/Cluster/UniGeneI.pm \ Bio/ClusterI.pm \ Bio/ClusterIO.pm \ Bio/ClusterIO/dbsnp.pm \ Bio/ClusterIO/unigene.pm \ Bio/CodonUsage/IO.pm \ Bio/CodonUsage/Table.pm \ Bio/Coordinate/Chain.pm \ Bio/Coordinate/Collection.pm \ Bio/Coordinate/ExtrapolatingPair.pm \ Bio/Coordinate/GeneMapper.pm \ Bio/Coordinate/Graph.pm \ Bio/Coordinate/MapperI.pm \ Bio/Coordinate/Pair.pm \ Bio/Coordinate/Result.pm \ Bio/Coordinate/Result/Gap.pm \ Bio/Coordinate/Result/Match.pm \ Bio/Coordinate/ResultI.pm \ Bio/Coordinate/Utils.pm \ Bio/DB/Ace.pm \ Bio/DB/Biblio/biofetch.pm \ Bio/DB/Biblio/soap.pm \ Bio/DB/BiblioI.pm \ Bio/DB/BioFetch.pm \ Bio/DB/CUTG.pm \ Bio/DB/DBFetch.pm \ Bio/DB/EMBL.pm \ Bio/DB/Failover.pm \ Bio/DB/Fasta.pm \ Bio/DB/FileCache.pm \ Bio/DB/Flat.pm \ Bio/DB/Flat/BDB.pm \ Bio/DB/Flat/BDB/embl.pm \ Bio/DB/Flat/BDB/fasta.pm \ Bio/DB/Flat/BDB/genbank.pm \ Bio/DB/Flat/BDB/swiss.pm \ Bio/DB/Flat/BDB/swissprot.pm \ Bio/DB/Flat/BinarySearch.pm \ Bio/DB/GDB.pm \ Bio/DB/GFF.pm \ Bio/DB/GFF/Adaptor/ace.pm \ Bio/DB/GFF/Adaptor/biofetch.pm \ Bio/DB/GFF/Adaptor/biofetch_oracle.pm \ Bio/DB/GFF/Adaptor/dbi.pm \ Bio/DB/GFF/Adaptor/dbi/caching_handle.pm \ Bio/DB/GFF/Adaptor/dbi/iterator.pm \ Bio/DB/GFF/Adaptor/dbi/mysql.pm \ Bio/DB/GFF/Adaptor/dbi/mysqlace.pm \ Bio/DB/GFF/Adaptor/dbi/mysqlopt.pm \ Bio/DB/GFF/Adaptor/dbi/oracle.pm \ Bio/DB/GFF/Adaptor/dbi/oracleace.pm \ Bio/DB/GFF/Adaptor/dbi/pg.pm \ Bio/DB/GFF/Adaptor/memory.pm \ Bio/DB/GFF/Adaptor/memory_iterator.pm \ Bio/DB/GFF/Aggregator.pm \ Bio/DB/GFF/Aggregator/alignment.pm \ Bio/DB/GFF/Aggregator/clone.pm \ Bio/DB/GFF/Aggregator/coding.pm \ Bio/DB/GFF/Aggregator/match.pm \ Bio/DB/GFF/Aggregator/none.pm \ Bio/DB/GFF/Aggregator/processed_transcript.pm \ Bio/DB/GFF/Aggregator/transcript.pm \ Bio/DB/GFF/Aggregator/ucsc_acembly.pm \ Bio/DB/GFF/Aggregator/ucsc_ensgene.pm \ Bio/DB/GFF/Aggregator/ucsc_genscan.pm \ Bio/DB/GFF/Aggregator/ucsc_refgene.pm \ Bio/DB/GFF/Aggregator/ucsc_sanger22.pm \ Bio/DB/GFF/Aggregator/ucsc_sanger22pseudo.pm \ Bio/DB/GFF/Aggregator/ucsc_softberry.pm \ Bio/DB/GFF/Aggregator/ucsc_twinscan.pm \ Bio/DB/GFF/Aggregator/ucsc_unigene.pm \ Bio/DB/GFF/Featname.pm \ Bio/DB/GFF/Feature.pm \ Bio/DB/GFF/Homol.pm \ Bio/DB/GFF/RelSegment.pm \ Bio/DB/GFF/Segment.pm \ Bio/DB/GFF/Typename.pm \ Bio/DB/GFF/Util/Binning.pm \ Bio/DB/GFF/Util/Rearrange.pm \ Bio/DB/GenBank.pm \ Bio/DB/GenPept.pm \ Bio/DB/InMemoryCache.pm \ Bio/DB/MeSH.pm \ Bio/DB/NCBIHelper.pm \ Bio/DB/Query/GenBank.pm \ Bio/DB/Query/WebQuery.pm \ Bio/DB/QueryI.pm \ Bio/DB/RandomAccessI.pm \ Bio/DB/RefSeq.pm \ Bio/DB/Registry.pm \ Bio/DB/SeqI.pm \ Bio/DB/SwissProt.pm \ Bio/DB/Taxonomy.pm \ Bio/DB/Taxonomy/entrez.pm \ Bio/DB/Taxonomy/flatfile.pm \ Bio/DB/Universal.pm \ Bio/DB/UpdateableSeqI.pm \ Bio/DB/WebDBSeqI.pm \ Bio/DB/XEMBL.pm \ Bio/DB/XEMBLService.pm \ Bio/DBLinkContainerI.pm \ Bio/Das/FeatureTypeI.pm \ Bio/Das/SegmentI.pm \ Bio/DasI.pm \ Bio/DescribableI.pm \ Bio/Event/EventGeneratorI.pm \ 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Bio/Search/Hit/GenericHit.pm \ Bio/Search/Hit/HMMERHit.pm \ Bio/Search/Hit/HitFactory.pm \ Bio/Search/Hit/HitI.pm \ Bio/Search/Hit/PsiBlastHit.pm \ Bio/Search/Iteration/GenericIteration.pm \ Bio/Search/Iteration/IterationI.pm \ Bio/Search/Processor.pm \ Bio/Search/Result/BlastResult.pm \ Bio/Search/Result/GenericResult.pm \ Bio/Search/Result/HMMERResult.pm \ Bio/Search/Result/ResultFactory.pm \ Bio/Search/Result/ResultI.pm \ Bio/Search/Result/WABAResult.pm \ Bio/Search/SearchUtils.pm \ Bio/SearchDist.pm \ Bio/SearchIO.pm \ Bio/SearchIO/EventHandlerI.pm \ Bio/SearchIO/FastHitEventBuilder.pm \ Bio/SearchIO/IteratedSearchResultEventBuilder.pm \ Bio/SearchIO/SearchResultEventBuilder.pm \ Bio/SearchIO/SearchWriterI.pm \ Bio/SearchIO/Writer/BSMLResultWriter.pm \ Bio/SearchIO/Writer/GbrowseGFF.pm \ Bio/SearchIO/Writer/HSPTableWriter.pm \ Bio/SearchIO/Writer/HTMLResultWriter.pm \ Bio/SearchIO/Writer/HitTableWriter.pm \ Bio/SearchIO/Writer/ResultTableWriter.pm \ 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Bio/Tools/EMBOSS/Palindrome.pm \ Bio/Tools/EPCR.pm \ Bio/Tools/ESTScan.pm \ Bio/Tools/Eponine.pm \ Bio/Tools/Est2Genome.pm \ Bio/Tools/FootPrinter.pm \ Bio/Tools/GFF.pm \ Bio/Tools/Gel.pm \ Bio/Tools/Geneid.pm \ Bio/Tools/Genemark.pm \ Bio/Tools/Genewise.pm \ Bio/Tools/Genomewise.pm \ Bio/Tools/Genscan.pm \ Bio/Tools/Glimmer.pm \ Bio/Tools/Grail.pm \ Bio/Tools/GuessSeqFormat.pm \ Bio/Tools/HMMER/Domain.pm \ Bio/Tools/HMMER/Results.pm \ Bio/Tools/HMMER/Set.pm \ Bio/Tools/Hmmpfam.pm \ Bio/Tools/IUPAC.pm \ Bio/Tools/Lucy.pm \ Bio/Tools/MZEF.pm \ Bio/Tools/OddCodes.pm \ Bio/Tools/Phylo/Molphy.pm \ Bio/Tools/Phylo/Molphy/Result.pm \ Bio/Tools/Phylo/PAML.pm \ Bio/Tools/Phylo/PAML/ModelResult.pm \ Bio/Tools/Phylo/PAML/Result.pm \ Bio/Tools/Phylo/Phylip/ProtDist.pm \ Bio/Tools/Prediction/Exon.pm \ Bio/Tools/Prediction/Gene.pm \ Bio/Tools/Primer/Assessor/Base.pm \ Bio/Tools/Primer/AssessorI.pm \ Bio/Tools/Primer/Feature.pm \ Bio/Tools/Primer/Pair.pm \ Bio/Tools/Primer3.pm \ Bio/Tools/Prints.pm \ Bio/Tools/Profile.pm \ Bio/Tools/Promoterwise.pm \ Bio/Tools/PrositeScan.pm \ Bio/Tools/Pseudowise.pm \ Bio/Tools/QRNA.pm \ Bio/Tools/RandomDistFunctions.pm \ Bio/Tools/RepeatMasker.pm \ Bio/Tools/RestrictionEnzyme.pm \ Bio/Tools/Run/RemoteBlast.pm \ Bio/Tools/Run/StandAloneBlast.pm \ Bio/Tools/Run/WrapperBase.pm \ Bio/Tools/Seg.pm \ Bio/Tools/SeqAnal.pm \ Bio/Tools/SeqPattern.pm \ Bio/Tools/SeqStats.pm \ Bio/Tools/SeqWords.pm \ Bio/Tools/SiRNA.pm \ Bio/Tools/Sigcleave.pm \ Bio/Tools/Signalp.pm \ Bio/Tools/Sim4/Exon.pm \ Bio/Tools/Sim4/Results.pm \ Bio/Tools/Tmhmm.pm \ Bio/Tools/WWW.pm \ Bio/Tools/dpAlign.pm \ Bio/Tools/pICalculator.pm \ Bio/Tools/pSW.pm \ Bio/Tree/AlleleNode.pm \ Bio/Tree/Node.pm \ Bio/Tree/NodeI.pm \ Bio/Tree/NodeNHX.pm \ Bio/Tree/RandomFactory.pm \ Bio/Tree/Statistics.pm \ Bio/Tree/Tree.pm \ Bio/Tree/TreeFunctionsI.pm \ Bio/Tree/TreeI.pm \ Bio/TreeIO.pm \ Bio/TreeIO/TreeEventBuilder.pm \ Bio/TreeIO/lintree.pm \ Bio/TreeIO/newick.pm \ Bio/TreeIO/nexus.pm \ Bio/TreeIO/nhx.pm \ Bio/TreeIO/svggraph.pm \ Bio/TreeIO/tabtree.pm \ Bio/UpdateableSeqI.pm \ Bio/Variation/AAChange.pm \ Bio/Variation/AAReverseMutate.pm \ Bio/Variation/Allele.pm \ Bio/Variation/DNAMutation.pm \ Bio/Variation/IO.pm \ Bio/Variation/IO/flat.pm \ Bio/Variation/IO/xml.pm \ Bio/Variation/RNAChange.pm \ Bio/Variation/SNP.pm \ Bio/Variation/SeqDiff.pm \ Bio/Variation/VariantI.pm \ Bio/WebAgent.pm \ biodatabases.pod \ biodesign.pod \ bioperl.pod \ bioscripts.pod \ bptutorial.pl HTMLEXT = html INST_MAN1DIR = blib/man1 INSTALLMAN1DIR = /usr/share/doclib/annex/man/man1 MAN1EXT = 1 INST_MAN3DIR = blib/man3 INSTALLMAN3DIR = /usr/share/doclib/annex/man/man3 MAN3EXT = 3 PERM_RW = 644 PERM_RWX = 755 # work around a famous dec-osf make(1) feature(?): makemakerdflt: all .SUFFIXES: .xs .c .C .cpp .cxx .cc $(OBJ_EXT) # Nick wanted to get rid of .PRECIOUS. I don't remember why. I seem to recall, that # some make implementations will delete the Makefile when we rebuild it. Because # we call false(1) when we rebuild it. So make(1) is not completely wrong when it # does so. Our milage may vary. # .PRECIOUS: Makefile # seems to be not necessary anymore .PHONY: all config static dynamic test linkext manifest # Where is the Config information that we are using/depend on CONFIGDEP = $(PERL_ARCHLIB)/Config.pm $(PERL_INC)/config.h # Where to put things: INST_LIBDIR = $(INST_LIB) INST_ARCHLIBDIR = $(INST_ARCHLIB) INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT) INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT) INST_STATIC = INST_DYNAMIC = INST_BOOT = EXPORT_LIST = PERL_ARCHIVE = TO_INST_PM = Bio/Align/AlignI.pm \ Bio/Align/DNAStatistics.pm \ Bio/Align/PairwiseStatistics.pm \ Bio/Align/StatisticsI.pm \ Bio/Align/Utilities.pm \ Bio/AlignIO.pm \ Bio/AlignIO/bl2seq.pm \ Bio/AlignIO/clustalw.pm \ Bio/AlignIO/emboss.pm \ Bio/AlignIO/fasta.pm \ Bio/AlignIO/maf.pm \ Bio/AlignIO/mase.pm \ Bio/AlignIO/mega.pm \ Bio/AlignIO/meme.pm \ Bio/AlignIO/metafasta.pm \ Bio/AlignIO/msf.pm \ Bio/AlignIO/nexus.pm \ Bio/AlignIO/pfam.pm \ Bio/AlignIO/phylip.pm \ Bio/AlignIO/prodom.pm \ 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$(INST_MAN1DIR)/.exists @$(NOOP) $(INST_MAN1DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h @$(MKPATH) $(INST_MAN1DIR) @$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN1DIR)/.exists -@$(CHMOD) $(PERM_RWX) $(INST_MAN1DIR) config :: $(INST_MAN3DIR)/.exists @$(NOOP) $(INST_MAN3DIR)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h @$(MKPATH) $(INST_MAN3DIR) @$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_MAN3DIR)/.exists -@$(CHMOD) $(PERM_RWX) $(INST_MAN3DIR) help: perldoc ExtUtils::MakeMaker Version_check: @$(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \ -MExtUtils::MakeMaker=Version_check \ -e "Version_check('$(MM_VERSION)')" # --- MakeMaker linkext section: linkext :: $(LINKTYPE) @$(NOOP) # --- MakeMaker dlsyms section: # --- MakeMaker dynamic section: ## $(INST_PM) has been moved to the all: target. ## It remains here for awhile to allow for old usage: "make dynamic" #dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT) $(INST_PM) dynamic :: Makefile $(INST_DYNAMIC) $(INST_BOOT) @$(NOOP) # --- MakeMaker dynamic_bs section: BOOTSTRAP = # --- MakeMaker dynamic_lib section: # --- MakeMaker static section: ## $(INST_PM) has been moved to the all: target. ## It remains here for awhile to allow for old usage: "make static" #static :: Makefile $(INST_STATIC) $(INST_PM) static :: Makefile $(INST_STATIC) @$(NOOP) # --- MakeMaker static_lib section: # --- MakeMaker htmlifypods section: htmlifypods : pure_all @$(NOOP) # --- MakeMaker manifypods section: manifypods : pure_all @$(NOOP) # --- MakeMaker processPL section: all :: bioscripts.pod @$(NOOP) bioscripts.pod :: doc/makedoc.PL $(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioscripts.pod all :: biodatabases.pod @$(NOOP) biodatabases.pod :: doc/makedoc.PL $(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodatabases.pod all :: biodesign.pod @$(NOOP) biodesign.pod :: doc/makedoc.PL $(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL biodesign.pod all :: bioperl.pod @$(NOOP) bioperl.pod :: doc/makedoc.PL $(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) doc/makedoc.PL bioperl.pod # --- MakeMaker installbin section: $(INST_SCRIPT)/.exists :: /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h @$(MKPATH) $(INST_SCRIPT) @$(EQUALIZE_TIMESTAMP) /usr/lib/perl-5.6.0/lib/5.6.0/alpha-dec_osf/CORE/perl.h $(INST_SCRIPT)/.exists -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT) EXE_FILES = ./scripts_temp/bp_load_gff.pl ./scripts_temp/bp_genbank2gff.pl ./scripts_temp/bp_bulk_load_gff.pl ./scripts_temp/bp_fast_load_gff.pl ./scripts_temp/bp_generate_histogram.pl ./scripts_temp/bp_pg_bulk_load_gff.pl ./scripts_temp/bp_process_gadfly.pl ./scripts_temp/bp_process_ncbi_human.pl ./scripts_temp/bp_process_sgd.pl ./scripts_temp/bp_process_wormbase.pl ./scripts_temp/bp_biofetch_genbank_proxy.pl ./scripts_temp/bp_bioflat_index.pl ./scripts_temp/bp_biogetseq.pl ./scripts_temp/bp_flanks.pl ./scripts_temp/bp_biblio.pl ./scripts_temp/bp_frend.pl ./scripts_temp/bp_feature_draw.pl ./scripts_temp/bp_search_overview.pl ./scripts_temp/bp_fetch.pl ./scripts_temp/bp_index.pl ./scripts_temp/bp_composite_LD.pl ./scripts_temp/bp_heterogeneity_test.pl ./scripts_temp/bp_filter_search.pl ./scripts_temp/bp_extract_feature_seq.pl ./scripts_temp/bp_seqconvert.pl ./scripts_temp/bp_split_seq.pl ./scripts_temp/bp_translate_seq.pl ./scripts_temp/bp_aacomp.pl ./scripts_temp/bp_chaos_plot.pl ./scripts_temp/bp_gccalc.pl ./scripts_temp/bp_oligo_count.pl ./scripts_temp/bp_local_taxonomydb_query.pl ./scripts_temp/bp_taxid4species.pl ./scripts_temp/bp_blast2tree.pl ./scripts_temp/bp_nrdb.pl ./scripts_temp/bp_mrtrans.pl ./scripts_temp/bp_sreformat.pl ./scripts_temp/bp_dbsplit.pl ./scripts_temp/bp_mask_by_search.pl ./scripts_temp/bp_mutate.pl ./scripts_temp/bp_pairwise_kaks.pl ./scripts_temp/bp_remote_blast.pl ./scripts_temp/bp_search2BSML.pl ./scripts_temp/bp_search2alnblocks.pl ./scripts_temp/bp_search2gff.pl ./scripts_temp/bp_search2tribe.pl ./scripts_temp/bp_seq_length.pl FIXIN = $(PERL) -I$(PERL_ARCHLIB) -I$(PERL_LIB) -MExtUtils::MakeMaker \ -e "MY->fixin(shift)" pure_all :: $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl @$(NOOP) realclean :: rm -f $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl $(INST_SCRIPT)/bp_pg_bulk_load_gff.pl $(INST_SCRIPT)/bp_sreformat.pl $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl $(INST_SCRIPT)/bp_local_taxonomydb_query.pl $(INST_SCRIPT)/bp_biogetseq.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_index.pl $(INST_SCRIPT)/bp_split_seq.pl $(INST_SCRIPT)/bp_remote_blast.pl $(INST_SCRIPT)/bp_aacomp.pl $(INST_SCRIPT)/bp_heterogeneity_test.pl $(INST_SCRIPT)/bp_frend.pl $(INST_SCRIPT)/bp_generate_histogram.pl $(INST_SCRIPT)/bp_process_sgd.pl $(INST_SCRIPT)/bp_mutate.pl $(INST_SCRIPT)/bp_filter_search.pl $(INST_SCRIPT)/bp_genbank2gff.pl $(INST_SCRIPT)/bp_bulk_load_gff.pl $(INST_SCRIPT)/bp_nrdb.pl $(INST_SCRIPT)/bp_blast2tree.pl $(INST_SCRIPT)/bp_chaos_plot.pl: ./scripts_temp/bp_chaos_plot.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_chaos_plot.pl cp ./scripts_temp/bp_chaos_plot.pl $(INST_SCRIPT)/bp_chaos_plot.pl $(FIXIN) $(INST_SCRIPT)/bp_chaos_plot.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_chaos_plot.pl $(INST_SCRIPT)/bp_composite_LD.pl: ./scripts_temp/bp_composite_LD.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_composite_LD.pl cp ./scripts_temp/bp_composite_LD.pl $(INST_SCRIPT)/bp_composite_LD.pl $(FIXIN) $(INST_SCRIPT)/bp_composite_LD.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_composite_LD.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl: ./scripts_temp/bp_pairwise_kaks.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_pairwise_kaks.pl cp ./scripts_temp/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_pairwise_kaks.pl $(FIXIN) $(INST_SCRIPT)/bp_pairwise_kaks.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_pairwise_kaks.pl $(INST_SCRIPT)/bp_flanks.pl: ./scripts_temp/bp_flanks.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_flanks.pl cp ./scripts_temp/bp_flanks.pl $(INST_SCRIPT)/bp_flanks.pl $(FIXIN) $(INST_SCRIPT)/bp_flanks.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_flanks.pl $(INST_SCRIPT)/bp_translate_seq.pl: ./scripts_temp/bp_translate_seq.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_translate_seq.pl cp ./scripts_temp/bp_translate_seq.pl $(INST_SCRIPT)/bp_translate_seq.pl $(FIXIN) $(INST_SCRIPT)/bp_translate_seq.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_translate_seq.pl $(INST_SCRIPT)/bp_feature_draw.pl: ./scripts_temp/bp_feature_draw.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_feature_draw.pl cp ./scripts_temp/bp_feature_draw.pl $(INST_SCRIPT)/bp_feature_draw.pl $(FIXIN) $(INST_SCRIPT)/bp_feature_draw.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_feature_draw.pl $(INST_SCRIPT)/bp_load_gff.pl: ./scripts_temp/bp_load_gff.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_load_gff.pl cp ./scripts_temp/bp_load_gff.pl $(INST_SCRIPT)/bp_load_gff.pl $(FIXIN) $(INST_SCRIPT)/bp_load_gff.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_load_gff.pl $(INST_SCRIPT)/bp_biblio.pl: ./scripts_temp/bp_biblio.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_biblio.pl cp ./scripts_temp/bp_biblio.pl $(INST_SCRIPT)/bp_biblio.pl $(FIXIN) $(INST_SCRIPT)/bp_biblio.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biblio.pl $(INST_SCRIPT)/bp_fast_load_gff.pl: ./scripts_temp/bp_fast_load_gff.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_fast_load_gff.pl cp ./scripts_temp/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_fast_load_gff.pl $(FIXIN) $(INST_SCRIPT)/bp_fast_load_gff.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fast_load_gff.pl $(INST_SCRIPT)/bp_search_overview.pl: ./scripts_temp/bp_search_overview.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_search_overview.pl cp ./scripts_temp/bp_search_overview.pl $(INST_SCRIPT)/bp_search_overview.pl $(FIXIN) $(INST_SCRIPT)/bp_search_overview.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search_overview.pl $(INST_SCRIPT)/bp_search2tribe.pl: ./scripts_temp/bp_search2tribe.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_search2tribe.pl cp ./scripts_temp/bp_search2tribe.pl $(INST_SCRIPT)/bp_search2tribe.pl $(FIXIN) $(INST_SCRIPT)/bp_search2tribe.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2tribe.pl $(INST_SCRIPT)/bp_fetch.pl: ./scripts_temp/bp_fetch.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_fetch.pl cp ./scripts_temp/bp_fetch.pl $(INST_SCRIPT)/bp_fetch.pl $(FIXIN) $(INST_SCRIPT)/bp_fetch.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_fetch.pl $(INST_SCRIPT)/bp_seq_length.pl: ./scripts_temp/bp_seq_length.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_seq_length.pl cp ./scripts_temp/bp_seq_length.pl $(INST_SCRIPT)/bp_seq_length.pl $(FIXIN) $(INST_SCRIPT)/bp_seq_length.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seq_length.pl $(INST_SCRIPT)/bp_search2gff.pl: ./scripts_temp/bp_search2gff.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_search2gff.pl cp ./scripts_temp/bp_search2gff.pl $(INST_SCRIPT)/bp_search2gff.pl $(FIXIN) $(INST_SCRIPT)/bp_search2gff.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2gff.pl $(INST_SCRIPT)/bp_extract_feature_seq.pl: ./scripts_temp/bp_extract_feature_seq.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_extract_feature_seq.pl cp 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$(INST_SCRIPT)/bp_dbsplit.pl $(FIXIN) $(INST_SCRIPT)/bp_dbsplit.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_dbsplit.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl: ./scripts_temp/bp_biofetch_genbank_proxy.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl cp ./scripts_temp/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(FIXIN) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_biofetch_genbank_proxy.pl $(INST_SCRIPT)/bp_bioflat_index.pl: ./scripts_temp/bp_bioflat_index.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_bioflat_index.pl cp ./scripts_temp/bp_bioflat_index.pl $(INST_SCRIPT)/bp_bioflat_index.pl $(FIXIN) $(INST_SCRIPT)/bp_bioflat_index.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_bioflat_index.pl $(INST_SCRIPT)/bp_search2alnblocks.pl: ./scripts_temp/bp_search2alnblocks.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_search2alnblocks.pl cp 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$(INST_SCRIPT)/bp_process_wormbase.pl cp ./scripts_temp/bp_process_wormbase.pl $(INST_SCRIPT)/bp_process_wormbase.pl $(FIXIN) $(INST_SCRIPT)/bp_process_wormbase.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_wormbase.pl $(INST_SCRIPT)/bp_search2BSML.pl: ./scripts_temp/bp_search2BSML.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_search2BSML.pl cp ./scripts_temp/bp_search2BSML.pl $(INST_SCRIPT)/bp_search2BSML.pl $(FIXIN) $(INST_SCRIPT)/bp_search2BSML.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_search2BSML.pl $(INST_SCRIPT)/bp_taxid4species.pl: ./scripts_temp/bp_taxid4species.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_taxid4species.pl cp ./scripts_temp/bp_taxid4species.pl $(INST_SCRIPT)/bp_taxid4species.pl $(FIXIN) $(INST_SCRIPT)/bp_taxid4species.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_taxid4species.pl $(INST_SCRIPT)/bp_mask_by_search.pl: ./scripts_temp/bp_mask_by_search.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_mask_by_search.pl cp ./scripts_temp/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mask_by_search.pl $(FIXIN) $(INST_SCRIPT)/bp_mask_by_search.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mask_by_search.pl $(INST_SCRIPT)/bp_mrtrans.pl: ./scripts_temp/bp_mrtrans.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_mrtrans.pl cp ./scripts_temp/bp_mrtrans.pl $(INST_SCRIPT)/bp_mrtrans.pl $(FIXIN) $(INST_SCRIPT)/bp_mrtrans.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_mrtrans.pl $(INST_SCRIPT)/bp_process_gadfly.pl: ./scripts_temp/bp_process_gadfly.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_process_gadfly.pl cp ./scripts_temp/bp_process_gadfly.pl $(INST_SCRIPT)/bp_process_gadfly.pl $(FIXIN) $(INST_SCRIPT)/bp_process_gadfly.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_process_gadfly.pl $(INST_SCRIPT)/bp_gccalc.pl: ./scripts_temp/bp_gccalc.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_gccalc.pl cp ./scripts_temp/bp_gccalc.pl $(INST_SCRIPT)/bp_gccalc.pl $(FIXIN) $(INST_SCRIPT)/bp_gccalc.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_gccalc.pl $(INST_SCRIPT)/bp_seqconvert.pl: ./scripts_temp/bp_seqconvert.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_seqconvert.pl cp ./scripts_temp/bp_seqconvert.pl $(INST_SCRIPT)/bp_seqconvert.pl $(FIXIN) $(INST_SCRIPT)/bp_seqconvert.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_seqconvert.pl $(INST_SCRIPT)/bp_oligo_count.pl: ./scripts_temp/bp_oligo_count.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_oligo_count.pl cp ./scripts_temp/bp_oligo_count.pl $(INST_SCRIPT)/bp_oligo_count.pl $(FIXIN) $(INST_SCRIPT)/bp_oligo_count.pl -@$(CHMOD) $(PERM_RWX) $(INST_SCRIPT)/bp_oligo_count.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl: ./scripts_temp/bp_process_ncbi_human.pl Makefile $(INST_SCRIPT)/.exists @rm -f $(INST_SCRIPT)/bp_process_ncbi_human.pl cp ./scripts_temp/bp_process_ncbi_human.pl $(INST_SCRIPT)/bp_process_ncbi_human.pl $(FIXIN) $(INST_SCRIPT)/bp_process_ncbi_human.pl -@$(CHMOD) $(PERM_RWX) 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Makefile : Makefile.PL $(CONFIGDEP) @echo "Makefile out-of-date with respect to $?" @echo "Cleaning current config before rebuilding Makefile..." -@$(RM_F) Makefile.old -@$(MV) Makefile Makefile.old -$(MAKE) -f Makefile.old clean $(DEV_NULL) || $(NOOP) $(PERL) "-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" Makefile.PL @echo "==> Your Makefile has been rebuilt. <==" @echo "==> Please rerun the make command. <==" false # To change behavior to :: would be nice, but would break Tk b9.02 # so you find such a warning below the dist target. #Makefile :: $(VERSION_FROM) # @echo "Warning: Makefile possibly out of date with $(VERSION_FROM)" # --- MakeMaker staticmake section: # --- MakeMaker makeaperl section --- MAP_TARGET = perl FULLPERL = /usr/bin/perl $(MAP_TARGET) :: static $(MAKE_APERL_FILE) $(MAKE) -f $(MAKE_APERL_FILE) $@ $(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) @echo Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET) @$(PERL) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) \ Makefile.PL DIR= \ MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \ MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= # --- MakeMaker test section: TEST_VERBOSE=0 TEST_TYPE=test_$(LINKTYPE) TEST_FILE = test.pl TEST_FILES = TESTDB_SW = -d testdb :: testdb_$(LINKTYPE) test :: $(TEST_TYPE) @echo 'No tests defined for $(NAME) extension.' test_dynamic :: pure_all testdb_dynamic :: pure_all PERL_DL_NONLAZY=1 $(FULLPERL) $(TESTDB_SW) -I$(INST_ARCHLIB) -I$(INST_LIB) -I$(PERL_ARCHLIB) -I$(PERL_LIB) $(TEST_FILE) test_ : test_dynamic test_static :: test_dynamic testdb_static :: testdb_dynamic # --- MakeMaker ppd section: # Creates a PPD (Perl Package Description) for a binary distribution. ppd: @$(PERL) -e "print qq{\n}. qq{\tbioperl\n}. qq{\tBioinformatics Toolkit\n}. qq{\tBioperl Team (bioperl-l\@bioperl.org)\n}. qq{\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\t\n}. qq{\t\n}. qq{\n}" > bioperl.ppd # --- MakeMaker pm_to_blib section: pm_to_blib: $(TO_INST_PM) @$(PERL) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)" \ "-I$(PERL_ARCHLIB)" "-I$(PERL_LIB)" -MExtUtils::Install \ -e "pm_to_blib({qw{$(PM_TO_BLIB)}},'$(INST_LIB)/auto')" @$(TOUCH) $@ # --- MakeMaker selfdocument section: # --- MakeMaker postamble section: show_tests : @echo 'type make test_ to run' @echo '' # End. -------------- next part -------------- ------------------------------- Dr. Wolf-Gerolf THIES ITG - Tox, Bau 439, Zi 507 Forschungszentrum Karlsruhe Postfach 3640 D-76021 Karlsruhe Tel: +49 7247 82-3139/-3547 Fax: +49 7247 82 3557 E-mail: thies@itg.fzk.de -------------------------------- From mwhahn at ucdavis.edu Mon Mar 1 16:13:29 2004 From: mwhahn at ucdavis.edu (Matthew Hahn) Date: Mon Mar 1 16:19:24 2004 Subject: Fwd: [Bioperl-l] Bio::PopGen::Statistics discrete calculations In-Reply-To: <1078175195.4043a5dbad588@webmail.duke.edu> References: <1078175195.4043a5dbad588@webmail.duke.edu> Message-ID: >----- Forwarded message from avilella ----- > Date: Mon, 01 Mar 2004 12:53:55 +0000 > From: avilella >Reply-To: avilella > Subject: [Bioperl-l] Bio::PopGen::Statistics discrete calculations > To: bioperl-ml > >Hi, > >I'm interested in calculating some of the statistics in >Bio::PopGen::Statistics in a discrete, position-wise, way. > >For example, > >I've done a quick implementation of the method "pi" that returns the >value of the statistic for each polymorphic positions instead of the >mean of all of them. It's "pi_discrete" method: > >http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-live/Bio/PopGen/Statistics.pm?rev=1.4&content-type=text/x-cvsweb-markup > Do you want to just calculate each site's heterozygosity? Otherwise, I'm not quite sure what 'pi' means in this context. The pi calculation currently implemented simply sums up each site's heterozygosity. >I would also like to have methods to do Sliding Window calculations for >these statistics. Something like: > >"Calculate tajima_D for windows of 100 polymorphisms that slide 10 >positions" > >Any comments about the logic, naming, interest of this methods? Sounds great--I'm sure it would get used. The only precaution I would give is that some of the formats for inputting the polymorphism data (i.e. prettybase files) do not have to include monomorphic sites. This would really mess with any kind of sliding window. cheers, Matt >Thanks, > > Albert. > >-- >Albert Vilella Bertran avilella_at_ebi_ac_uk >EMBL Outstation, European Bioinformatics Institute >Wellcome Trust Genome Campus, Hinxton >Cambs. CB10 1SD, United Kingdom >Phone: +44 (0)1223 494 448 FAX: +44 (0)1223 494 468 > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > >----- End forwarded message ----- -- Matthew W. Hahn Center for Population Biology 2320 Storer Hall University of California Davis, CA 95616 From hlapp at gnf.org Mon Mar 1 23:16:31 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Mar 1 23:22:21 2004 Subject: [Bioperl-l] load_seqdatabase.pl problem In-Reply-To: <40433322.2080403@univ-montp2.fr> Message-ID: <62B81678-6C00-11D8-B838-000A959EB4C4@gnf.org> I suspect the database wasn't fresh at the time you loaded the NCBI taxonomy. Specifically, the offending species probably was already in there through some sequence load. Alternatively, the EMBL SeqIO parser fails to parse out the NCBI taxonID and the species name slightly mismatches with the one in the NCBI taxonomy database. What is the result if you issue the following query: select t.* from taxon t, taxon_name tn where tn.taxon_id = t.taxon_id and tn.name = 'Aspergillus oryzae' and tn.name_class = 'scientific name'; -hilmar On Monday, March 1, 2004, at 04:57 AM, Eric Bazin wrote: > Hi. > > I try to import embl sequence datas in a biosql schema using the perl > script "load_seqdatabase.pl". Previously I loaded without any problem > the taxon schema from the NCBI with load_ncbi_taxonomy.pl. Can anybody > give > me a help for this? > > This is what I received: > > bash#./load_seqdatabase.pl --dbname polymorphix --format embl > /home/eric/polybase.dat > > Could not store AB022832: > ------------- EXCEPTION ------------- > MSG: Unique key query in Bio::DB::BioSQL::SpeciesAdaptor returned 3 > rows > instead of 1. Query was [name_class="scie > ntific name",binomial="Aspergillus oryzae"] > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Ba > sePersistenceAdaptor.pm:960 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/Bas > ePersistenceAdaptor.pm:856 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence > Adaptor.pm:183 > STACK Bio::DB::Persistent::PersistentObject::create > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj > ect.pm:243 > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistence > Adaptor.pm:170 > [root@thaler biosql]# :BasePersistenceAdaptor::store > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceA > daptor.pm:253 > STACK Bio::DB::Persistent::PersistentObject::store > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObje > ct.pm:270 > STACK (eval) ./load_seqdatabase.pl:517 > STACK toplevel ./load_seqdatabase.pl:500 > > -------------------------------------- > > Thanks a lot > > Eric bazin > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From cuddles21sapphire at hotmail.com Tue Mar 2 06:24:09 2004 From: cuddles21sapphire at hotmail.com (mauro) Date: Tue Mar 2 04:35:42 2004 Subject: [Bioperl-l] 8 times longer than V_I A_G R_A?? Message-ID: <1078226649-20222@excite.com> Find out more about the new drug that puts V I A G R A to shame!! http://drugsbusiness.com/sv/index.php?pid=eph9106 niki kathytacobell tanya blondie gibson concept promethe joel chinaqwerty12 larry spain angels dan utopia Get off this list by writing to http://drugsbusiness.com/sv/applepie.php From avilella at ebi.ac.uk Tue Mar 2 04:33:13 2004 From: avilella at ebi.ac.uk (avilella) Date: Tue Mar 2 04:39:37 2004 Subject: Fwd: [Bioperl-l] Bio::PopGen::Statistics discrete calculations In-Reply-To: References: <1078175195.4043a5dbad588@webmail.duke.edu> Message-ID: <1078219993.2607.24.camel@localhost.localdomain> > >I'm interested in calculating some of the statistics in > >Bio::PopGen::Statistics in a discrete, position-wise, way. > > > >For example, > > > >I've done a quick implementation of the method "pi" that returns the > >value of the statistic for each polymorphic positions instead of the > >mean of all of them. It's "pi_discrete" method: > > > >http://www.ebi.ac.uk/cvs/cvspublic/wallace/bioperl-live/Bio/PopGen/Statistics.pm?rev=1.4&content-type=text/x-cvsweb-markup > > > > > Do you want to just calculate each site's heterozygosity? Otherwise, > I'm not quite sure what 'pi' means in this context. The pi > calculation currently implemented simply sums up each site's > heterozygosity. Well, in pi_discrete I save the name of the marker in the key of the hash, which for MSA files, using Bio::PopGen::Utilities::aln_to_population is the position in the alignment: for( my $i = 0; $i < $aln->length; $i++ ) { # my $nm = "Site-$i"; my $nm = sprintf "Site-%09d", $i; Apart from that, yes*, it's just heterozygosity in sliding windows of width=1 sliding with jump=1 position each time. *pi being a bad example of the statistic_discrete methods. > >I would also like to have methods to do Sliding Window calculations for > >these statistics. Something like: > > > >"Calculate tajima_D for windows of 100 polymorphisms that slide 10 > >positions" > > > >Any comments about the logic, naming, interest of this methods? > > > Sounds great--I'm sure it would get used. The only precaution I > would give is that some of the formats for inputting the polymorphism > data (i.e. prettybase files) do not have to include monomorphic > sites. This would really mess with any kind of sliding window. I would say that there are two kinds of windows concerning to that: "Real position windows": where the window refers to the position in the alignment (either, mono- or polymorphic) "Polymorphic pos. windows": where the window refers to, e.g., the first 10 polymorphisms in the prettybase file. Obviously, with this second option, the "real" width of the window is going to be different each time. But if the name of the marker in the prettybase file informs about the position, like "Site-$i", then one can, roughly, calculate the midpoint for those polymorphisms. And about the prettybase format, I would like to have a conversor in bioperl from Bio::AlignIO aligments to prettybase "polymorphisms" or markers. Which would be the best place for that? Maybe in Bio::PopGen::Utilities? Feedback is welcomed, Thanks in advance, Albert. > > > > > cheers, > Matt > > > > >Thanks, > > > > Albert. > > > >-- > >Albert Vilella Bertran avilella_at_ebi_ac_uk > >EMBL Outstation, European Bioinformatics Institute > >Wellcome Trust Genome Campus, Hinxton > >Cambs. CB10 1SD, United Kingdom > >Phone: +44 (0)1223 494 448 FAX: +44 (0)1223 494 468 > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > >----- End forwarded message ----- > From khoueiry at ibsm.cnrs-mrs.fr Tue Mar 2 06:00:34 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Tue Mar 2 06:06:28 2004 Subject: [Bioperl-l] Sequence search Message-ID: <40446952.508@ibsm.cnrs-mrs.fr> Hi all, I'm searching in bioperl for methods that can detect in a protein sequence a subseq rich in a special amino acids. In other way, I want to find _per example_ if there is subsequence of 12 aa (sliding window) that contains at least 7 (valin + leucine) in a given sequence of 400 aa. I need to progress amino acid by amino acid using my sliding window I appreciate any help, Thanks -- --------------------------------- Pierre Khoueiry khoueiry@ibsm.cnrs-mrs.fr LCB - CNRS 31, Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France --------------------------------- From heikki at ebi.ac.uk Tue Mar 2 08:04:59 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Mar 2 08:10:51 2004 Subject: [Bioperl-l] Sequence search In-Reply-To: <40446952.508@ibsm.cnrs-mrs.fr> References: <40446952.508@ibsm.cnrs-mrs.fr> Message-ID: <200403021304.59378.heikki@ebi.ac.uk> Pierre, The closest we have is a Bio::Tools::SeqPattern, but it does not do the pattern matching. That could be added if we decide what exactly and how generic we want to implement. Ideas anyone? The code below shows one simple approach to the problem. More advanced algorthms exist, but this one is simple to work with if you want to go a head and solve your immediate problem. Yours, -Heikki ############################################## #!/usr/bin/perl -w use strict; my $s= "abjabjabjbkakjkjbkajkjanakjnakjnakjnakjnakjaankjankajakjna"; my $verbose = 0; my $length = 7; my $pattern = '[ak]'; my $threshold = 5; my $offset =0; while (1) { my $subs = substr $s, $offset, $length; last unless length($subs) eq $length; my $subsori = $subs; my $c = $subs =~ tr/$pattern/1/; print "\t", $subsori, " $c\n" if $verbose; print $subsori, " $c\n" if $c >= $threshold; $offset++; } ############################################## On Tuesday 02 Mar 2004 11:00, KHOUEIRY pierre wrote: > Hi all, > I'm searching in bioperl for methods that can detect in a protein > sequence a subseq rich in a special amino acids. In other way, I want to > find _per example_ if there is subsequence of 12 aa (sliding window) > that contains at least 7 (valin + leucine) in a given sequence of 400 > aa. I need to progress amino acid by amino acid using my sliding window > I appreciate any help, > Thanks -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From Anthony.Underwood at hpa.org.uk Tue Mar 2 08:30:06 2004 From: Anthony.Underwood at hpa.org.uk (SRMD, Col - Underwood, Anthony) Date: Tue Mar 2 08:20:55 2004 Subject: [Bioperl-l] Trace coordinates from scf files Message-ID: <427DA33A6101484BA7A72934AF90DF73051AA817@exchange1.phls.org.uk> Hi Bioperlers and Chad As a follow up to my last message on the bioperl-mailing list: I can see that the follwing methods do the following $seq->length() returns the length in bases of the sequence held within the scf file $seq->trace_length() this returns the number of points for the trace data print $seq->baseat("64") returns the base at position 64 in the sequence print $seq->qualat("64") returns the quality at position 64 in the sequence $seq->peak_indices() returns the peaks heights at each of the sequence positions however I find the $seq->trace("G") method a bit mysterious the array returned has $seq->trace_length() elements and the values are cumulative ( I think I may be dealing with a version 2 scf file). I understand that the trace values should be calculated based on delta values. something like $current_delta=$current_value-$previous_value $delta_delta=$current_delta-$previous_delta This doesn't quite work. Please could anybody enlighten me on how the trace values can be convrted into points that plotted as sequential "Y" values would represent points on a curve that resemble the traces when viewed in a an application such as Chromas. Many thanks, Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 f: 0208 3583138 e: anthony.underwood@hpa.org.uk From john.herbert at clinical-pharmacology.oxford.ac.uk Tue Mar 2 09:45:06 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Tue Mar 2 09:51:03 2004 Subject: [Bioperl-l] Partial BioPerl installations Message-ID: Hello. Is there away to only install specific parts of BioPerl on to your system. My problem is I have limited space on my machine and therefore don't want to install the whole of BioPerl if I am only going to use certain objects. I realise some classes will have super classes and all will have to be installed but I am assuming this will not need a full BioPerl install. Any information on how I could install just specific classes from BioPerl would be much appreciated, thank you. Kind regards, John Herbert, From heikki at ebi.ac.uk Tue Mar 2 11:11:26 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Mar 2 11:17:17 2004 Subject: [Bioperl-l] Partial BioPerl installations In-Reply-To: References: Message-ID: <200403021611.26589.heikki@ebi.ac.uk> John, This s something that have been discussed but no definite action has been taken. Bioperl core is still one monolithic package. However, if you really are tight with space there are some things you can do. I am assuming you are using anonymous CVS access and setting PERL5LIB to point your perl to the bioperl modules. The whole bioperl core takes ~25M. 1. Remove everything else that CVS and Bio subdirectories. This takes the disk space down to 12M. Run 'cvs update' within the Bio directory and you can keep up to date. If you need to run tests, examples or read documentation, you can do 'cvs update' in the main directory. 2. If all you need is the basic sequence manipulation classes, you can, possibly, remove a number of subdirectories under Bio. For example, if you do not directly need these, could try removing them: CodonUsage Coordinate Das Graphics LiveSeq Map MapIO Matrix Ontology Phenotype PopGen Tree TreeIO Variation Note that I am only guessing here. If you try removing these, keep a log and be prepared to restore modules from cvs. If you really try this, please report back to the list. We'd be interested in knowing if and what works. Yours, -Heikki On Tuesday 02 Mar 2004 14:45, john herbert wrote: > Hello. > Is there away to only install specific parts of BioPerl on to your > system. My problem is I have limited space on my machine and therefore > don't want to install the whole of BioPerl if I am only going to use > certain objects. > > I realise some classes will have super classes and all will have to be > installed but I am assuming this will not need a full BioPerl install. > > Any information on how I could install just specific classes from > BioPerl would be much appreciated, thank you. > > Kind regards, > > John Herbert, > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From john.herbert at clinical-pharmacology.oxford.ac.uk Tue Mar 2 11:24:22 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Tue Mar 2 11:30:47 2004 Subject: [Bioperl-l] Partial BioPerl installations Message-ID: Thanks for the info Heikki, very helpful. One question arises, could I change the Perl library location to my own custom location instead of PERL5LIB? Thanks, John. >>> Heikki Lehvaslaiho 02/03/2004 16:11:26 >>> John, This s something that have been discussed but no definite action has been taken. Bioperl core is still one monolithic package. However, if you really are tight with space there are some things you can do. I am assuming you are using anonymous CVS access and setting PERL5LIB to point your perl to the bioperl modules. The whole bioperl core takes ~25M. 1. Remove everything else that CVS and Bio subdirectories. This takes the disk space down to 12M. Run 'cvs update' within the Bio directory and you can keep up to date. If you need to run tests, examples or read documentation, you can do 'cvs update' in the main directory. 2. If all you need is the basic sequence manipulation classes, you can, possibly, remove a number of subdirectories under Bio. For example, if you do not directly need these, could try removing them: CodonUsage Coordinate Das Graphics LiveSeq Map MapIO Matrix Ontology Phenotype PopGen Tree TreeIO Variation Note that I am only guessing here. If you try removing these, keep a log and be prepared to restore modules from cvs. If you really try this, please report back to the list. We'd be interested in knowing if and what works. Yours, -Heikki On Tuesday 02 Mar 2004 14:45, john herbert wrote: > Hello. > Is there away to only install specific parts of BioPerl on to your > system. My problem is I have limited space on my machine and therefore > don't want to install the whole of BioPerl if I am only going to use > certain objects. > > I realise some classes will have super classes and all will have to be > installed but I am assuming this will not need a full BioPerl install. > > Any information on how I could install just specific classes from > BioPerl would be much appreciated, thank you. > > Kind regards, > > John Herbert, > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From john.herbert at clinical-pharmacology.oxford.ac.uk Tue Mar 2 11:31:39 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Tue Mar 2 11:37:41 2004 Subject: [Bioperl-l] Partial BioPerl installations Message-ID: Please ignore my last question, I looked up what the PERL5LIB variable does. Sorry, John. >>> "john herbert" 02/03/2004 16:24:22 >>> Thanks for the info Heikki, very helpful. One question arises, could I change the Perl library location to my own custom location instead of PERL5LIB? Thanks, John. >>> Heikki Lehvaslaiho 02/03/2004 16:11:26 >>> John, This s something that have been discussed but no definite action has been taken. Bioperl core is still one monolithic package. However, if you really are tight with space there are some things you can do. I am assuming you are using anonymous CVS access and setting PERL5LIB to point your perl to the bioperl modules. The whole bioperl core takes ~25M. 1. Remove everything else that CVS and Bio subdirectories. This takes the disk space down to 12M. Run 'cvs update' within the Bio directory and you can keep up to date. If you need to run tests, examples or read documentation, you can do 'cvs update' in the main directory. 2. If all you need is the basic sequence manipulation classes, you can, possibly, remove a number of subdirectories under Bio. For example, if you do not directly need these, could try removing them: CodonUsage Coordinate Das Graphics LiveSeq Map MapIO Matrix Ontology Phenotype PopGen Tree TreeIO Variation Note that I am only guessing here. If you try removing these, keep a log and be prepared to restore modules from cvs. If you really try this, please report back to the list. We'd be interested in knowing if and what works. Yours, -Heikki On Tuesday 02 Mar 2004 14:45, john herbert wrote: > Hello. > Is there away to only install specific parts of BioPerl on to your > system. My problem is I have limited space on my machine and therefore > don't want to install the whole of BioPerl if I am only going to use > certain objects. > > I realise some classes will have super classes and all will have to be > installed but I am assuming this will not need a full BioPerl install. > > Any information on how I could install just specific classes from > BioPerl would be much appreciated, thank you. > > Kind regards, > > John Herbert, > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From chad at dieselwurks.com Tue Mar 2 15:40:05 2004 From: chad at dieselwurks.com (Chad Matsalla) Date: Tue Mar 2 15:46:00 2004 Subject: [Bioperl-l] Re: Trace coordinates from scf files In-Reply-To: <427DA33A6101484BA7A72934AF90DF73051AA817@exchange1.phls.org.uk> References: <427DA33A6101484BA7A72934AF90DF73051AA817@exchange1.phls.org.uk> Message-ID: > Please does anyone have experience with using the > Bio::Seq::SequenceTrace and Bio::SeqIO::scf modules to extract peak > values for the different traces (G,A,T and C) which can then be > plotted using a graphics module along with the bases themselves at the > appropriate positions. I'm a little unclear as to how the trace, peak > indices, peak_index_at, base_at etc methods work. Hi All, You can do that very easily. Check the method Bio::Seq::SequenceTrace->scf_dump(). It demonstrates how this can be done. There is a line in t/sequencetrace that calls that method but in the interest of brevity iof output it is commented out. Remove the pound for line 119 and you will get output like this.[1] See also the internal method Bio::Seq::SequenceTrace->_dump_traces($transformed): ' - if a scalar is included as an argument (any scalar), this procedure will dump the _delta'd trace. If you don't know what that means you should not be using this.' Note that scf_dump calls _dump_traces to produce output like this.[1] Hope that helps, Chad Matsalla [1] $ make test_sequencetrace TEST_VERBOSE=1 Count a c g t 0 0 0 0 0 1 0 0 7 0 2 0 0 28 0 3 0 0 91 0 4 0 0 203 0 5 0 0 357 0 6 0 0 525 0 7 0 0 560 0 8 0 0 525 0 9 0 0 357 0 10 0 0 203 0 11 0 0 91 0 12 0 0 28 0 13 7 0 7 0 14 28 0 0 0 15 91 0 0 0 16 203 0 0 0 17 357 0 0 0 18 525 0 0 0 19 560 0 0 0 20 525 0 0 0 21 357 0 0 0 22 203 0 0 0 23 91 0 0 0 24 28 0 0 0 25 7 0 0 7 26 0 0 0 28 27 0 0 0 91 28 0 0 0 203 29 0 0 0 357 30 0 0 0 525 31 0 0 0 560 32 0 0 0 525 33 0 0 0 357 34 0 0 0 203 35 0 0 0 91 36 0 0 0 28 ... From facemann at yahoo.com Tue Mar 2 19:07:48 2004 From: facemann at yahoo.com (Andy Hammer) Date: Tue Mar 2 19:13:38 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <20040303000748.14298.qmail@web13426.mail.yahoo.com> My RemoteBlast results are differing from my web page blast. Is there a way to view the HEADER values from NCBI's Blast page so I can duplicate them with RemoteBlast? __________________________________ Do you Yahoo!? Yahoo! Search - Find what you’re looking for faster http://search.yahoo.com From chauser at duke.edu Tue Mar 2 19:13:06 2004 From: chauser at duke.edu (Charles Hauser) Date: Tue Mar 2 19:18:58 2004 Subject: [Bioperl-l] Root::IO tempfile error Message-ID: <1078272786.2378.61.camel@pandorina> All, I'm working on a web blast script and it appears that Bio::SeqIO is not writing the temp file for the input sequence. (I'm using CVS version of bioperl updated this am) If I output $tempfile, Bio::Root::IO appears to be creating it: /scratch/B3ltaJkxr4 but if I look in /scratch nada, and if I let the script execute blast and attempt to open the results($tempfile.bls.txt) I get the server error below. ideas? thanks Charles relevant snippet of code: use constant TEMPOUTDIR => '/scratch'; my $io = new Bio::Root::IO; my ($tfh,$tempfile) = $io->tempfile(-DIR => TEMPOUTDIR); my $out = new Bio::SeqIO(-fh => $tfh, -format => 'fasta'); $out->write_seq($seq); $out->close(); [snip set up blast params ] my $blastexe = "$prog -i $tempfile -o $tempfile.bls.txt -d ".BLASTDIR."/$db E=$evalue $options"; `$blastexe`; my $parser = new Bio::SearchIO(-file => "$tempfile.bls.txt", -format => 'blast'); ------------- EXCEPTION ------------- MSG: Could not open /scratch/B3ltaJkxr4.bls.txt: No such file or directory STACK Bio::Root::IO::_initialize_io /usr/local/src/bioperl/core/Bio/Root/IO.pm:273 STACK Bio::Root::IO::new /usr/local/src/bioperl/core/Bio/Root/IO.pm:213 STACK Bio::SearchIO::new /usr/local/src/bioperl/core/Bio/SearchIO.pm:135 STACK Bio::SearchIO::new /usr/local/src/bioperl/core/Bio/SearchIO.pm:167 STACK toplevel /var/www/cgi-bin/BLAST/foo.pl:217 From Marc.Logghe at devgen.com Wed Mar 3 03:23:33 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Wed Mar 3 03:30:01 2004 Subject: [Bioperl-l] Root::IO tempfile error Message-ID: Hi Charles, You have to pass the UNLINK argument, saying you don't want to delete the file as soon as the filehandle is closed. By default it is 1. This should work: my ($tfh,$tempfile) = $io->tempfile(-DIR => TEMPOUTDIR, -UNLINK => 0); HTH, Marc > -----Original Message----- > From: Charles Hauser [mailto:chauser@duke.edu] > Sent: woensdag 3 maart 2004 1:13 > To: BioPerl-List > Subject: [Bioperl-l] Root::IO tempfile error > > > All, > > I'm working on a web blast script and it appears that > Bio::SeqIO is not > writing the temp file for the input sequence. > (I'm using CVS version of bioperl updated this am) > > If I output $tempfile, Bio::Root::IO appears to be creating it: > > /scratch/B3ltaJkxr4 > > but if I look in /scratch nada, and if I let the script execute blast > and attempt to open the results($tempfile.bls.txt) I get the server > error below. > > ideas? > > thanks Charles > > > relevant snippet of code: > > use constant TEMPOUTDIR => '/scratch'; > > my $io = new Bio::Root::IO; > my ($tfh,$tempfile) = $io->tempfile(-DIR => TEMPOUTDIR); > my $out = new Bio::SeqIO(-fh => $tfh, -format => 'fasta'); > $out->write_seq($seq); > $out->close(); > > [snip set up blast params ] > > my $blastexe = "$prog -i $tempfile -o $tempfile.bls.txt > -d ".BLASTDIR."/$db E=$evalue $options"; > `$blastexe`; > > my $parser = new Bio::SearchIO(-file => "$tempfile.bls.txt", > -format => 'blast'); > > > > > ------------- EXCEPTION ------------- > MSG: Could not open /scratch/B3ltaJkxr4.bls.txt: No such file > or directory > STACK Bio::Root::IO::_initialize_io > /usr/local/src/bioperl/core/Bio/Root/IO.pm:273 > STACK Bio::Root::IO::new > /usr/local/src/bioperl/core/Bio/Root/IO.pm:213 > STACK Bio::SearchIO::new > /usr/local/src/bioperl/core/Bio/SearchIO.pm:135 > STACK Bio::SearchIO::new > /usr/local/src/bioperl/core/Bio/SearchIO.pm:167 > STACK toplevel /var/www/cgi-bin/BLAST/foo.pl:217 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From michael.watson at bbsrc.ac.uk Wed Mar 3 05:16:04 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Wed Mar 3 05:23:59 2004 Subject: [Bioperl-l] Validate Fasta Message-ID: <20B7EB075F2D4542AFFAF813E98ACD9302822751@cl-exsrv1.irad.bbsrc.ac.uk> Hi I have searched the archives and only come up with one answer, and it didn't work - I want to validate a FASTA sequence (DNA). What I mean is that if I am given a perfect FASTA sequence, then thats ok, but if there are ANY whitespace characters, or any other characters that really shouldn't be there, I want it to throw an error. The script below was suggested by Jason in 2002: use Bio::SeqIO; my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); eval { LOOP: while( my $seq = $in->next_seq ) { $out->write_seq($seq); } }; if( $@) { print "There's an Error!\n"; goto LOOP; } I actually fired this at one of my scripts, a perl script that clearly wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA sequence characters. Here is the result: >#!/usr/bin/perl my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" /mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") ;system("/bin/gzip$location/$name.$date.tar");} This is undoubtedly a wonderfully FASTA formatted perl script, but... Anyone? Any ideas? Thanks in advance for the help! Mick From john.herbert at clinical-pharmacology.oxford.ac.uk Wed Mar 3 05:45:16 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Wed Mar 3 05:51:25 2004 Subject: [Bioperl-l] Validate Fasta Message-ID: Hello Michael. Im not a BioPerl extra-ordinaire programmer (so anyone correct me if I am wrong) but I think the -format flag should help here. Try my $in = Bio::SeqIO->new(-file => "rubbish.fasta", -format => 'Fasta'); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta", -format => 'Fasta'); I am pretty sure if you put this change in your code and run it on your very nice Perl fasta sequence, it will complain. Kind regards, JOhn. >>> "michael watson (IAH-C)" 03/03/2004 10:16:04 >>> Hi I have searched the archives and only come up with one answer, and it didn't work - I want to validate a FASTA sequence (DNA). What I mean is that if I am given a perfect FASTA sequence, then thats ok, but if there are ANY whitespace characters, or any other characters that really shouldn't be there, I want it to throw an error. The script below was suggested by Jason in 2002: use Bio::SeqIO; my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); eval { LOOP: while( my $seq = $in->next_seq ) { $out->write_seq($seq); } }; if( $@) { print "There's an Error!\n"; goto LOOP; } I actually fired this at one of my scripts, a perl script that clearly wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA sequence characters. Here is the result: >#!/usr/bin/perl my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" /mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") ;system("/bin/gzip$location/$name.$date.tar");} This is undoubtedly a wonderfully FASTA formatted perl script, but... Anyone? Any ideas? Thanks in advance for the help! Mick _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From michael.watson at bbsrc.ac.uk Wed Mar 3 05:52:58 2004 From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C)) Date: Wed Mar 3 06:02:48 2004 Subject: [Bioperl-l] Validate Fasta Message-ID: <20B7EB075F2D4542AFFAF813E98ACD9302822754@cl-exsrv1.irad.bbsrc.ac.uk> Thanks for youe help, but I am afraid not.... -----Original Message----- From: john herbert [mailto:john.herbert@clinical-pharmacology.oxford.ac.uk] Sent: 03 March 2004 10:45 To: michael.watson@bbsrc.ac.uk; bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Validate Fasta Hello Michael. Im not a BioPerl extra-ordinaire programmer (so anyone correct me if I am wrong) but I think the -format flag should help here. Try my $in = Bio::SeqIO->new(-file => "rubbish.fasta", -format => 'Fasta'); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta", -format => 'Fasta'); I am pretty sure if you put this change in your code and run it on your very nice Perl fasta sequence, it will complain. Kind regards, JOhn. >>> "michael watson (IAH-C)" 03/03/2004 10:16:04 >>> Hi I have searched the archives and only come up with one answer, and it didn't work - I want to validate a FASTA sequence (DNA). What I mean is that if I am given a perfect FASTA sequence, then thats ok, but if there are ANY whitespace characters, or any other characters that really shouldn't be there, I want it to throw an error. The script below was suggested by Jason in 2002: use Bio::SeqIO; my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); eval { LOOP: while( my $seq = $in->next_seq ) { $out->write_seq($seq); } }; if( $@) { print "There's an Error!\n"; goto LOOP; } I actually fired this at one of my scripts, a perl script that clearly wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA sequence characters. Here is the result: >#!/usr/bin/perl my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" /mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") ;system("/bin/gzip$location/$name.$date.tar");} This is undoubtedly a wonderfully FASTA formatted perl script, but... Anyone? Any ideas? Thanks in advance for the help! Mick _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From john.herbert at clinical-pharmacology.oxford.ac.uk Wed Mar 3 06:10:11 2004 From: john.herbert at clinical-pharmacology.oxford.ac.uk (john herbert) Date: Wed Mar 3 06:16:20 2004 Subject: [Bioperl-l] Validate Fasta Message-ID: Interestingly, it also does not complain if you convert the fasta Perl to EMBL format either :-) ID #!/usr/bin/perlstandard; AA; UNK; 527 BP. XX AC unknown; XX DE XX FH Key Location/Qualifiers FH XX SQ Sequence 527 BP; 38 A; 19 C; 5 G; 29 T; 436 other; my$backups ={'mysql'= "/mick/mys ql/",'apac he'="/res/ upity/apac 60 he",'mwats on'="/res/ upity/mwat son",'www' ="/www/doc s",'ensemb 120 l'="/too/f ools/ensem bl",'cgi'= "/www/cgi- bin/"};my$ location=" 180 /mick/back ups";my$da te=`date`; my@date=sp lit(/\s+/, $date);my$ 240 date=join( "_",@date[ 0..2],$dat e[$#date]) ;print"$da te\n";#whi 300 le(my($nam e,$dir)=ea ch%{$backu ps}){forea ch$name(qw (apachemys 360 qlmwatsonw wwensemblc gi)){$dir= $backups-{ $name};pri nt"tarzipp 420 ing$dir\n" ;system("/ bin/tar-c$ dir$locati on/$name.$ date.tar") 480 ;system("/ bin/gzip$l ocation/$n ame.$date. tar");} 527 // >>> "michael watson (IAH-C)" 03/03/2004 10:52:58 >>> Thanks for youe help, but I am afraid not.... -----Original Message----- From: john herbert [mailto:john.herbert@clinical-pharmacology.oxford.ac.uk] Sent: 03 March 2004 10:45 To: michael.watson@bbsrc.ac.uk; bioperl-l@portal.open-bio.org Subject: Re: [Bioperl-l] Validate Fasta Hello Michael. Im not a BioPerl extra-ordinaire programmer (so anyone correct me if I am wrong) but I think the -format flag should help here. Try my $in = Bio::SeqIO->new(-file => "rubbish.fasta", -format => 'Fasta'); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta", -format => 'Fasta'); I am pretty sure if you put this change in your code and run it on your very nice Perl fasta sequence, it will complain. Kind regards, JOhn. >>> "michael watson (IAH-C)" 03/03/2004 10:16:04 >>> Hi I have searched the archives and only come up with one answer, and it didn't work - I want to validate a FASTA sequence (DNA). What I mean is that if I am given a perfect FASTA sequence, then thats ok, but if there are ANY whitespace characters, or any other characters that really shouldn't be there, I want it to throw an error. The script below was suggested by Jason in 2002: use Bio::SeqIO; my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); eval { LOOP: while( my $seq = $in->next_seq ) { $out->write_seq($seq); } }; if( $@) { print "There's an Error!\n"; goto LOOP; } I actually fired this at one of my scripts, a perl script that clearly wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA sequence characters. Here is the result: >#!/usr/bin/perl my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" /mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") ;system("/bin/gzip$location/$name.$date.tar");} This is undoubtedly a wonderfully FASTA formatted perl script, but... Anyone? Any ideas? Thanks in advance for the help! Mick _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From ak at ebi.ac.uk Wed Mar 3 06:26:21 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Wed Mar 3 06:32:17 2004 Subject: [Bioperl-l] Validate Fasta In-Reply-To: References: Message-ID: <20040303112621.GA601@ebi.ac.uk> The only difference is (I think) that Michales code will use my Bio::Tools::GuessSeqFormat module to guess that the format is FastA (using BioPerl 1.4). Currently, the guesser will say "fasta" if the first line of the file matches /^>\w/ (and no other format matches for the first line), or if any other line matches /^[A-IK-NP-Z]+$/i (and no other format matches the same line). I think that sequence file format validation ought to be an optional part of Bio::SeqIO or a separate module. I haven't looked into Bio::SeqIO to see what goes on in there though... My module just provides a rough guess. Andreas On Wed, Mar 03, 2004 at 10:45:16AM +0000, john herbert wrote: > Hello Michael. > Im not a BioPerl extra-ordinaire programmer (so anyone correct me if I > am wrong) but I think the -format flag should help here. > > Try > > my $in = Bio::SeqIO->new(-file => "rubbish.fasta", -format => > 'Fasta'); > my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta", -format => > 'Fasta'); > > I am pretty sure if you put this change in your code and run it on your > very nice Perl fasta sequence, it will complain. > > Kind regards, > > JOhn. > > > >>> "michael watson (IAH-C)" 03/03/2004 > 10:16:04 >>> > Hi > > I have searched the archives and only come up with one answer, and it > didn't work - I want to validate a FASTA sequence (DNA). What I mean is > that if I am given a perfect FASTA sequence, then thats ok, but if there > are ANY whitespace characters, or any other characters that really > shouldn't be there, I want it to throw an error. The script below was > suggested by Jason in 2002: > > use Bio::SeqIO; > > my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); > my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); > > eval { > LOOP: while( my $seq = $in->next_seq ) { > $out->write_seq($seq); > } > > }; > if( $@) { > print "There's an Error!\n"; > goto LOOP; > } > > I actually fired this at one of my scripts, a perl script that clearly > wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non DNA > sequence characters. Here is the result: > > >#!/usr/bin/perl > my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac > he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb > l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" > /mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ > date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi > le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys > qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp > ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") > ;system("/bin/gzip$location/$name.$date.tar");} > > This is undoubtedly a wonderfully FASTA formatted perl script, but... > > Anyone? Any ideas? > > Thanks in advance for the help! > > Mick > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- |-][-| Andreas K?h?ri |[==]| |[--]| EMBL, European Bioinformatics Institute |=][=| |-][-| Wellcome Trust Genome Campus |[==]| |[--]| Hinxton, Cambridgeshire, CB10 1SD |=][=| |-][-| United Kingdom |[==]| From Richard.Adams at ed.ac.uk Wed Mar 3 06:26:44 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Wed Mar 3 06:32:34 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <4045C0F4.3090709@ed.ac.uk> 1. Submit your sequence to blast 2. Wait till you get the "Your request has been successfulyy submitted" page. 3. Go back to the submission page- all the options are now in the URL. I'd be interested to know what the differences are... Is it the raw report that's different or after you've parsed them through SearchIO? Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From james.wasmuth at ed.ac.uk Wed Mar 3 06:23:01 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Mar 3 06:33:14 2004 Subject: [Bioperl-l] Validate Fasta In-Reply-To: <4045BFD8.50103@ed.ac.uk> References: <4045BFD8.50103@ed.ac.uk> Message-ID: <4045C015.3070104@ed.ac.uk> from my understanding the validator was built for speed, rather than complete accuracy. It WILL fail if there is no header, but when checking the actual sequence it uses (or used) a number of general rules. They were something along the lines of: if 80% G T C A then DNA something with U's in it is RNA and anything else is protein. Forgive me if I got that wrong, it was a while back that I remember this from. If you want to check the sequence then write one... for DNA: unless ($seq=~/^[GCTA\n]+$/) { print "Error!\n"; } james > > > john herbert wrote: > >>Interestingly, it also does not complain if you convert the fasta Perl >>to EMBL format either :-) >> >>ID #!/usr/bin/perlstandard; AA; UNK; 527 BP. >>XX >>AC unknown; >>XX >>DE >>XX >>FH Key Location/Qualifiers >>FH >>XX >>SQ Sequence 527 BP; 38 A; 19 C; 5 G; 29 T; 436 other; >> my$backups ={'mysql'= "/mick/mys ql/",'apac he'="/res/ upity/apac >> 60 >> he",'mwats on'="/res/ upity/mwat son",'www' ="/www/doc s",'ensemb >> 120 >> l'="/too/f ools/ensem bl",'cgi'= "/www/cgi- bin/"};my$ location=" >> 180 >> /mick/back ups";my$da te=`date`; my@date=sp lit(/\s+/, $date);my$ >> 240 >> date=join( "_",@date[ 0..2],$dat e[$#date]) ;print"$da te\n";#whi >> 300 >> le(my($nam e,$dir)=ea ch%{$backu ps}){forea ch$name(qw (apachemys >> 360 >> qlmwatsonw wwensemblc gi)){$dir= $backups-{ $name};pri nt"tarzipp >> 420 >> ing$dir\n" ;system("/ bin/tar-c$ dir$locati on/$name.$ date.tar") >> 480 >> ;system("/ bin/gzip$l ocation/$n ame.$date. tar");} >> 527 >>// >> >> >> >> >> >>>>>"michael watson (IAH-C)" 03/03/2004 >>>>> >>>>> >>10:52:58 >>> >>Thanks for youe help, but I am afraid not.... >> >>-----Original Message----- >>From: john herbert >>[mailto:john.herbert@clinical-pharmacology.oxford.ac.uk] >>Sent: 03 March 2004 10:45 >>To: michael.watson@bbsrc.ac.uk; bioperl-l@portal.open-bio.org >>Subject: Re: [Bioperl-l] Validate Fasta >> >> >>Hello Michael. >>Im not a BioPerl extra-ordinaire programmer (so anyone correct me if I >>am wrong) but I think the -format flag should help here. >> >>Try >> >>my $in = Bio::SeqIO->new(-file => "rubbish.fasta", -format => >>'Fasta'); >>my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta", -format => >>'Fasta'); >> >>I am pretty sure if you put this change in your code and run it on >>your >>very nice Perl fasta sequence, it will complain. >> >>Kind regards, >> >>JOhn. >> >> >> >> >>>>>"michael watson (IAH-C)" 03/03/2004 >>>>> >>>>> >>10:16:04 >>> >>Hi >> >>I have searched the archives and only come up with one answer, and it >>didn't work - I want to validate a FASTA sequence (DNA). What I mean >>is >>that if I am given a perfect FASTA sequence, then thats ok, but if >>there >>are ANY whitespace characters, or any other characters that really >>shouldn't be there, I want it to throw an error. The script below was >>suggested by Jason in 2002: >> >>use Bio::SeqIO; >> >>my $in = Bio::SeqIO->new(-file => "rubbish.fasta"); >>my $out = Bio::SeqIO->new(-file => ">rubbish2.fasta"); >> >>eval { >> LOOP: while( my $seq = $in->next_seq ) { >> $out->write_seq($seq); >> } >> >>}; >>if( $@) { >> print "There's an Error!\n"; >> goto LOOP; >>} >> >>I actually fired this at one of my scripts, a perl script that clearly >>wasn't a fasta sequence - it has #'s, \ts, \ns and all sorts of non >>DNA >>sequence characters. Here is the result: >> >> >> >>>#!/usr/bin/perl >>> >>> >>my$backups={'mysql'="/mick/mysql/",'apache'="/res/upity/apac >>he",'mwatson'="/res/upity/mwatson",'www'="/www/Docs",'ensemb >>l'="/too/fools/ensembl",'cgi'="/www/cgi-bin/"};my$location=" >>/mick/backups";my$date=`date`;my@date=split(/\s+/,$date);my$ >>date=join("_",@date[0..2],$date[$#date]);print"$date\n";#whi >>le(my($name,$dir)=each%{$backups}){foreach$name(qw(apachemys >>qlmwatsonwwwensemblcgi)){$dir=$backups-{$name};print"tarzipp >>ing$dir\n";system("/bin/tar-c$dir$location/$name.$date.tar") >>;system("/bin/gzip$location/$name.$date.tar");} >> >>This is undoubtedly a wonderfully FASTA formatted perl script, but... >> >>Anyone? Any ideas? >> >>Thanks in advance for the help! >> >>Mick >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > >-- >Nematode Bioinformatics || >Blaxter Nematode Genomics Group || >School of Biological Sciences || >Ashworth Laboratories || >King's Buildings || tel: +44 131 650 7403 >University of Edinburgh || web: www.nematodes.org >Edinburgh || >EH9 3JT || >UK || > >"I have not failed. I've just found 10,000 ways that don't work." > --- Thomas Edison > > -- Nematode Bioinformatics || Blaxter Nematode Genomics Group || School of Biological Sciences || Ashworth Laboratories || King's Buildings || tel: +44 131 650 7403 University of Edinburgh || web: www.nematodes.org Edinburgh || EH9 3JT || UK || "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison From 9904982 at sms.ed.ac.uk Wed Mar 3 08:39:12 2004 From: 9904982 at sms.ed.ac.uk (martin) Date: Wed Mar 3 08:48:31 2004 Subject: [Bioperl-l] Fetching > 500 sequences In-Reply-To: <200403011427.35507.rnilsson@clarku.edu> References: <200403011427.35507.rnilsson@clarku.edu> Message-ID: <1078321151.9199.11.camel@adorus.cap.ed.ac.uk> Hi, I've experienced a similar problem with the 500 sequence limit. I've not found a way round it; my solution has been to download the sequences you want in GenBank format using SRS from the ncbi website, then open it thus: my $stream=Bio::SeqIO->new(-file => 'filename.genbank', -format => 'GenBank'); #process each record in turn.. while (my $seq=$stream->next_seq()){ do_something } hope this helps. Martin On Mon, 2004-03-01 at 19:27, henrik nilsson wrote: > Hi, > > It seems that I have problems with fetching more than 500 sequences from > Genbank using Bioperl. It looks like the script (attached below) fetches all > the 7000+ sequences, but only 500 make it to the output file. Is there any > way to get all these 7000+ sequences written to the file - that is, is it > possible to sidestep the 500 seq. limit? > > Thanks for your time, > > Rolf > > > > > Please find the script below. When I run it, I get > > Writing accession number AJ406491 > ... etc ... > Writing accession number AJ406489 > Writing accession number AJ406471 > Writing accession number AJ406465 > Writing accession number AJ406461 > Total number of records found = 7053 > > but when I type > > [rolf@localhost dir]$ cat data.gb | grep 'BASE COUNT' | wc -l > 500 > [rolf@localhost dir]$ > > It is clear that only 500 seq. were written to the file. > > #!/usr/bin/perl -w > use strict; > use Bio::DB::GenBank; > use Bio::DB::Query::GenBank; > use IO::String; > use Bio::SeqIO; > use Bio::Seq::RichSeq; > > > my $query_string = 'Boletales'; > > my $query = Bio::DB::Query::GenBank->new(-db=>'nucleotide', > -query=>$query_string); > my $out = Bio::SeqIO->new(-file=>">data.gb", -format=>'genbank'); > > my $count = $query->count; > > my $gb = new Bio::DB::GenBank(); > > my $stream = $gb->get_Stream_by_query($query); > > while (my $seq = $stream->next_seq) { > print "Writing accession number ", $seq->accession_number,"\n"; > $out->write_seq($seq); > } > > print "Total number of records found = $count\n"; > > exit; > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Martin Jones Blaxter Nematode Genomics Lab ICAPB Ashworth Labs Kings Buildings University of Edinburgh Edinburgh 0131 650 6761 9904982@sms.ed.ac.uk From tintin21public at hotmail.com Wed Mar 3 11:16:59 2004 From: tintin21public at hotmail.com (emory) Date: Wed Mar 3 09:28:02 2004 Subject: [Bioperl-l] 8 times longer than V_I A_G R_A?? Message-ID: <1078330619-15212@excite.com> Find out more about the new drug that puts V I A G R A to shame!! http://drugsbusiness.com/sv/index.php?pid=eph9106 church imagelulu dan alison cookies robinhoo olivier dickhead barrykingdom dougie aylmer chevy cyrano boogie Get off this list by writing to http://drugsbusiness.com/sv/applepie.php From off2w0rk at yahoo.com Tue Mar 2 20:45:12 2004 From: off2w0rk at yahoo.com (facemann) Date: Wed Mar 3 11:07:05 2004 Subject: [Bioperl-l] Sequence search Message-ID: <20040303014512.67475.qmail@web41303.mail.yahoo.com> Its not BioPerl, but you might consider PatScan. Its a good search program written in C and I think it uses perl. Check it out at http://www-unix.mcs.anl.gov/compbio/PatScan/HTML/ --------------------------------- Do you Yahoo!? Yahoo! Search - Find what you’re looking for faster. From off2w0rk at yahoo.com Tue Mar 2 21:03:02 2004 From: off2w0rk at yahoo.com (facemann) Date: Wed Mar 3 11:07:06 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <20040303020302.79270.qmail@web41310.mail.yahoo.com> Ah... Solved the header problem. Merely check all the option you desire on the NCBI web page and hit the "Get URL" button at the bottom of the page. Now all the choices are shown. --------------------------------- Do you Yahoo!? Yahoo! Search - Find what you’re looking for faster. From off2w0rk at yahoo.com Tue Mar 2 23:10:15 2004 From: off2w0rk at yahoo.com (facemann) Date: Wed Mar 3 11:07:10 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <20040303041015.26947.qmail@web41314.mail.yahoo.com> I have found the HEADER values and matched them but my scores still differ. This is causing a bit of head scratching... I have matched everything that I thought could cause a difference and a few that shouldn't make the slightest difference. My HEADER code: my @params = ( '-prog' => $prog, '-data' => $db, '-expect' => $e_val, '-readmethod' => 'SearchIO' ); my $factory = Bio::Tools::Run::RemoteBlast->new(@params); $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = 'Pairwise'; $Bio::Tools::Run::RemoteBlast::HEADER{'AUTO_FORMAT'} = 'Semiauto'; $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'nr'; $Bio::Tools::Run::RemoteBlast::HEADER{'HITLIST_SIZE'} = '3'; $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10'; $Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} = '11'; $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'Alignment'; $Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'plain'; # the following line locks up the query #$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'all'; $Bio::Tools::Run::RemoteBlast::HEADER{'GET_SEQUENCE'} = 'on'; $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'on'; $Bio::Tools::Run::RemoteBlast::HEADER{'PAGE'} = 'Nucleotides'; delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'}; print $factory->header, "\n"; --------------------------------- Do you Yahoo!? Yahoo! Search - Find what you’re looking for faster. From chapmanb at uga.edu Wed Mar 3 10:51:17 2004 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Mar 3 11:07:11 2004 Subject: [Bioperl-l] Fetching > 500 sequences In-Reply-To: <1078321151.9199.11.camel@adorus.cap.ed.ac.uk> References: <200403011427.35507.rnilsson@clarku.edu> <1078321151.9199.11.camel@adorus.cap.ed.ac.uk> Message-ID: <20040303155117.GA51845@evostick.agtec.uga.edu> Hi Rolf, Martin; > > It seems that I have problems with fetching more than 500 sequences from > > Genbank using Bioperl. It looks like the script (attached below) fetches all > > the 7000+ sequences, but only 500 make it to the output file. Is there any > > way to get all these 7000+ sequences written to the file - that is, is it > > possible to sidestep the 500 seq. limit? I actually debugged and fixed this problem recently for Biopython -- it looks like a change in the way EUtils works. If you pass 'retmax' to the eutils URL then it will only give you back at max 500 sequences, no matter what you pass for this parameter. The fix I found that worked was to not pass 'retmax'. The attached patch to Bio/DB/Query/GenBank.pm should fix the problem, if similar symptoms equal similar fixes in this case. An actual Perl/BioPerl person should look at this, though, as I'm not to be trusted for coding Perl :-). Hope this helps. Brad -------------- next part -------------- *** Bio/DB/Query/GenBank.pm.orig Tue Sep 9 17:29:00 2003 --- Bio/DB/Query/GenBank.pm Wed Mar 3 10:44:21 2004 *************** *** 197,203 **** $method = 'get'; $base = ESEARCH; push @params,('term' => $self->query); ! push @params,('retmax' => $self->{'_count'} || MAXENTRY); ($method,$base,@params); } --- 197,204 ---- $method = 'get'; $base = ESEARCH; push @params,('term' => $self->query); ! # Providing 'retmax' limits queries to 500 sequences ! # push @params,('retmax' => $self->{'_count'} || MAXENTRY); ($method,$base,@params); } From tan10 at psu.edu Wed Mar 3 16:03:45 2004 From: tan10 at psu.edu (Dr. Todd Naumann) Date: Wed Mar 3 11:09:45 2004 Subject: [Bioperl-l] Bio::Graphics::Glyph::translation.pm Message-ID: <1078347825.4592.39.camel@gentiBk> Hi, I am trying to use the translation glyph and I am running into problems. When I run the program below with glyph=>'dna' I get a picture of double stranded DNA sequence as I expected. When I try to use glyph=>'translation' I get the following error message: Can't locate object method "translate" via package "Bio::SeqFeature::Generic" at /usr/lib/perl5/site_perl/5.8.2/Bio/Graphics/Glyph/translation.pm line 134, line 118. I tried to find another SeqFeature object that has a translate method but did not have any luck. If someone could point me in the right direction I would really appreciate it. -Todd #!/usr/bin/perl use strict; use warnings; use Bio::Graphics; use Bio::SeqFeature::Generic; use Bio::SeqIO; # initialize the graphics panel my $panel = Bio::Graphics::Panel->new(-length => 80, -width => 800, -pad_left => 10, -pad_right => 10, ); # make the feature object my $feature = Bio::SeqFeature::Generic->new(-start=>1, -end=>60, ); # create a sequence object my $seqIO_object = Bio::SeqIO->new(-file => 'test_sequence.gb', -format => 'genbank', ); my $seq_object = $seqIO_object->next_seq(); # attach sequence object to feature $feature->attach_seq($seq_object); # add track to panel $panel->add_track($feature, -glyph => 'translation', -fgcolor => 'black', ); print $panel->png; exit; ============================ Todd Naumann Dept. of Chemistry Penn State University University Park, PA 16802 From brian_osborne at cognia.com Wed Mar 3 12:04:19 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Mar 3 12:10:13 2004 Subject: [Bioperl-l] Fetching > 500 sequences In-Reply-To: <20040303155117.GA51845@evostick.agtec.uga.edu> Message-ID: Brad, Thank you, I'll apply the patch in bioperl-live. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Brad Chapman Sent: Wednesday, March 03, 2004 10:51 AM To: bioperl Subject: Re: [Bioperl-l] Fetching > 500 sequences Hi Rolf, Martin; > > It seems that I have problems with fetching more than 500 sequences from > > Genbank using Bioperl. It looks like the script (attached below) fetches all > > the 7000+ sequences, but only 500 make it to the output file. Is there any > > way to get all these 7000+ sequences written to the file - that is, is it > > possible to sidestep the 500 seq. limit? I actually debugged and fixed this problem recently for Biopython -- it looks like a change in the way EUtils works. If you pass 'retmax' to the eutils URL then it will only give you back at max 500 sequences, no matter what you pass for this parameter. The fix I found that worked was to not pass 'retmax'. The attached patch to Bio/DB/Query/GenBank.pm should fix the problem, if similar symptoms equal similar fixes in this case. An actual Perl/BioPerl person should look at this, though, as I'm not to be trusted for coding Perl :-). Hope this helps. Brad From paeruginosa at hotmail.com Wed Mar 3 14:51:59 2004 From: paeruginosa at hotmail.com (Andrew Walsh) Date: Wed Mar 3 14:57:50 2004 Subject: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) Message-ID: Hello, My question is not really related to a specific Bioperl library, so I apologize. If there is a specific 'BLAST' newsgroup, I will be happy to post there. But I was hoping somebody on the Bioperl list had some experience doing nucleic acid searches with small word sizes. I would like to search for small (5-7) bp matches between an oligo sequence and a ~100,000 mRNA database. I've tried doing this with WU-BLAST and NCBI-BLAST. NCBI-BLAST does not allow word sizes below 7, so I've tried lots of different command line parameters for WU-BLAST. I've tried these searches with versions 2.0a19 (alpha) and 2.0 of WU-BLAST. I get quite strange results when I start lowering the word size below the default (11). For example, with the alpha version, I get more hits with a word size of 10 than I do with a word size of 7. With the beta version, I get the same number of hits with word sizes 10 and 7. I've checked this by hand, and the 'missing' hits do in fact have stretches of 7 continuous bps matching. Here is an example of one of the command lines I've tried running: blastn human_refseq.fasta seq3.fasta W=5 S=5 M=1 V=100000 B=100000 I've tried adjusting every parameter I thought would affect the search results, but still cannot recover the 'missing' hits. Maybe BLAST is the wrong tool for this. I'd just like something that's fast. If anyone has some advice, it would be greatly appreciated. Thanks a lot, Andrew _________________________________________________________________ Add photos to your messages with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=dept/features&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From jbedell at oriongenomics.com Wed Mar 3 15:59:16 2004 From: jbedell at oriongenomics.com (Joseph Bedell) Date: Wed Mar 3 16:05:21 2004 Subject: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) Message-ID: <434AF352F9D03C4C896782B8CC78BC7636B4CB@VADER.oriongenomics.com> Hi Andrew, I'm cross-posting your question to the Sequence Search Mailing List (SSML). This should be a good place for a discussion of your problem. https://bioinformatics.org/mailman/listinfo/ssml-general Are you looking for only 5-7bp matches with no extension? How big is your oligo? One parameter that would need adjustment is E which should probably be set outrageously high (1e-10?). Can you share the seq3.fasta sequence? I could try blasting against refseq too or against some sequence that you know it should hit. Regards, Joey ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Joseph A Bedell, Ph.D. Director, Bioinformatics Orion Genomics, LLC 4041 Forest Park Ave. St. Louis, MO 63108 Office:(314)615-6979; Fax:(314)615-6975 Mobile:(314)518-1343 http://www.oriongenomics.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >bounces@portal.open-bio.org] On Behalf Of Andrew Walsh >Sent: Wednesday, March 03, 2004 1:52 PM >To: bioperl-l@portal.open-bio.org >Subject: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) > >Hello, > >My question is not really related to a specific Bioperl library, so I >apologize. If there is a specific 'BLAST' newsgroup, I will be happy to >post there. But I was hoping somebody on the Bioperl list had some >experience doing nucleic acid searches with small word sizes. > >I would like to search for small (5-7) bp matches between an oligo >sequence >and a ~100,000 mRNA database. I've tried doing this with WU-BLAST and >NCBI-BLAST. NCBI-BLAST does not allow word sizes below 7, so I've tried >lots of different command line parameters for WU-BLAST. > >I've tried these searches with versions 2.0a19 (alpha) and 2.0 of WU-BLAST. > >I get quite strange results when I start lowering the word size below the >default (11). For example, with the alpha version, I get more hits with a >word size of 10 than I do with a word size of 7. With the beta version, I >get the same number of hits with word sizes 10 and 7. I've checked this by >hand, and the 'missing' hits do in fact have stretches of 7 continuous bps >matching. > >Here is an example of one of the command lines I've tried running: >blastn human_refseq.fasta seq3.fasta W=5 S=5 M=1 V=100000 B=100000 > >I've tried adjusting every parameter I thought would affect the search >results, but still cannot recover the 'missing' hits. > >Maybe BLAST is the wrong tool for this. I'd just like something that's >fast. If anyone has some advice, it would be greatly appreciated. > >Thanks a lot, > >Andrew > >_________________________________________________________________ >Add photos to your messages with MSN 8. Get 2 months FREE*. >http://join.msn.com/?page=dept/features&pgmarket=en- >ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgma rket >%3den-ca > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l From karplus at soe.ucsc.edu Wed Mar 3 16:14:47 2004 From: karplus at soe.ucsc.edu (Kevin Karplus) Date: Wed Mar 3 16:20:47 2004 Subject: [ssml] RE: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) In-Reply-To: <434AF352F9D03C4C896782B8CC78BC7636B4CB@VADER.oriongenomics.com> (jbedell@oriongenomics.com) References: <434AF352F9D03C4C896782B8CC78BC7636B4CB@VADER.oriongenomics.com> Message-ID: <200403032114.i23LElJ1014377@cheep.cse.ucsc.edu> If searching for an exact match to a 5-mer, the approximate-match tools are a poor choice. You're much better off just reading the flat file and scanning the sequence with a standard string-match algorithm. You can probably even use the built-in regular-expression search in perl. That should be reasonably fast for a single search. The Bioperl wrappers for reading the files should make this a pretty trivial program to write, though they might make things a little too slow for heavy-duty use. If you need more speed, you could write a c or c++ program to do the i/o and use the gnu regular-expression package to do the searching. If you have many different 5-mers to search for, you could build an index, listing for each 5-mer all the sequences that contain that 5-mer. Building the index would take only one pass over the data and would allow very fast lookup. Again, one could build a prototype quickly in perl, and reimplement in a faster language if it turns out to be necessary. Kevin Karplus karplus@soe.ucsc.edu http://www.soe.ucsc.edu/~karplus life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck (lapsed) Professor of Biomolecular Engineering, University of California, Santa Cruz Undergraduate and Graduate Director, Bioinformatics Affiliations for identification only. From basu at pharm.sunysb.edu Wed Mar 3 17:45:44 2004 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Wed Mar 3 17:51:28 2004 Subject: [Bioperl-l] Functionality of Bio::DB::Flat module Message-ID: <40466018.7050007@pharm.sunysb.edu> Hi, I am trying to create some obda compliant indexed fasta sequence file using the Bio::DB::Flat module. Earlier i have used the Bio::Index::Fasta module and provided my own id_parser using the callback subroutine. However, i could'nt find any way to use the same with Bio::DB::Flat module. So, does the Bio::DB::Flat module lacks this functionality. Is there is any way to get around of this problem. Thanks in advance. -siddhartha From dmb at mrc-dunn.cam.ac.uk Wed Mar 3 17:49:11 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed Mar 3 17:53:14 2004 Subject: [ssml] RE: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) In-Reply-To: <434AF352F9D03C4C896782B8CC78BC7636B4CB@VADER.oriongenomics.com> Message-ID: One solution which springs to mind (but isn't yet 'off the shelf') is to customize cd-hit a bit. By default cd-hit clusters sequences, but it does this using a 'words in common' heuristic to filter sequences which are likely to be below a certain identity threshold. If you need heavy duty calculation, and you are OK with c / c++, modifing cd-hit would be the best bet (and the cd-hit project is trying to attract developers!). Cheers, Dan. On Wed, 3 Mar 2004, Joseph Bedell wrote: > Hi Andrew, > > I'm cross-posting your question to the Sequence Search Mailing List > (SSML). This should be a good place for a discussion of your problem. > > https://bioinformatics.org/mailman/listinfo/ssml-general > > Are you looking for only 5-7bp matches with no extension? How big is > your oligo? One parameter that would need adjustment is E which should > probably be set outrageously high (1e-10?). Can you share the seq3.fasta > sequence? I could try blasting against refseq too or against some > sequence that you know it should hit. > > Regards, > Joey > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Joseph A Bedell, Ph.D. > Director, Bioinformatics > Orion Genomics, LLC > 4041 Forest Park Ave. > St. Louis, MO 63108 > Office:(314)615-6979; Fax:(314)615-6975 > Mobile:(314)518-1343 > http://www.oriongenomics.com > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > >-----Original Message----- > >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > >bounces@portal.open-bio.org] On Behalf Of Andrew Walsh > >Sent: Wednesday, March 03, 2004 1:52 PM > >To: bioperl-l@portal.open-bio.org > >Subject: [Bioperl-l] Small word sizes with BLAST (WU, NCBI) > > > >Hello, > > > >My question is not really related to a specific Bioperl library, so I > >apologize. If there is a specific 'BLAST' newsgroup, I will be happy > to > >post there. But I was hoping somebody on the Bioperl list had some > >experience doing nucleic acid searches with small word sizes. > > > >I would like to search for small (5-7) bp matches between an oligo > >sequence > >and a ~100,000 mRNA database. I've tried doing this with WU-BLAST and > >NCBI-BLAST. NCBI-BLAST does not allow word sizes below 7, so I've > tried > >lots of different command line parameters for WU-BLAST. > > > >I've tried these searches with versions 2.0a19 (alpha) and 2.0 of > WU-BLAST. > > > >I get quite strange results when I start lowering the word size below > the > >default (11). For example, with the alpha version, I get more hits > with a > >word size of 10 than I do with a word size of 7. With the beta > version, I > >get the same number of hits with word sizes 10 and 7. I've checked > this by > >hand, and the 'missing' hits do in fact have stretches of 7 continuous > bps > >matching. > > > >Here is an example of one of the command lines I've tried running: > >blastn human_refseq.fasta seq3.fasta W=5 S=5 M=1 V=100000 B=100000 > > > >I've tried adjusting every parameter I thought would affect the search > >results, but still cannot recover the 'missing' hits. > > > >Maybe BLAST is the wrong tool for this. I'd just like something that's > >fast. If anyone has some advice, it would be greatly appreciated. > > > >Thanks a lot, > > > >Andrew > > > >_________________________________________________________________ > >Add photos to your messages with MSN 8. Get 2 months FREE*. > >http://join.msn.com/?page=dept/features&pgmarket=en- > >ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgma > rket > >%3den-ca > > > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > ssml-general mailing list > ssml-general@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/ssml-general > From lawso1n98 at hotmail.com Thu Mar 4 01:15:17 2004 From: lawso1n98 at hotmail.com (dean) Date: Thu Mar 4 01:21:09 2004 Subject: [Bioperl-l] Save up to 80% on your medications! Message-ID: <1078380917-23422@excite.com> Buy the drugs you need at huge discounts from Offshore Pharmacy! http://bigdiscounts.selcydc.com/s95/index.php?id=s95 This weeks specials include great deals on: - V i a g r a Soft Tabs - (Takes effect in a quarter of the time!) - Super V i a g r a - (Lasts 8 times longer!) - U l t r a m - (Pain Relief) - S o m a - (Muscle Relaxants) - Z y b a n - (Stop Smoking) - P r o z a c - (Anti-Depressant) - X a n a x - (Anti-Depressant) - V a l i u m - (Anxiety Relief) http://bigdiscounts.selcydc.com/s95/index.php?id=s95 pollard deliver indiana jtwalton sstberna tulip mjkuzia thesis Golferklopfer drojek shells njashley sillars rock adrian schwarz vicky3 cvdors Get off this list by writing to getmeoff731@excitemail.com From ildhdbu at ezagenda.com Thu Mar 4 03:04:38 2004 From: ildhdbu at ezagenda.com (Franklin Wilkerson) Date: Thu Mar 4 03:10:19 2004 Subject: [Bioperl-l] RE[2]: earn . Message-ID: <200403038929.HMS94564@gate7.ezagenda.com> Top quality software stripped from it's Expensive. Extra's gives you the lowest Possible price - Guaran1eed! http://www.goodsoftwarenow.biz/lnow/?showman The 10 All-Time Best Software Products at Rock Bottom Prices! -s-t-o-p- http://goodsoftwarenow.biz/re/clean.php?seaside ----0125611139935041814-- From Richard.Adams at ed.ac.uk Thu Mar 4 03:28:24 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Thu Mar 4 03:34:13 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <4046E8A8.3050700@ed.ac.uk> Can you send the output from web and scripted versions and your input sequence? It's harder to fix otherwise. Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From mbatesalann at netscape.net Thu Mar 4 06:35:36 2004 From: mbatesalann at netscape.net (mbatesalann@netscape.net) Date: Thu Mar 4 06:34:32 2004 Subject: [Bioperl-l] REPLY SOON Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From t.goetz at dkfz-heidelberg.de Thu Mar 4 08:58:59 2004 From: t.goetz at dkfz-heidelberg.de (Thomas =?iso-8859-1?q?G=F6tz?=) Date: Thu Mar 4 08:56:48 2004 Subject: [Bioperl-l] PubMed and UTF8 Message-ID: <200403041458.59119.t.goetz@dkfz-heidelberg.de> a little bit offtopic maybe, but I thought this would be the best place to ask ;) I want to automatically download abstracts from PubMed for database storage. As many author's names contain umlauts (e.g. german Umlaute ?,?,? etc.) I also want to catch them. Right now I'm using LWP::Simple and get($URL) to download articles, but umlauts aren't displayed correctly that way. Anybody could give me a hint on how to solve that? Tia, Tom -- Thomas G?tz German Cancer Research Center Central Spectroscopic Department - B090 Im Neuenheimer Feld 280 D-69120 Heidelberg Tel. +49-6221-424670 Fax +49-6221-42524670 Email: t.goetz@dkfz-heidelberg.de http://www.dkfz.de/spec/ From Nathan.Agrin at umassmed.edu Thu Mar 4 09:54:12 2004 From: Nathan.Agrin at umassmed.edu (Agrin, Nathan) Date: Thu Mar 4 09:59:51 2004 Subject: [Bioperl-l] Clickable Glyphs... Message-ID: <89AA811FD79DC94788093B23DA79E71FD9AC0A@edunivmail02.ad.umassmed.edu> I finally got Bio::Graphics to start generating some images for me. 2 quick questions I can't seem to resolve. Is there anyway to have the description of the track placed to the right of the track, instead of under it? Is there a way to keep tracks from aligning on the same vertical plane? I am trying to visualize some interpro hits and I want each type of conserved region to exist on its own track in box form with a straight line connecting and/or taking up the remainder of the track. I'm hoping these are just some basic options I've over looked. Thanks, Nate -----Original Message----- From: Lincoln Stein [mailto:lstein@cshl.edu] Sent: Thursday, February 19, 2004 5:09 AM To: Jonathan Greenwood; bioperl-l@bioperl.org Subject: Re: [Bioperl-l] Clickable Glyphs... -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Get the latest CVS version of bioperl-live and read the section of the Bio::Graphics::Panel manual page labeled "Creating Imagemaps." Essentially what you need to do is to replace the section after you create the panel with this: my ($url,$map,$mapname) - $panel->image_and_map( -root => '/var/www/html', -url => '/tmpimages'); print $q->header(),$q->start_html('A Bitmap Rendering'); print $q->img({-src=>$url,-usemap=>"#$mapname"); print $map; print $q->end_html; I'm frankly more fond of the function-oriented CGI calls, so I would bring in the standard functions and then: print header(), start_html('A Bitmap Rendering'), img({-src=>$url,-usemap=>"#$mapname"), $map, end_html(); Lincoln On Wednesday 18 February 2004 05:53 pm, Jonathan Greenwood wrote: > Hi, I've submitted my code with the email, what I'm trying to do is > to render a Genbank file as a png file, I need to make each glyph > clickable(I'm also displaying this page online)...any help with the > new changes to Bio::Graphics::Panel would be appreciated...many > thanks... > > Sincerely, > > Jonathan Greenwood > email: jonathon@mgcheo.med.uottawa.ca > > code: > #! /usr/local/bin/perl -wT > > use strict; > use Bio::Graphics; > use Bio::SeqIO; > use Bio::SeqFeature::Generic; > use CGI; > use CGI::Pretty; > > my $file = 'x65306.gb'; > my $io = Bio::SeqIO->new(-file=>$file); > my $seq = $io->next_seq; > my $wholeseq = Bio::SeqFeature::Generic->new(-start=>1, > > -end=>$seq->length); > my @features = $seq->all_SeqFeatures; > my $q = new CGI; > > # sort features by their primary tags > my %sorted_features; > for my $f (@features) { > my $tag = $f->primary_tag; > push @{$sorted_features{$tag}},$f; > } > > print $q->header( 'text/html' ); > print $q->start_html('A Vector Rendering'); > > my $panel = Bio::Graphics::Panel->new(-length => $seq->length, > -width => 1000, > -pad_left => 10, > -pad_right => 10, > -key_color => 'white', > -key_spacing => 15, > -key_style => 'bottom', > -spacing => -0.25, > -box_subparts => 'true' > ); > > my ($url,$map,$mapname) = $panel->image_and_map(-root => > '/webfiles/cgi-bin', > -url => '/tmpimages', > ); > > $panel->add_track($wholeseq, > -glyph => 'arrow', > -bump => +1, > -double => 1, > -tick => 2 > ); > > $panel->add_track($wholeseq, > -glyph => 'generic', > -bgcolor => 'purple', > -height => 12, > -key => 'Whole Sequence', > -title => 'Whole Sequence' > ); > > # special feature > if ($sorted_features{CDS}) { > $panel->add_track($sorted_features{CDS}, > -glyph => 'transcript2', > -bgcolor => 'orange', > -bump => +1, > -height => 12, > -key => 'CDS', > -label => \&gene_label, > -title => 'CDS', > -link => 'feature1.html#CDS' > ); > delete $sorted_features{'CDS'}; > } > > #general case > my @colors = qw(wheat blue yellow green cyan chartreuse magenta > gray); my $idx = 0; > for my $tag (sort keys %sorted_features) { > my $features = $sorted_features{$tag}; > $panel->add_track($features, > -glyph => 'generic', > -bgcolor => $colors[$idx++ % @colors], > -fgcolor => 'black', > -font2color => 'red', > -key => "${tag}s", > -bump => +1, > -height => 12, > -label => \&gene_label, > -description => \&generic_description, > -title => \&gene_label, > -link => 'feature1.html#$tag', > ); > } > > print $q->img({-src=>$url,-usemap=>"#$mapname"}); > print $q->$map; > print $q->($panel->png); > > print $q->exit_html; > > exit; > > sub gene_label { > my $feature = shift; > my @notes; > foreach (qw(product gene)) { > next unless $feature->has_tag($_); > @notes = $feature->each_tag_value($_); > last; > } > $notes[0]; > } > > sub generic_description { > my $feature = shift; > my $description; > foreach ($feature->all_tags) { > my @values = $feature->each_tag_value($_); > $description .= $_ eq 'note' ? "@values" : "$_=@values; "; > } > $description =~ s/; $//; # get rid of last > $description; > } > > _________________________________________________________________ > The new MSN 8: smart spam protection and 2 months FREE* > http://join.msn.com/?page=features/junkmail > http://join.msn.com/?page=dept/bcomm&pgmarket=en-ca&RU=http%3a%2f%2 >fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFANIss0CIvUP7P+AkRAmh/AJ9SaY4MIZPS5vW5gE5xzaw7AzrjaQCdHJdE S+2+MS2vScLrVTd+C3V4mME= =MBei -----END PGP SIGNATURE----- _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From parrot21orchid at hotmail.com Thu Mar 4 23:41:27 2004 From: parrot21orchid at hotmail.com (johnnie) Date: Thu Mar 4 10:46:22 2004 Subject: [Bioperl-l] This Drug puts VlAGRA to shame!! Message-ID: <1078461687-28857@excite.com> The Biggest New Drug since V1agra! Many times as powerful. http://newmedformula.com/sv/index.php?pid=eph9106 -A quicker more stable erection -More enjoyable sex for both -Longer sex -Known to add length to you erection -Lasts up to 36 hours (not a thrity-six hour erection, but enhancement for thirty-six) We have it at a discounted savings. Save when you go through our site on all your orders. http://newmedformula.com/sv/index.php?pid=eph9106 playboy dashatrumpet pearl bmw playboy paula cuddles ladybug cosmosmookie sting1 surf asdfghjk hornet abcdef Get off this list go to http://newmedformula.com/sv/applepie.php From allenday at ucla.edu Thu Mar 4 12:50:00 2004 From: allenday at ucla.edu (Allen Day) Date: Thu Mar 4 12:55:51 2004 Subject: [Bioperl-l] PubMed and UTF8 In-Reply-To: <200403041458.59119.t.goetz@dkfz-heidelberg.de> Message-ID: have you tried using Bio::DB::Biblio::eutils in bioperl-live? that pulls pubmed info from NCBI's eutils utilities directly. i'm not sure if it handles umlautes any better than the ebi's soap biblio server, but it may be worth a look... -allen On Thu, 4 Mar 2004, Thomas G?tz wrote: > a little bit offtopic maybe, but I thought this would be the best place to > ask ;) > > I want to automatically download abstracts from PubMed for database storage. > As many author's names contain umlauts (e.g. german Umlaute ?,?,? etc.) I > also want to catch them. Right now I'm using LWP::Simple and get($URL) to > download articles, but umlauts aren't displayed correctly that way. > > Anybody could give me a hint on how to solve that? > Tia, > Tom > > From ahammer at genetics.utah.edu Thu Mar 4 13:00:26 2004 From: ahammer at genetics.utah.edu (andy hammer) Date: Thu Mar 4 13:06:14 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <001501c40212$93304ea0$4696659b@WSP> SOLVED. I am submitting no code because the issue was with the "keyboard to floor interface". :-( Once my head was on straight both BLAST and RemoteBlast.pm work perfectly. Thank you for your time and suggestions. Andy Hammer University of Utah Dept. of Human Genetics Gesteland & Atkins Lab From sjmiller at email.arizona.edu Thu Mar 4 13:13:21 2004 From: sjmiller at email.arizona.edu (Susan J. Miller) Date: Thu Mar 4 13:19:09 2004 Subject: [Bioperl-l] Broken link in bptutorial Message-ID: <404771C1.8060302@email.arizona.edu> In the BioPerl Tutorial Introduction Overview section http://www.bioperl.org/Core/Latest/bptutorial.html#i._introduction the link http://bioperl.org/Core/Latest/bioscripts.html does not work because there is punctuation included in the URL. -- Regards, -susan Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories Bio West 228 University of Arizona Tucson, AZ 85721 (520) 626-2597 From Annie.Law at nrc-cnrc.gc.ca Thu Mar 4 15:16:37 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Thu Mar 4 15:22:36 2004 Subject: [Bioperl-l] Bioperl-DB error Message-ID: <10C94843061E094A98C02EB77CFC328722FE0F@nrcmrdex1d.imsb.nrc.ca> Hi Hilmar, I would appreciate help on the following. Previously, I had errors with the make tests of both Bioperl-DB And Bioperl-1.4. I went to CVS bioperl-live and dowloaded again the Head branch of bioperl-db and bioperl-schema. As well from bioperl-live I downloaded the bioperl-1.4 from branch 1.4. I have bioperl installed in two places. I think it should be okay since the Errors that I am receiving have reduced. I not sure how to get rid of the initial install or if it matters. 1) When I performed the make test for bioperl-db all of the tests passed but there seems to be one warning and I am concerned That this will affect what I want to do which is to load unigene information into the annotation database that I am creating With the perl script load_seqdatabase.pl. Should I be concerned about this warning? [root@ bioperl-db]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/cluster....... t/cluster.......ok 1/160 t/cluster.......ok 2/160 t/cluster.......ok 3/160 t/cluster.......ok 4/160 t/cluster.......ok 5/160 t/cluster.......ok 6/160 t/cluster.......ok 7/160 etc... t/cluster.......ok 154/160 t/cluster.......ok 155/160 -------------------- WARNING --------------------- MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=1) --------------------------------------------------- t/cluster.......ok 160/160 t/cluster.......ok t/comment....... All tests successful. Files=15, Tests=930, 93 wallclock secs (31.64 cusr + 1.26 csys = 32.90 CPU) 2) I started with an empty database and I loaded the NCBI taxonomy into the database, then the GO information then locuslink (I used The --safe and --lookup options and did not get any errors). Loading locuslink information to half a day to a day. Next I loaded unigene information and it is taking three days and is still not finished?! (I meant to use the option --mergeobjs but forgot when I ran the script but I don't think that this will make a difference in terms of execution time) Something strange that is happening is that when I use mysqlcc to refresh what the current state of the database is the number of bioentries increases and then decreases. However the general overall trend is that the number of bioentries is increasing. Is this correct or is something wrong happening. I am wondering if loading of unigene information is affected by the warning I got from the make test in bioperl-db MSG: failed to store one or more child objects for an instance of class Bio::Cluster::UniGene (PK=1). If so, I am not sure how to Resolve the problem. 3) On a related note every time including the initial time that I load the database with load_ontology.pl, or load_seqdatbase.pl I use the option lookup. I want to create annotation database so I am loading first with NCBI taxonomy databse, then GO, then locuslink, then unigene. I want find out the annotation for some clones from ESTs. I think I only need to use the mergobjs option when I load the unigene information? I read the documentation of mergobjs in the load_seqdatbase.pl script but would appreciate an example of how this works. 4) Also after I intalled Bioperl-1.4 again I decreased the number of failed tests but still there Where 3 test failures and I am not sure if I should be concerned about these. t/AlignIO....................ok 75/80Bio::AlignIO: largemultifasta cannot be found Exception ------------- EXCEPTION ------------- MSG: Failed to load module Bio::AlignIO::largemultifasta. Can't locate Bio/Seq/LargeLocatableSeq.pm in @INC (@INC contains: t /usr/lib/bioperl-live/blib/lib /usr/lib/bioperl-live/blib/arch /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/lib/bioperl-live/blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. BEGIN failed--compilation aborted at /usr/lib/bioperl-live/blib/lib/Bio/AlignIO/largemultifasta.pm line 69, line 28. Compilation failed in require at /usr/lib/bioperl-live/blib/lib/Bio/Root/Root.pm line 394, line 28. STACK Bio::Root::Root::_load_module /usr/lib/bioperl-live/blib/lib/Bio/Root/Root.pm:396 STACK (eval) /usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:420 STACK Bio::AlignIO::_load_format_module /usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:419 STACK Bio::AlignIO::new /usr/lib/bioperl-live/blib/lib/Bio/AlignIO.pm:347 STACK toplevel t/AlignIO.t:283 -------------------------------------- For more information about the AlignIO system please see the AlignIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_aln" on an undefined value at t/AlignIO.t line 285, line 28. t/AlignIO....................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 76-80 Failed 5/80 tests, 93.75% okay t/AlignStats................. -the other error I got was t/GeneCoordinateMap per.......ok 70/113 t/GeneCoordinateMapper.......ok 71/113 -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- -------------------- WARNING --------------------- MSG: sorted sublocation array requested but root location doesn't define seq_id (at least one sublocation does!) --------------------------------------------------- t/GeneCoordinateMapper.......ok 72/113 t/GeneCoordinateMapper.......ok 73/113 t/GeneCoordinateMapper.......ok 74/113 ---the next error was t/tutorial...................ok 9/21 t/tutorial...................ok 10/21 ------------- EXCEPTION ------------- MSG: WebDBSeqI Request Error: HTTP/1.1 500 Internal Server Error Connection: close Date: Mon, 23 Feb 2004 15:59:50 GMT Via: 1.1 eutils.ncbi.nih.gov Server: Apache Content-Type: text/html Client-Date: Mon, 23 Feb 2004 16:05:33 GMT Client-Response-Num: 1 Client-Transfer-Encoding: chunked X-Cache: MISS from eutils.ncbi.nih.gov
NCBI/xpubmed3 - WWW Error 500 Diagnostic

Server Error

Your request could not be processed due to a problem on our Web server. This could be a transient problem, please try the query again. If it doesn't clear up within a reasonable period of time, e-mail a short description of your query and the diagnostic information shown below to:

pubmed@nlm.nih.gov - for problems with PubMed
info@ncbi.nlm.nih.gov - for problems with other services

Thank you for your assistance. We will try to fix the problem as soon as possible.
Diagnostic Information:
    Error: 500
    URL: http://eutils.ncbi.nlm.nih.gov/entrez/viewer.fcgi?WebEnvRq=1&save=efetch&db= nucleotide&val=gb%7CAF303112&retmode=text&dopt=gb&tmpl=__reset&tool=bioperl& usehistory=n
    User agent: bioperl-Bio_DB_GenBank/1.4
    Client: 130.14.29.13
    Server: xpubmed3
    Time: Mon Feb 23 11:00:20 EST 2004

NOTE: The above is an internal URL which may differ from the one you used to address the page.

Rev. 05/09/00 STACK Bio::DB::WebDBSeqI::_stream_request Bio/DB/WebDBSeqI.pm:728 STACK Bio::DB::WebDBSeqI::get_seq_stream Bio/DB/WebDBSeqI.pm:460 STACK Bio::DB::NCBIHelper::get_Stream_by_acc Bio/DB/NCBIHelper.pm:415 STACK Bio::DB::WebDBSeqI::get_Seq_by_acc Bio/DB/WebDBSeqI.pm:181 STACK Bio::DB::GenBank::get_Seq_by_acc Bio/DB/GenBank.pm:216 STACK main::__ANON__ /usr/lib/bioperl-live/blib/lib/bptutorial.pl:2920 STACK main::run_examples /usr/lib/bioperl-live/blib/lib/bptutorial.pl:4144 STACK toplevel t/tutorial.t:23 -------------------------------------- -------------------- WARNING --------------------- MSG: acc (gb|AF303112) does not exist --------------------------------------------------- Can't call method "display_id" on an undefined value at /usr/lib/bioperl-live/blib/lib/bptutorial.pl line 2921. t/tutorial...................dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 11-21 Failed 11/21 tests, 47.62% okay Failed Test Stat Wstat Total Fail Failed List of Failed ---------------------------------------------------------------------------- --- t/AlignIO.t 2 512 80 5 6.25% 76-80 t/DB.t 78 ?? % ?? t/tutorial.t 255 65280 21 11 52.38% 11-21 122 subtests skipped. Failed 3/180 test scripts, 98.33% okay. 7/8305 subtests failed, 99.92% okay. 5) I have been loading the database with the following command. I would like to know if the format option should be SeqIO:locuslink or should it simply be locuslink? Perl /root/bioperl-db/scripts/biosql/load_seqdatabase.pl --dbuser=root --dbpass=ms22a --dbname=annotatedata --namespace LocusLink --format SeqIO::locuslink /var/lib/mysql/LL_tmpl thanks very much, Annie. From barry.moore at genetics.utah.edu Thu Mar 4 15:30:49 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Mar 4 15:36:39 2004 Subject: [Bioperl-l] Getting values from a GenBank File Message-ID: <404791F9.2030103@genetics.utah.edu> While learning BioPerl, I've spent a good bit of time trying to figure out where some bit of information in a GenBank file might be tucked away in that RichSeq object, and how the hell to get at it. I finally decided it was time to sift through that object and find out what's in there and where it is. Along the way I wrote down what I found, and then added a bit to it to try and turn it into something that I would like to have found when I first started learning Bioperl. The result is a "GeneBank-file-centric" crib sheet for Bioperl. The document is centered around a "standard" GenBank file where each seperate item of information is marked-up with numbers and codes that refer to information later in the document about how to get at that particular value in using BioPerl. It also includes a script at the end that can be modified easily to get at all the major stuff in the GenBank file. This document is aimed at beginners to BioPerl, but assumes a working knowledge of Perl. The file is, of course, free to be used by anyone in anyway that they wish. I'd appreciate any corrections or improvements if you find errors or shortcomings. Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT ----------------------------------------------------------------------------------- How to get values in a GenBank file with BioPerl This is a guide to accessing the value of each item in a GenBank file with BioPerl. Underneath each value in the sample GenBank file there is a number and a 3-letter code. The 3-letter code represents the object where the associated value is stored. Table 1 at the end of this file gives the object for each code. By looking up the numbers in Table 2 at the end of this file you will find the object where this information can be called from, and the method to get (and usually set) the value. Some values may be stored by, and accessible by methods in more than one object. There is perl code at the end that you can use as a starting point to get at all of the objects and their methods. ----------------------------------------------------------------------------------- LOCUS NM_079543 1821 bp mRNA linear INV 10-DEC-2003 1-BSR 2-BPS 3-BSR 4-BSR 5-BSR 6-BSR DEFINITION Drosophila melanogaster alpha-Esterase-3 CG1257-PA (alpha-Est3) mRNA, complete cds. 7-BPS ACCESSION NM_079543 XX_123456 8-BPS 9-BSR VERSION NM_079543.2 GI:24644853 | | 10-BPS 11-BSR KEYWORDS Esterases 12-BSR SOURCE Drosophila melanogaster (fruit fly) 13-BSC ORGANISM Drosophila melanogaster 14-BSC 15-BSC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila. 16-BSC REFERENCE 1 (bases 1 to 1821) 17-BAR 18-BAR AUTHORS Adams,M.D. et al.(additional authors deleted for brevity) 19-BAR TITLE The genome sequence of Drosophila melanogaster 20-BAR JOURNAL Science 287 (5461), 2185-2195 (2000) 21-BAR MEDLINE 20196006 22-BAR PUBMED 10731132 23-BAR COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. This record is derived from an annotated genomic sequence (NT_033777). The reference sequence was derived from CG1257-RA. On Nov 6, 2002 this sequence version replaced gi:17737826. 24-BAC FEATURES Location/Qualifiers source 1..1821 25-BLS 26-BLS /organism="Drosophila melanogaster" 27-BSG /mol_type="mRNA" /db_xref="taxon:7227" /chromosome="3R" /note="genotype: y[1]; cn[1] bw[1] sp[1]; Rh6[1]" gene 1..1821 /gene="alpha-Est3" /locus_tag="CG1257" /note="alpha-Esterase-3; synonyms: B, aE3, CG1257, alphaE3, alpha-Ests, fragment B; go_function: carboxylesterase activity [goid 0004091] [evidence NAS]" /map="84D9-84D9" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" CDS 119..1750 /gene="alpha-Est3" /locus_tag="CG1257" /EC_number="3.1.1.1" /note="alpha-Est3 gene product" /codon_start=1 /product="alpha-Esterase-3 CG1257-PA" /protein_id="NP_524267.2" /db_xref="GI:24644854" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" /translation="MESLQVNTTSGPVLGKQCTGVYGDEYVSFERIPYAQPPVGHLRF MAPLPVEPWSQPLDCTKPGQKPLQFNHYSKQLEGVEDCLYLNVYAKELDSPRPLPLIV FFFGGGFEKGDPTKELHSPDYFMMRDVVVVTVSYRVGPLGFLSLNDPAVGVPGNAGLK DQLLAMEWIKENAERFNGDPKNVTAFGESAGAASVHYLMLNPKAEGLFHKAILQSGNV LCSWALCTIKNLPHRLAVNLGMESAEHVTDAMVLDFLQKLPGEKLVRPYLLSAEEHLD DCVFQFGPMVEPYKTEHCALPNHPQELLDKAWGNRIPVLMSGTSFEGLLMYARVQMAP YLLTSLKKEPEHMLPLDVKRNLPQALARHLGQRLQETHFGGNDPSAMSPESLKAYCEY ASYKVFWHPILKTLRSRVKSSSASTYLYRFDFDSPTFNHQRLKYCGDKLRGVAHVDDH SYLWYGDFSWKLDKHTPEFLTIERMIDMLTSFARTSNPNCKLIQDQLPRAKEWKPLNS KSALECLNISENIKMMELPELQKLRVWESVCQSTG" ORIGIN 1 gtactatggc aaatggtact atgggcagtc gcgataataa taataaatga ggctttaaat 61 gtttttccac tacaagataa aaagttacga gtgcgcaccg agcatttagt agacgaacat 28-BPS ... (additional sequence deleted for brevity) // ----------------------------------------------------------------------------------- Table 1. Object Key BPS - Bio::PrimarySeq BSR - Bio::Seq::RichSeq BSC - Bio::Species BAC - Bio::Annotation::Comment BAR - Bio::Annotation::Reference BLS - Bio::Location::Simple BSG - Bio::SeqFeature::Generic ----------------------------------------------------------------------------------- Table 2. Usage key 1. Bio::Seq::RichSeq $scalar = $self->display_name() or ->display_id() 2. Bio::PrimarySeq $scalar = $self->length() 3. Bio::Seq::RichSeq $scalar = $self->molecule() 4. Bio::PrimarySeq $scalar = $self->is_circular 5. Bio::Seq::RichSeq $scalar = $self->division() 6. Bio::seq::Richseq @array = $self->get_dates 7. Bio::PrimarySeq $scalar = $self->description() 8. Bio::PrimarySeq $scalar = $self->accession_number() Bio::Seq::RichSeq $scalar = $self->accession() 9. Bio::Seq::RichSeq @array = $self->get_secondary_accessions 10. Bio::PrimarySeq $scalar = $self->version() Bio::Seq::RichSeq $scalar = $self->seq_version() 11. Bio::PrimarySeq $scalar = $self->primary_id() 12. Bio::Seq::RichSeq @array = $self->get_keywords 13. Bio::Species $scalar = $self->common_name() 14. Bio::Species $scalar = $self->genus() 15. Bio::Species $scalar = $self->species() 16. Bio::Species @array = $self->classification() 17. Bio::Annotation::Reference $scalar = $self->start() 18. Bio::Annotation::Reference $scalar = $self->end() 19. Bio::Annotation::Reference $scalar = $self->authors() 20. Bio::Annotation::Reference $scalar = $self->title() 21. Bio::Annotation::Reference $scalar = $self->location() 22. Bio::Annotation::Reference $scalar = $self->medline() 23. Bio::Annotation::Reference $scalar = $self->pubmed() 24. Bio::Annotation::Comment $scalar = $self->text() or ->as_text 25. Bio::SeqFeature::Generic $scalar = $self->start() 26. Bio::SeqFeature::Generic $scalar = $self->end() 27. Bio::SeqFeature::Generic Get all features from the features table using a variation on the code below. You will need to vary the primary_tag (e.g. source, gene, CDS) and the get_tag_values (e.g. organism, db_xref, chromosome, note, gene, locus_tag, go_function, map, EC_number, codon_start, protein_id, etc.). If there is more than one primary tag associated with a give value (e.g. more than one gene) then you will have to step through the @source_feats array to find what you want rather than simply shifting the first scalar off the top. my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); 28. Bio::PrimarySeq $scalar = $self->seq() ----------------------------------------------------------------------------------- #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::DB::GenBank; #use Bio::DB::GenPept or Bio::DB::RefSeq if needed #Get some sequence IDs either like below, or read in from a file. Note that #this sample script works with the accession numbers below (at least at the time #it was written). If you add different accession numbers, and you get errors, #you may be calling for something that the sequence doesn't have. You'll have #to add your own error trapping code to handle that. my @ids = ('U59228', 'AB039327', 'BC035972'); #Create the GenBank database object to read from the database. my $gb = new Bio::DB::GenBank(); #Create a sequence stream to pass the sequences from the database to the program. my $seqio = $gb->get_Stream_by_id(\@ids); #Loop over all of the sequences that you requested. while (my $seq = $seqio->next_seq) { #Here is how you get methods directly from the RichSeq object. Replace #'display_name' with any other method in Table 2. that can be called on #either the RichSeq object directly, or the PrimarySeq object which it has #inherited. print $seq->display_name,"\n"; #Here is how to access the classification data from the species object. my $species = $seq->species; print $species->common_name,"\n"; my @class = $species->classification; print "@class\n"; #Here is a general way to call things that are stored as a Bio::SeqFeature:: #Generic object. Replace 'source' with any other of the "major" headings in #the feature table (e.g gene, CDS, etc.) and replace 'organism' with any of #the tag values found under that heading (mol_type, locus_tag, gene, etc.) my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); print "@mol_type\n"; #Here is a general way to call things that are stored as some type of a #Bio::Annotation oject. This includes reference information, and comments. #Replace reference with 'comment' to get the comment, and replace #$ref->authors with $ref->title (or location, medline, etc.) to get other #reference categories my $ann = $seq->annotation(); my @references = ($ann->get_Annotations('reference')); my $ref = shift @references; my ($title, $authors, $location, $pubmed, $reference); if (defined $ref) { $authors = $ref->authors; print "$authors\n"; } print "\n"; } ----------------------------------------------------------------------------------- This file is without copyright. It may be reproduced, edited, and redistributed at will without notice to the author, however I would appreciate it if any corrections or improvements were sent to barry.moore@genetics.utah.edu From hlapp at gnf.org Thu Mar 4 16:10:06 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Mar 4 16:15:49 2004 Subject: [Bioperl-l] Re: Bioperl-DB error In-Reply-To: <10C94843061E094A98C02EB77CFC328722FE0F@nrcmrdex1d.imsb.nrc.ca> Message-ID: <4F9FD8AC-6E20-11D8-A997-000A959EB4C4@gnf.org> On Thursday, March 4, 2004, at 12:16 PM, Law, Annie wrote: > > I have bioperl installed in two places. I think it should be okay > since the > Errors that I am receiving have reduced. I not sure how to get rid of > the > initial install or if it matters. Brian may be the better person to answer this, but if you just remove the Bio/ directory where it got installed then you should have purged most of bioperl (and bioperl-db too). There's a few files more that get installed into the root directory for site libraries/modules in perl, but if you're uncomfortable picking them then there's no harm really. It'd actually be useful to have an 'uninstall' command. Any comments or ideas anybody has had on that already? Maybe there already is and I'm just missing it? As for having two bioperls around and one of them is installed, be careful with that. I just recently found myself duped by believing that in this situation if you set PERL5LIB to point to your uninstalled bioperl perl will pick up the uninstalled version instead of the installed. This is not true - it will pick up the installed one if it can find one. To discern from where it is going to take the bioperl modules you'll have to use the -I option to perl. Unless somebody else has a better suggestion ... > > Should > I be concerned about this warning? > > t/cluster.......ok 155/160 > -------------------- WARNING --------------------- > MSG: failed to store one or more child objects for an instance of class > Bio::Cluster::UniGene (PK=1) > --------------------------------------------------- > > No, don't worry. The warning reflects the fact that one of the associations failed to insert because it was already there. I turned off the DBI warnings on failed statements, so you don't see that precede a bioperl-style warning anymore. > > All tests successful. > Files=15, Tests=930, 93 wallclock secs (31.64 cusr + 1.26 csys = > 32.90 CPU) > That's the important message to watch out for. > 2) I started with an empty database and I loaded the NCBI taxonomy > into the > database, then the GO information then locuslink (I used > The --safe and --lookup options and did not get any errors). Loading > locuslink information to half a day to a day. Sounds about what I get. The script can report progress every n entries using the --logchunk option, check out the POD. It will report some speed statistics along. > > Next I loaded unigene information and it is taking three days and is > still > not finished?! (I meant to use the option --mergeobjs but forgot when > I ran > the script but I don't think that this will make a difference in terms > of > execution time) Human and mouse unigene releases take a *very* long time to load, each takes about 2-2.5 days for me. The thing with unigene that makes it very heavy is that every cluster member becomes its own bioentry (as it is a sequence - but it won't have an actual sequence associated as the unigene SeqIO parser currently doesn't use the file that would contain them). So, when it finishes you will find several million bioentries, even though there are already 120k clusters. If you turn on progress reporting you'll see that the speed also varies widely depending on where in the file the script is. The reason is that some cluster are *huge* with tens of thousands of members. Such a single cluster will lead to tens of thousands of bioentries being created for it alone. When you load unigene the first time it doesn't really matter which combination you use for merging or look-up since none will be found anyway. Once you update though, and you don't purge Unigene from the database before, this is critical, because otherwise a large cluster will not just take a long time to insert, but also to look up. A very useful combination of options for unigene is --flatlookup (see the POD) and --mergeobjs="del-assocs-sql.pl". The latter will delete the associations partially using SQL instead of traversing object trees and deleting one association at a time. (It is therefore also specific to the schema version I wrote it for, which is Oracle, but can be ported easily to work with the mysql and pg versions. Let me know once you are there.) Also, what to keep in mind is that sequence loading can be trivially parallelized by firing up different load_seqdatabase's in parallel on different targets simultaneously. How many parallel processes are beneficial depends on your number of CPUs and what your RDBMS can handle. (e.g. I always run human and mouse unigene in parallel) Also, you can run Unigene and LL in parallel, if you've got the necessary CPU power on the db-server end. > Something strange that is happening is that when I use > mysqlcc to refresh what the current state of the database is the > number of > bioentries increases and then decreases. I don't know about mysqlcc and hence can't comment ... > I am wondering if loading of unigene information is affected by the > warning > I got from the make test in bioperl-db No, it's not, don't worry. > 3) On a related note every time including the initial time that I load > the > database with load_ontology.pl, or load_seqdatbase.pl I use the option > lookup. I want to create annotation database so I am loading first > with > NCBI taxonomy databse, then GO, then locuslink, then unigene. I want > find > out the annotation for some clones from ESTs. I think I only need to > use > the mergobjs option when I load the unigene information? If the database is empty or doesn't contain yet the datasource you're trying to load then there is no point in using --lookup (or --mergeobjs). In fact, it'll hurt, although really not much -- what will happen is that for every bioentry a look-up (SELECT query) is generated which you already know won't return anything. The lookup is fast though - should be at or below 0.01 seconds, but again that may depend on the load on the database. As for --mergeobjs, there are a couple implementations provided in the repository. Check those out to see how it works, e.g. update-on-new-date.pl, update-on-new-version.pl, freshen-annot.pl, and merge-unique-ann.pl. It's not difficult to write your own if you have other requirements. > I read the documentation of mergobjs in the load_seqdatbase.pl script > but > would appreciate an example of how this works. > > 4) Also after I intalled Bioperl-1.4 again I decreased the number of > failed > tests but still there Where 3 test failures and I am not sure if I > should be > concerned about these. > > Failed Test Stat Wstat Total Fail Failed List of Failed > ----------------------------------------------------------------------- > ----- > --- > t/AlignIO.t 2 512 80 5 6.25% 76-80 > t/DB.t 78 ?? % ?? > t/tutorial.t 255 65280 21 11 52.38% 11-21 > 122 subtests skipped. > Failed 3/180 test scripts, 98.33% okay. 7/8305 subtests failed, 99.92% > okay. > I'll leave this one to Brian, Heikki, Jason, or whoever can provide insight. > > 5) I have been loading the database with the following command. I > would like > to know if the format option should be SeqIO:locuslink or should it > simply > be locuslink? > Either will work. SeqIO::locuslink is more precise, but since SeqIO is (and will remain) the default, locuslink will work too. Only for ClusterIO formats you have to prepend the ClusterIO:: to the name of the format (e.g. unigene). Hth, -hilmar > Perl /root/bioperl-db/scripts/biosql/load_seqdatabase.pl --dbuser=root > --dbpass=ms22a --dbname=annotatedata --namespace LocusLink > --format SeqIO::locuslink /var/lib/mysql/LL_tmpl > > > thanks very much, > Annie. > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From jason at cgt.duhs.duke.edu Thu Mar 4 16:15:22 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Mar 4 16:21:14 2004 Subject: [Bioperl-l] getting a subtree In-Reply-To: <4172.152.14.14.253.1078434268.squirrel@webmail.ncsu.edu> References: <4172.152.14.14.253.1078434268.squirrel@webmail.ncsu.edu> Message-ID: Deng - here is some code to answer your question. use Bio::Tree::Tree; use Bio::TreeIO; # get a tree somehow # choose the subnodes for finding the lca somehow # get the least common ancestor my $node = $tree->get_lca( -nodes => \@nodes ); # build a new tree with its root at $node my $subtree = Bio::Tree::Tree->new(-root => $node, -nodelete => 1); my $out = Bio::TreeIO->new(-format=>'newick'); $out->write_tree($subtree); -jason -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Thu Mar 4 16:46:59 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Mar 4 16:52:59 2004 Subject: [Bioperl-l] Broken link in bptutorial In-Reply-To: <404771C1.8060302@email.arizona.edu> Message-ID: Susan, I thought I'd gotten all of those! Thanks for the tip. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Susan J. Miller Sent: Thursday, March 04, 2004 1:13 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Broken link in bptutorial In the BioPerl Tutorial Introduction Overview section http://www.bioperl.org/Core/Latest/bptutorial.html#i._introduction the link http://bioperl.org/Core/Latest/bioscripts.html does not work because there is punctuation included in the URL. -- Regards, -susan Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories Bio West 228 University of Arizona Tucson, AZ 85721 (520) 626-2597 _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From morten at binf.ku.dk Thu Mar 4 10:57:11 2004 From: morten at binf.ku.dk (Morten Lindow) Date: Thu Mar 4 21:30:04 2004 Subject: [Bioperl-l] Unusual behaviour of SeqIO::tigr In-Reply-To: References: Message-ID: <404751D7.6030406@binf.ku.dk> I am trying to build a table of genomic features from the tigrxml-format of a rice (pseudo)chromosome. However the tigr-parser seem to behave differently from genbank/embl: tigr.pm considers every TU/etc an individual sequence, and hence resets its coordinate system every time it starts on a new TU. My question is: Is there a bioperl-way to get to the global coordinates, like when I am parsing a genbankfile of a whole chromosome? my $tigrin = Bio::SeqIO->new( -format => 'tigr', -file => 'chr01.xml'); while (my $seq = $tigrin->next_seq){ #I would expect this loop to run only once foreach my $feat ( $seq->get_SeqFeatures ) { foreach my $location ($feat->location->each_Location){ print $location->to_FTstring, "\n"; #blablabla } } } cheers, Morten From off2w0rk at yahoo.com Wed Mar 3 21:37:12 2004 From: off2w0rk at yahoo.com (facemann) Date: Thu Mar 4 21:30:37 2004 Subject: [Bioperl-l] RemoteBlast VS Traditional Browser Blast Message-ID: <20040304023712.83186.qmail@web41306.mail.yahoo.com> SOLVED. I had a problem with my "keyboard to floor interface". BLAST & RemoteBlast.pm work just fine. Thank you for you time. --------------------------------- Do you Yahoo!? Yahoo! Search - Find what you’re looking for faster. From advil21dundee at hotmail.com Fri Mar 5 04:25:50 2004 From: advil21dundee at hotmail.com (berry) Date: Fri Mar 5 04:31:39 2004 Subject: [Bioperl-l] 36 H0UR V1=AG-RA Message-ID: <1078478750-5189@excite.com> Did you know That the normal cost for Super V i a g r a is $20, per dose? We are running a hot special!! T0DAY Its only an amazing $3.00 Shipped world wide! DISC0UNT 0RDER: http://healthypolicy.com/sv/index.php?pid=eph9106 laura biologygretchen dirk percy diana praise corrado vicky bensongray abcdef molly1 mantra rufus joel Get off this list by going to http://healthypolicy.com/sv/applepie.php From heikki at ebi.ac.uk Fri Mar 5 05:39:44 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Fri Mar 5 05:45:34 2004 Subject: [Bioperl-l] Getting values from a GenBank File In-Reply-To: <404791F9.2030103@genetics.utah.edu> References: <404791F9.2030103@genetics.utah.edu> Message-ID: <200403051039.45640.heikki@ebi.ac.uk> Barry, I like your RichSeq breakdown! It would make a great addition into BioPerl howtos. Would you be interested in converting it into DocBook yourself? -Heikki On Thursday 04 Mar 2004 20:30, Barry Moore wrote: > While learning BioPerl, I've spent a good bit of time trying to figure > out where some bit of information in a GenBank file might be tucked away > in that RichSeq object, and how the hell to get at it. I finally > decided it was time to sift through that object and find out what's in > there and where it is. Along the way I wrote down what I found, and > then added a bit to it to try and turn it into something that I would > like to have found when I first started learning Bioperl. The result is > a "GeneBank-file-centric" crib sheet for Bioperl. The document is > centered around a "standard" GenBank file where each seperate item of > information is marked-up with numbers and codes that refer to > information later in the document about how to get at that particular > value in using BioPerl. It also includes a script at the end that can > be modified easily to get at all the major stuff in the GenBank file. > This document is aimed at beginners to BioPerl, but assumes a working > knowledge of Perl. The file is, of course, free to be used by anyone in > anyway that they wish. I'd appreciate any corrections or improvements > if you find errors or shortcomings. > > Barry -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From Alexandre.Irrthum at icr.ac.uk Fri Mar 5 06:26:28 2004 From: Alexandre.Irrthum at icr.ac.uk (Alexandre Irrthum) Date: Fri Mar 5 06:32:44 2004 Subject: [Bioperl-l] bl2seq overflow Message-ID: Hello bioperl people, I have a strange problem here. I am trying to blast (bl2seq) EST sequences against a reference cDNA. In this test, the EST file comprises > 2000 sequences. Here is the skeleton of the program (sorry if it's formatted improperly): #! /usr/bin/perl use warnings; use strict; use Bio::Tools::Run::StandAloneBlast; use Bio::SeqIO; my $factory = Bio::Tools::Run::StandAloneBlast->new(program =>'blastn'); my $refseqio = Bio::SeqIO->new(-file => 'refseq.fasta', -format => 'Fasta'); my $refseq = $refseqio->next_seq(); my $estseqio = Bio::SeqIO->new(-file => 'ests.fasta', -format => 'Fasta'); my $count = 0; while (my $estseq = $estseqio->next_seq()) { $count++; my $report = $factory->bl2seq($estseq, $refseq); if (my $hsp = $report->next_feature()) { my $query_seq = $hsp->querySeq(); my $sbjct_seq = $hsp->sbjctSeq(); print "COUNT: $count\n"; print "QUERY: $query_seq\n"; print "SBJCT: $sbjct_seq\n"; } } The program crashes with the following message, after successfully blasting 1020 sequences. Always after 1020 blasts, even when I reorganize the EST input file. --------------program output------------------- Can't locate Carp/Heavy.pm in @INC (@INC contains:/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at/usr/lib/perl5/5.8.0/Carp.pm line 178, line 1021. I don't know why bioperl cannot find Carp and Carp::heavy, since they are in /usr/lib/perl5/5.8.0/. Anyhow, when I add "use Carp;" and "useCarp::Heavy;", I get this: ---------------program output--------------- Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp file/tmp/C5b2L4SloO: Too many open files at/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 659 There are no blast temporary files in /tmp. I'm clueless. Many thanks to the bioperl developers for the fantastic tool they've built us. alex From matthias.wahl at gsf.de Fri Mar 5 07:16:10 2004 From: matthias.wahl at gsf.de (Matthias Wahl) Date: Fri Mar 5 07:16:36 2004 Subject: [Bioperl-l] bl2seq overflow References: Message-ID: <40486F8A.7020601@gsf.de> One possible solution is to use the old bioperl 0.7 version. This one works with unlimited number of sequences. But you might have to change your code to be compatible with the old version. Matthias Alexandre Irrthum wrote: >Hello bioperl people, > >I have a strange problem here. I am trying to blast (bl2seq) EST >sequences against a reference cDNA. In this test, the EST file comprises > > >>2000 sequences. Here is the skeleton of the program (sorry if it's >> >> >formatted improperly): > >#! /usr/bin/perl > >use warnings; >use strict; >use Bio::Tools::Run::StandAloneBlast; >use Bio::SeqIO; > >my $factory = Bio::Tools::Run::StandAloneBlast->new(program =>'blastn'); >my $refseqio = Bio::SeqIO->new(-file => 'refseq.fasta', > -format => 'Fasta'); >my $refseq = $refseqio->next_seq(); >my $estseqio = Bio::SeqIO->new(-file => 'ests.fasta', >-format => 'Fasta'); >my $count = 0; >while (my $estseq = $estseqio->next_seq()) { $count++; >my $report = $factory->bl2seq($estseq, $refseq); >if (my $hsp = $report->next_feature()) { >my $query_seq = $hsp->querySeq(); >my $sbjct_seq = $hsp->sbjctSeq(); >print "COUNT: $count\n"; >print "QUERY: $query_seq\n"; >print "SBJCT: $sbjct_seq\n"; >} >} > >The program crashes with the following message, after successfully >blasting 1020 sequences. Always after 1020 blasts, even when I >reorganize the EST input file. > >--------------program output------------------- >Can't locate Carp/Heavy.pm in @INC (@INC >contains:/usr/lib/perl5/5.8.0/i386-linux-thread-multi >/usr/lib/perl5/5.8.0/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/site_perl/5.8.0 >/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.0 >/usr/lib/perl5/vendor_perl/usr/lib/perl5/5.8.0/i386-linux-thread-multi >/usr/lib/perl5/5.8.0 .) at/usr/lib/perl5/5.8.0/Carp.pm line 178, >line 1021. > >I don't know why bioperl cannot find Carp and Carp::heavy, since they >are in /usr/lib/perl5/5.8.0/. Anyhow, when I add "use Carp;" and >"useCarp::Heavy;", I get this: > >---------------program output--------------- >Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp >file/tmp/C5b2L4SloO: Too many open files >at/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 659 > >There are no blast temporary files in /tmp. I'm clueless. > >Many thanks to the bioperl developers for the fantastic tool they've >built us. > >alex >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- Matthias Wahl GSF-National Research Center for Environment and Health Institute of Developmental Genetics Ingolstaedter Landstrasse 1 D-85764 Neuherberg Germany TEL: ++49 89 3187-4117,-2638 FAX: ++49 89 3187-3099 E-mail: matthias.wahl@gsf.de WWW: http://www.gsf.de/idg From brian_osborne at cognia.com Fri Mar 5 07:52:56 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Mar 5 07:58:48 2004 Subject: [Bioperl-l] Getting values from a GenBank File In-Reply-To: <404791F9.2030103@genetics.utah.edu> Message-ID: Barry, This is good. I've also been talking to another Bioperl-er who's writing a script that creates an output very much like your Tables, where the input is any type of format (Genbank, Locuslink, and so on). So you could write your own HOWTO, yes, but in my opinion the better idea is to marry the existing HOWTO, your tables, and this incoming script somehow. I'm convinced that having too much on a single topic ("you could read the FAQ 2.6 or the HOWTO or the module documentation for Bio::That or Bio::This or the bptutorial section 3.4...") is not good. Bioperl is under-documented, generally, but you'll also find places where there's documentation scattered all over the place on a given topic. The advice is inconsistent, one section gets outdated, the authors move on, these sorts of things happen. My suggestion would be to wait a moment until my colleague's script appears, then let's write something coherent that's easy to maintain. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Barry Moore Sent: Thursday, March 04, 2004 3:31 PM To: bioperl Subject: [Bioperl-l] Getting values from a GenBank File While learning BioPerl, I've spent a good bit of time trying to figure out where some bit of information in a GenBank file might be tucked away in that RichSeq object, and how the hell to get at it. I finally decided it was time to sift through that object and find out what's in there and where it is. Along the way I wrote down what I found, and then added a bit to it to try and turn it into something that I would like to have found when I first started learning Bioperl. The result is a "GeneBank-file-centric" crib sheet for Bioperl. The document is centered around a "standard" GenBank file where each seperate item of information is marked-up with numbers and codes that refer to information later in the document about how to get at that particular value in using BioPerl. It also includes a script at the end that can be modified easily to get at all the major stuff in the GenBank file. This document is aimed at beginners to BioPerl, but assumes a working knowledge of Perl. The file is, of course, free to be used by anyone in anyway that they wish. I'd appreciate any corrections or improvements if you find errors or shortcomings. Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT ---------------------------------------------------------------------------- ------- How to get values in a GenBank file with BioPerl This is a guide to accessing the value of each item in a GenBank file with BioPerl. Underneath each value in the sample GenBank file there is a number and a 3-letter code. The 3-letter code represents the object where the associated value is stored. Table 1 at the end of this file gives the object for each code. By looking up the numbers in Table 2 at the end of this file you will find the object where this information can be called from, and the method to get (and usually set) the value. Some values may be stored by, and accessible by methods in more than one object. There is perl code at the end that you can use as a starting point to get at all of the objects and their methods. ---------------------------------------------------------------------------- ------- LOCUS NM_079543 1821 bp mRNA linear INV 10-DEC-2003 1-BSR 2-BPS 3-BSR 4-BSR 5-BSR 6-BSR DEFINITION Drosophila melanogaster alpha-Esterase-3 CG1257-PA (alpha-Est3) mRNA, complete cds. 7-BPS ACCESSION NM_079543 XX_123456 8-BPS 9-BSR VERSION NM_079543.2 GI:24644853 | | 10-BPS 11-BSR KEYWORDS Esterases 12-BSR SOURCE Drosophila melanogaster (fruit fly) 13-BSC ORGANISM Drosophila melanogaster 14-BSC 15-BSC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila. 16-BSC REFERENCE 1 (bases 1 to 1821) 17-BAR 18-BAR AUTHORS Adams,M.D. et al.(additional authors deleted for brevity) 19-BAR TITLE The genome sequence of Drosophila melanogaster 20-BAR JOURNAL Science 287 (5461), 2185-2195 (2000) 21-BAR MEDLINE 20196006 22-BAR PUBMED 10731132 23-BAR COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. This record is derived from an annotated genomic sequence (NT_033777). The reference sequence was derived from CG1257-RA. On Nov 6, 2002 this sequence version replaced gi:17737826. 24-BAC FEATURES Location/Qualifiers source 1..1821 25-BLS 26-BLS /organism="Drosophila melanogaster" 27-BSG /mol_type="mRNA" /db_xref="taxon:7227" /chromosome="3R" /note="genotype: y[1]; cn[1] bw[1] sp[1]; Rh6[1]" gene 1..1821 /gene="alpha-Est3" /locus_tag="CG1257" /note="alpha-Esterase-3; synonyms: B, aE3, CG1257, alphaE3, alpha-Ests, fragment B; go_function: carboxylesterase activity [goid 0004091] [evidence NAS]" /map="84D9-84D9" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" CDS 119..1750 /gene="alpha-Est3" /locus_tag="CG1257" /EC_number="3.1.1.1" /note="alpha-Est3 gene product" /codon_start=1 /product="alpha-Esterase-3 CG1257-PA" /protein_id="NP_524267.2" /db_xref="GI:24644854" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" /translation="MESLQVNTTSGPVLGKQCTGVYGDEYVSFERIPYAQPPVGHLRF MAPLPVEPWSQPLDCTKPGQKPLQFNHYSKQLEGVEDCLYLNVYAKELDSPRPLPLIV FFFGGGFEKGDPTKELHSPDYFMMRDVVVVTVSYRVGPLGFLSLNDPAVGVPGNAGLK DQLLAMEWIKENAERFNGDPKNVTAFGESAGAASVHYLMLNPKAEGLFHKAILQSGNV LCSWALCTIKNLPHRLAVNLGMESAEHVTDAMVLDFLQKLPGEKLVRPYLLSAEEHLD DCVFQFGPMVEPYKTEHCALPNHPQELLDKAWGNRIPVLMSGTSFEGLLMYARVQMAP YLLTSLKKEPEHMLPLDVKRNLPQALARHLGQRLQETHFGGNDPSAMSPESLKAYCEY ASYKVFWHPILKTLRSRVKSSSASTYLYRFDFDSPTFNHQRLKYCGDKLRGVAHVDDH SYLWYGDFSWKLDKHTPEFLTIERMIDMLTSFARTSNPNCKLIQDQLPRAKEWKPLNS KSALECLNISENIKMMELPELQKLRVWESVCQSTG" ORIGIN 1 gtactatggc aaatggtact atgggcagtc gcgataataa taataaatga ggctttaaat 61 gtttttccac tacaagataa aaagttacga gtgcgcaccg agcatttagt agacgaacat 28-BPS ... (additional sequence deleted for brevity) // ---------------------------------------------------------------------------- ------- Table 1. Object Key BPS - Bio::PrimarySeq BSR - Bio::Seq::RichSeq BSC - Bio::Species BAC - Bio::Annotation::Comment BAR - Bio::Annotation::Reference BLS - Bio::Location::Simple BSG - Bio::SeqFeature::Generic ---------------------------------------------------------------------------- ------- Table 2. Usage key 1. Bio::Seq::RichSeq $scalar = $self->display_name() or ->display_id() 2. Bio::PrimarySeq $scalar = $self->length() 3. Bio::Seq::RichSeq $scalar = $self->molecule() 4. Bio::PrimarySeq $scalar = $self->is_circular 5. Bio::Seq::RichSeq $scalar = $self->division() 6. Bio::seq::Richseq @array = $self->get_dates 7. Bio::PrimarySeq $scalar = $self->description() 8. Bio::PrimarySeq $scalar = $self->accession_number() Bio::Seq::RichSeq $scalar = $self->accession() 9. Bio::Seq::RichSeq @array = $self->get_secondary_accessions 10. Bio::PrimarySeq $scalar = $self->version() Bio::Seq::RichSeq $scalar = $self->seq_version() 11. Bio::PrimarySeq $scalar = $self->primary_id() 12. Bio::Seq::RichSeq @array = $self->get_keywords 13. Bio::Species $scalar = $self->common_name() 14. Bio::Species $scalar = $self->genus() 15. Bio::Species $scalar = $self->species() 16. Bio::Species @array = $self->classification() 17. Bio::Annotation::Reference $scalar = $self->start() 18. Bio::Annotation::Reference $scalar = $self->end() 19. Bio::Annotation::Reference $scalar = $self->authors() 20. Bio::Annotation::Reference $scalar = $self->title() 21. Bio::Annotation::Reference $scalar = $self->location() 22. Bio::Annotation::Reference $scalar = $self->medline() 23. Bio::Annotation::Reference $scalar = $self->pubmed() 24. Bio::Annotation::Comment $scalar = $self->text() or ->as_text 25. Bio::SeqFeature::Generic $scalar = $self->start() 26. Bio::SeqFeature::Generic $scalar = $self->end() 27. Bio::SeqFeature::Generic Get all features from the features table using a variation on the code below. You will need to vary the primary_tag (e.g. source, gene, CDS) and the get_tag_values (e.g. organism, db_xref, chromosome, note, gene, locus_tag, go_function, map, EC_number, codon_start, protein_id, etc.). If there is more than one primary tag associated with a give value (e.g. more than one gene) then you will have to step through the @source_feats array to find what you want rather than simply shifting the first scalar off the top. my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); 28. Bio::PrimarySeq $scalar = $self->seq() ---------------------------------------------------------------------------- ------- #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::DB::GenBank; #use Bio::DB::GenPept or Bio::DB::RefSeq if needed #Get some sequence IDs either like below, or read in from a file. Note that #this sample script works with the accession numbers below (at least at the time #it was written). If you add different accession numbers, and you get errors, #you may be calling for something that the sequence doesn't have. You'll have #to add your own error trapping code to handle that. my @ids = ('U59228', 'AB039327', 'BC035972'); #Create the GenBank database object to read from the database. my $gb = new Bio::DB::GenBank(); #Create a sequence stream to pass the sequences from the database to the program. my $seqio = $gb->get_Stream_by_id(\@ids); #Loop over all of the sequences that you requested. while (my $seq = $seqio->next_seq) { #Here is how you get methods directly from the RichSeq object. Replace #'display_name' with any other method in Table 2. that can be called on #either the RichSeq object directly, or the PrimarySeq object which it has #inherited. print $seq->display_name,"\n"; #Here is how to access the classification data from the species object. my $species = $seq->species; print $species->common_name,"\n"; my @class = $species->classification; print "@class\n"; #Here is a general way to call things that are stored as a Bio::SeqFeature:: #Generic object. Replace 'source' with any other of the "major" headings in #the feature table (e.g gene, CDS, etc.) and replace 'organism' with any of #the tag values found under that heading (mol_type, locus_tag, gene, etc.) my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); print "@mol_type\n"; #Here is a general way to call things that are stored as some type of a #Bio::Annotation oject. This includes reference information, and comments. #Replace reference with 'comment' to get the comment, and replace #$ref->authors with $ref->title (or location, medline, etc.) to get other #reference categories my $ann = $seq->annotation(); my @references = ($ann->get_Annotations('reference')); my $ref = shift @references; my ($title, $authors, $location, $pubmed, $reference); if (defined $ref) { $authors = $ref->authors; print "$authors\n"; } print "\n"; } ---------------------------------------------------------------------------- ------- This file is without copyright. It may be reproduced, edited, and redistributed at will without notice to the author, however I would appreciate it if any corrections or improvements were sent to barry.moore@genetics.utah.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason at cgt.duhs.duke.edu Fri Mar 5 08:18:57 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 5 08:24:47 2004 Subject: [Bioperl-l] bl2seq overflow In-Reply-To: References: Message-ID: What version of bioperl - this problem of not cleaning up tempfiles was supposed to be resolved in 1.4 You might add $factory->io->_io_cleanup(); At the beginning of your sequence loop while ( my $estseq = $estseqio->next_seq ) { } On Fri, 5 Mar 2004, Alexandre Irrthum wrote: > Hello bioperl people, > > I have a strange problem here. I am trying to blast (bl2seq) EST > sequences against a reference cDNA. In this test, the EST file comprises > > 2000 sequences. Here is the skeleton of the program (sorry if it's > formatted improperly): > > #! /usr/bin/perl > > use warnings; > use strict; > use Bio::Tools::Run::StandAloneBlast; > use Bio::SeqIO; > > my $factory = Bio::Tools::Run::StandAloneBlast->new(program =>'blastn'); > my $refseqio = Bio::SeqIO->new(-file => 'refseq.fasta', > -format => 'Fasta'); > my $refseq = $refseqio->next_seq(); > my $estseqio = Bio::SeqIO->new(-file => 'ests.fasta', > -format => 'Fasta'); > my $count = 0; > while (my $estseq = $estseqio->next_seq()) { $count++; > my $report = $factory->bl2seq($estseq, $refseq); > if (my $hsp = $report->next_feature()) { > my $query_seq = $hsp->querySeq(); > my $sbjct_seq = $hsp->sbjctSeq(); > print "COUNT: $count\n"; > print "QUERY: $query_seq\n"; > print "SBJCT: $sbjct_seq\n"; > } > } > > The program crashes with the following message, after successfully > blasting 1020 sequences. Always after 1020 blasts, even when I > reorganize the EST input file. > > --------------program output------------------- > Can't locate Carp/Heavy.pm in @INC (@INC > contains:/usr/lib/perl5/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/5.8.0/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl/usr/lib/perl5/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/5.8.0 .) at/usr/lib/perl5/5.8.0/Carp.pm line 178, > line 1021. > > I don't know why bioperl cannot find Carp and Carp::heavy, since they > are in /usr/lib/perl5/5.8.0/. Anyhow, when I add "use Carp;" and > "useCarp::Heavy;", I get this: > > ---------------program output--------------- > Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp > file/tmp/C5b2L4SloO: Too many open files > at/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 659 > > There are no blast temporary files in /tmp. I'm clueless. > > Many thanks to the bioperl developers for the fantastic tool they've > built us. > > alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Fri Mar 5 08:20:08 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 5 08:26:35 2004 Subject: [Bioperl-l] bl2seq overflow In-Reply-To: <40486F8A.7020601@gsf.de> References: <40486F8A.7020601@gsf.de> Message-ID: I doubt this will fix it - there is no coded limit in bioperl - it has to do with the creation of tempfiles and not being cleaned up properly until perl exits instead of within a loop of factory->bl2seq calls. On Fri, 5 Mar 2004, Matthias Wahl wrote: > One possible solution is to use the old bioperl 0.7 version. This one > works with unlimited number of sequences. But you might have to change > your code to be compatible with the old version. > > Matthias > > Alexandre Irrthum wrote: > > >Hello bioperl people, > > > >I have a strange problem here. I am trying to blast (bl2seq) EST > >sequences against a reference cDNA. In this test, the EST file comprises > > > > > >>2000 sequences. Here is the skeleton of the program (sorry if it's > >> > >> > >formatted improperly): > > > >#! /usr/bin/perl > > > >use warnings; > >use strict; > >use Bio::Tools::Run::StandAloneBlast; > >use Bio::SeqIO; > > > >my $factory = Bio::Tools::Run::StandAloneBlast->new(program =>'blastn'); > >my $refseqio = Bio::SeqIO->new(-file => 'refseq.fasta', > > -format => 'Fasta'); > >my $refseq = $refseqio->next_seq(); > >my $estseqio = Bio::SeqIO->new(-file => 'ests.fasta', > >-format => 'Fasta'); > >my $count = 0; > >while (my $estseq = $estseqio->next_seq()) { $count++; > >my $report = $factory->bl2seq($estseq, $refseq); > >if (my $hsp = $report->next_feature()) { > >my $query_seq = $hsp->querySeq(); > >my $sbjct_seq = $hsp->sbjctSeq(); > >print "COUNT: $count\n"; > >print "QUERY: $query_seq\n"; > >print "SBJCT: $sbjct_seq\n"; > >} > >} > > > >The program crashes with the following message, after successfully > >blasting 1020 sequences. Always after 1020 blasts, even when I > >reorganize the EST input file. > > > >--------------program output------------------- > >Can't locate Carp/Heavy.pm in @INC (@INC > >contains:/usr/lib/perl5/5.8.0/i386-linux-thread-multi > >/usr/lib/perl5/5.8.0/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/site_perl/5.8.0 > >/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.0 > >/usr/lib/perl5/vendor_perl/usr/lib/perl5/5.8.0/i386-linux-thread-multi > >/usr/lib/perl5/5.8.0 .) at/usr/lib/perl5/5.8.0/Carp.pm line 178, > >line 1021. > > > >I don't know why bioperl cannot find Carp and Carp::heavy, since they > >are in /usr/lib/perl5/5.8.0/. Anyhow, when I add "use Carp;" and > >"useCarp::Heavy;", I get this: > > > >---------------program output--------------- > >Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp > >file/tmp/C5b2L4SloO: Too many open files > >at/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 659 > > > >There are no blast temporary files in /tmp. I'm clueless. > > > >Many thanks to the bioperl developers for the fantastic tool they've > >built us. > > > >alex > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From matthias.wahl at gsf.de Fri Mar 5 08:47:23 2004 From: matthias.wahl at gsf.de (Matthias Wahl) Date: Fri Mar 5 08:47:48 2004 Subject: [Bioperl-l] bl2seq overflow References: <40486F8A.7020601@gsf.de> Message-ID: <404884EB.90006@gsf.de> At least it worked with my programs (blasting 30,000 sequences against database). At that time, 1.4 was not yet available. Jason Stajich wrote: >I doubt this will fix it - there is no coded limit in bioperl - it has to >do with the creation of tempfiles and not being cleaned up properly until >perl exits instead of within a loop of factory->bl2seq calls. > > >On Fri, 5 Mar 2004, Matthias Wahl wrote: > > > >>One possible solution is to use the old bioperl 0.7 version. This one >>works with unlimited number of sequences. But you might have to change >>your code to be compatible with the old version. >> >>Matthias >> >>Alexandre Irrthum wrote: >> >> >> >>>Hello bioperl people, >>> >>>I have a strange problem here. I am trying to blast (bl2seq) EST >>>sequences against a reference cDNA. In this test, the EST file comprises >>> >>> >>> >>> >>>>2000 sequences. Here is the skeleton of the program (sorry if it's >>>> >>>> >>>> >>>> >>>formatted improperly): >>> >>>#! /usr/bin/perl >>> >>>use warnings; >>>use strict; >>>use Bio::Tools::Run::StandAloneBlast; >>>use Bio::SeqIO; >>> >>>my $factory = Bio::Tools::Run::StandAloneBlast->new(program =>'blastn'); >>>my $refseqio = Bio::SeqIO->new(-file => 'refseq.fasta', >>> -format => 'Fasta'); >>>my $refseq = $refseqio->next_seq(); >>>my $estseqio = Bio::SeqIO->new(-file => 'ests.fasta', >>>-format => 'Fasta'); >>>my $count = 0; >>>while (my $estseq = $estseqio->next_seq()) { $count++; >>>my $report = $factory->bl2seq($estseq, $refseq); >>>if (my $hsp = $report->next_feature()) { >>>my $query_seq = $hsp->querySeq(); >>>my $sbjct_seq = $hsp->sbjctSeq(); >>>print "COUNT: $count\n"; >>>print "QUERY: $query_seq\n"; >>>print "SBJCT: $sbjct_seq\n"; >>>} >>>} >>> >>>The program crashes with the following message, after successfully >>>blasting 1020 sequences. Always after 1020 blasts, even when I >>>reorganize the EST input file. >>> >>>--------------program output------------------- >>>Can't locate Carp/Heavy.pm in @INC (@INC >>>contains:/usr/lib/perl5/5.8.0/i386-linux-thread-multi >>>/usr/lib/perl5/5.8.0/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/site_perl/5.8.0 >>>/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.0 >>>/usr/lib/perl5/vendor_perl/usr/lib/perl5/5.8.0/i386-linux-thread-multi >>>/usr/lib/perl5/5.8.0 .) at/usr/lib/perl5/5.8.0/Carp.pm line 178, >>>line 1021. >>> >>>I don't know why bioperl cannot find Carp and Carp::heavy, since they >>>are in /usr/lib/perl5/5.8.0/. Anyhow, when I add "use Carp;" and >>>"useCarp::Heavy;", I get this: >>> >>>---------------program output--------------- >>>Error in tempfile() using /tmp/XXXXXXXXXX: Could not create temp >>>file/tmp/C5b2L4SloO: Too many open files >>>at/usr/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 659 >>> >>>There are no blast temporary files in /tmp. I'm clueless. >>> >>>Many thanks to the bioperl developers for the fantastic tool they've >>>built us. >>> >>>alex >>>_______________________________________________ >>>Bioperl-l mailing list >>>Bioperl-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >>> >>> >>> >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu > > > > -- Matthias Wahl GSF-National Research Center for Environment and Health Institute of Developmental Genetics Ingolstaedter Landstrasse 1 D-85764 Neuherberg Germany TEL: ++49 89 3187-4117,-2638 FAX: ++49 89 3187-3099 E-mail: matthias.wahl@gsf.de WWW: http://www.gsf.de/idg From barry.moore at genetics.utah.edu Fri Mar 5 09:30:06 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Mar 5 09:35:53 2004 Subject: [Bioperl-l] Getting values from a GenBank File In-Reply-To: References: Message-ID: <40488EEE.7040407@genetics.utah.edu> O.K. Sounds good. Barry Brian Osborne wrote: >Barry, > >This is good. I've also been talking to another Bioperl-er who's writing a >script that creates an output very much like your Tables, where the input is >any type of format (Genbank, Locuslink, and so on). So you could write your >own HOWTO, yes, but in my opinion the better idea is to marry the existing >HOWTO, your tables, and this incoming script somehow. > >I'm convinced that having too much on a single topic ("you could read the >FAQ 2.6 or the HOWTO or the module documentation for Bio::That or Bio::This >or the bptutorial section 3.4...") is not good. Bioperl is under-documented, >generally, but you'll also find places where there's documentation scattered >all over the place on a given topic. The advice is inconsistent, one section >gets outdated, the authors move on, these sorts of things happen. > >My suggestion would be to wait a moment until my colleague's script appears, >then let's write something coherent that's easy to maintain. > >Brian O. > >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Barry Moore >Sent: Thursday, March 04, 2004 3:31 PM >To: bioperl >Subject: [Bioperl-l] Getting values from a GenBank File > >While learning BioPerl, I've spent a good bit of time trying to figure >out where some bit of information in a GenBank file might be tucked away >in that RichSeq object, and how the hell to get at it. I finally >decided it was time to sift through that object and find out what's in >there and where it is. Along the way I wrote down what I found, and >then added a bit to it to try and turn it into something that I would >like to have found when I first started learning Bioperl. The result is >a "GeneBank-file-centric" crib sheet for Bioperl. The document is >centered around a "standard" GenBank file where each seperate item of >information is marked-up with numbers and codes that refer to >information later in the document about how to get at that particular >value in using BioPerl. It also includes a script at the end that can >be modified easily to get at all the major stuff in the GenBank file. >This document is aimed at beginners to BioPerl, but assumes a working >knowledge of Perl. The file is, of course, free to be used by anyone in >anyway that they wish. I'd appreciate any corrections or improvements >if you find errors or shortcomings. > >Barry >-- > >Barry Moore >Dept. of Human Genetics >University of Utah >Salt Lake City, UT > >---------------------------------------------------------------------------- >------- > > How to get values in a GenBank file with BioPerl > >This is a guide to accessing the value of each item in a GenBank file >with BioPerl. >Underneath each value in the sample GenBank file there is a number and a >3-letter >code. The 3-letter code represents the object where the associated >value is stored. >Table 1 at the end of this file gives the object for each code. By >looking up the >numbers in Table 2 at the end of this file you will find the object >where this >information can be called from, and the method to get (and usually set) >the value. >Some values may be stored by, and accessible by methods in more than one >object. >There is perl code at the end that you can use as a starting point to >get at all of >the objects and their methods. >---------------------------------------------------------------------------- >------- >LOCUS NM_079543 1821 bp mRNA linear INV >10-DEC-2003 > 1-BSR 2-BPS 3-BSR 4-BSR 5-BSR 6-BSR >DEFINITION Drosophila melanogaster alpha-Esterase-3 CG1257-PA (alpha-Est3) > mRNA, complete cds. > 7-BPS >ACCESSION NM_079543 XX_123456 > 8-BPS 9-BSR >VERSION NM_079543.2 GI:24644853 > | | > 10-BPS 11-BSR >KEYWORDS Esterases > 12-BSR >SOURCE Drosophila melanogaster (fruit fly) > 13-BSC > ORGANISM Drosophila melanogaster > 14-BSC 15-BSC > Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; > Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; > Ephydroidea; Drosophilidae; Drosophila. > 16-BSC >REFERENCE 1 (bases 1 to 1821) > 17-BAR 18-BAR > AUTHORS Adams,M.D. et al.(additional authors deleted for brevity) > 19-BAR > TITLE The genome sequence of Drosophila melanogaster > 20-BAR > JOURNAL Science 287 (5461), 2185-2195 (2000) > 21-BAR > MEDLINE 20196006 > 22-BAR > PUBMED 10731132 > 23-BAR >COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to >final > NCBI review. This record is derived from an annotated genomic > sequence (NT_033777). The reference sequence was derived from > CG1257-RA. > On Nov 6, 2002 this sequence version replaced gi:17737826. > 24-BAC >FEATURES Location/Qualifiers > source 1..1821 > 25-BLS 26-BLS > /organism="Drosophila melanogaster" > 27-BSG > /mol_type="mRNA" > /db_xref="taxon:7227" > /chromosome="3R" > /note="genotype: y[1]; cn[1] bw[1] sp[1]; Rh6[1]" > gene 1..1821 > /gene="alpha-Est3" > /locus_tag="CG1257" > /note="alpha-Esterase-3; synonyms: B, aE3, CG1257, > alphaE3, alpha-Ests, fragment B; > go_function: carboxylesterase activity [goid 0004091] > [evidence NAS]" > /map="84D9-84D9" > /db_xref="FLYBASE:FBgn0015571" > /db_xref="GeneID:40907" > /db_xref="LocusID:40907" > CDS 119..1750 > /gene="alpha-Est3" > /locus_tag="CG1257" > /EC_number="3.1.1.1" > /note="alpha-Est3 gene product" > /codon_start=1 > /product="alpha-Esterase-3 CG1257-PA" > /protein_id="NP_524267.2" > /db_xref="GI:24644854" > /db_xref="FLYBASE:FBgn0015571" > /db_xref="GeneID:40907" > /db_xref="LocusID:40907" > >/translation="MESLQVNTTSGPVLGKQCTGVYGDEYVSFERIPYAQPPVGHLRF > >MAPLPVEPWSQPLDCTKPGQKPLQFNHYSKQLEGVEDCLYLNVYAKELDSPRPLPLIV > >FFFGGGFEKGDPTKELHSPDYFMMRDVVVVTVSYRVGPLGFLSLNDPAVGVPGNAGLK > >DQLLAMEWIKENAERFNGDPKNVTAFGESAGAASVHYLMLNPKAEGLFHKAILQSGNV > >LCSWALCTIKNLPHRLAVNLGMESAEHVTDAMVLDFLQKLPGEKLVRPYLLSAEEHLD > >DCVFQFGPMVEPYKTEHCALPNHPQELLDKAWGNRIPVLMSGTSFEGLLMYARVQMAP > >YLLTSLKKEPEHMLPLDVKRNLPQALARHLGQRLQETHFGGNDPSAMSPESLKAYCEY > >ASYKVFWHPILKTLRSRVKSSSASTYLYRFDFDSPTFNHQRLKYCGDKLRGVAHVDDH > >SYLWYGDFSWKLDKHTPEFLTIERMIDMLTSFARTSNPNCKLIQDQLPRAKEWKPLNS > KSALECLNISENIKMMELPELQKLRVWESVCQSTG" >ORIGIN > 1 gtactatggc aaatggtact atgggcagtc gcgataataa taataaatga ggctttaaat > 61 gtttttccac tacaagataa aaagttacga gtgcgcaccg agcatttagt agacgaacat > 28-BPS >... (additional sequence deleted for brevity) >// >---------------------------------------------------------------------------- >------- >Table 1. Object Key >BPS - Bio::PrimarySeq >BSR - Bio::Seq::RichSeq >BSC - Bio::Species >BAC - Bio::Annotation::Comment >BAR - Bio::Annotation::Reference >BLS - Bio::Location::Simple >BSG - Bio::SeqFeature::Generic >---------------------------------------------------------------------------- >------- >Table 2. Usage key >1. Bio::Seq::RichSeq $scalar = $self->display_name() or >->display_id() >2. Bio::PrimarySeq $scalar = $self->length() >3. Bio::Seq::RichSeq $scalar = $self->molecule() >4. Bio::PrimarySeq $scalar = $self->is_circular >5. Bio::Seq::RichSeq $scalar = $self->division() >6. Bio::seq::Richseq @array = $self->get_dates >7. Bio::PrimarySeq $scalar = $self->description() >8. Bio::PrimarySeq $scalar = $self->accession_number() > Bio::Seq::RichSeq $scalar = $self->accession() >9. Bio::Seq::RichSeq @array = $self->get_secondary_accessions >10. Bio::PrimarySeq $scalar = $self->version() > Bio::Seq::RichSeq $scalar = $self->seq_version() >11. Bio::PrimarySeq $scalar = $self->primary_id() >12. Bio::Seq::RichSeq @array = $self->get_keywords >13. Bio::Species $scalar = $self->common_name() >14. Bio::Species $scalar = $self->genus() >15. Bio::Species $scalar = $self->species() >16. Bio::Species @array = $self->classification() >17. Bio::Annotation::Reference $scalar = $self->start() >18. Bio::Annotation::Reference $scalar = $self->end() >19. Bio::Annotation::Reference $scalar = $self->authors() >20. Bio::Annotation::Reference $scalar = $self->title() >21. Bio::Annotation::Reference $scalar = $self->location() >22. Bio::Annotation::Reference $scalar = $self->medline() >23. Bio::Annotation::Reference $scalar = $self->pubmed() >24. Bio::Annotation::Comment $scalar = $self->text() or ->as_text >25. Bio::SeqFeature::Generic $scalar = $self->start() >26. Bio::SeqFeature::Generic $scalar = $self->end() >27. Bio::SeqFeature::Generic > >Get all features from the features table using a variation on the code >below. >You will need to vary the primary_tag (e.g. source, gene, CDS) and the >get_tag_values (e.g. organism, db_xref, chromosome, note, gene, locus_tag, >go_function, map, EC_number, codon_start, protein_id, etc.). If there >is more >than one primary tag associated with a give value (e.g. more than one >gene) then >you will have to step through the @source_feats array to find what you >want rather >than simply shifting the first scalar off the top. > >my @source_feats = grep { $_->primary_tag eq 'source' } >$seq->get_SeqFeatures(); >my $source_feat = shift @source_feats; >my @mol_type = $source_feat->get_tag_values('mol_type'); > >28. Bio::PrimarySeq $scalar = $self->seq() >---------------------------------------------------------------------------- >------- >#!/usr/bin/perl > >use strict; >use warnings; >use Bio::SeqIO; >use Bio::DB::GenBank; #use Bio::DB::GenPept or Bio::DB::RefSeq if needed > >#Get some sequence IDs either like below, or read in from a file. Note that >#this sample script works with the accession numbers below (at least at >the time >#it was written). If you add different accession numbers, and you get >errors, >#you may be calling for something that the sequence doesn't have. >You'll have >#to add your own error trapping code to handle that. >my @ids = ('U59228', 'AB039327', 'BC035972'); > >#Create the GenBank database object to read from the database. >my $gb = new Bio::DB::GenBank(); > >#Create a sequence stream to pass the sequences from the database to the >program. >my $seqio = $gb->get_Stream_by_id(\@ids); > >#Loop over all of the sequences that you requested. >while (my $seq = $seqio->next_seq) { > > #Here is how you get methods directly from the RichSeq object. Replace > #'display_name' with any other method in Table 2. that can be called on > #either the RichSeq object directly, or the PrimarySeq object which it has > #inherited. > print $seq->display_name,"\n"; > > #Here is how to access the classification data from the species object. > my $species = $seq->species; > print $species->common_name,"\n"; > my @class = $species->classification; > print "@class\n"; > > #Here is a general way to call things that are stored as a >Bio::SeqFeature:: > #Generic object. Replace 'source' with any other of the "major" >headings in > #the feature table (e.g gene, CDS, etc.) and replace 'organism' with >any of > #the tag values found under that heading (mol_type, locus_tag, gene, etc.) > my @source_feats = grep { $_->primary_tag eq 'source' } >$seq->get_SeqFeatures(); > my $source_feat = shift @source_feats; > my @mol_type = $source_feat->get_tag_values('mol_type'); > print "@mol_type\n"; > > #Here is a general way to call things that are stored as some type of a > #Bio::Annotation oject. This includes reference information, and >comments. > #Replace reference with 'comment' to get the comment, and replace > #$ref->authors with $ref->title (or location, medline, etc.) to get other > #reference categories > my $ann = $seq->annotation(); > my @references = ($ann->get_Annotations('reference')); > my $ref = shift @references; > my ($title, $authors, $location, $pubmed, $reference); > if (defined $ref) { > $authors = $ref->authors; > print "$authors\n"; > } > print "\n"; >} >---------------------------------------------------------------------------- >------- >This file is without copyright. It may be reproduced, edited, and >redistributed at >will without notice to the author, however I would appreciate it if any >corrections >or improvements were sent to barry.moore@genetics.utah.edu > > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From abrusan at mpil-ploen.mpg.de Fri Mar 5 12:07:02 2004 From: abrusan at mpil-ploen.mpg.de (Gyoergy Abrusan) Date: Fri Mar 5 12:11:42 2004 Subject: [Bioperl-l] CpG frequency Message-ID: <4048B3B6.3040000@mpil-ploen.mpg.de> Dear All, I am a biologiist with quite "moderate" knowledge in bioinformatics. I would like to ask whether a script for estimating CpG frequencies (no. of CG pairs/no. of nucleotides) in files containing several DNA sequences (fasta format) exist in the bioperl database. Thanking you in advance. kind regards, Gyorgy Abrusan From rsucgang at bcm.tmc.edu Fri Mar 5 12:10:31 2004 From: rsucgang at bcm.tmc.edu (richard sucgang phd) Date: Fri Mar 5 12:16:29 2004 Subject: [Bioperl-l] CpG frequency In-Reply-To: <4048B3B6.3040000@mpil-ploen.mpg.de> References: <4048B3B6.3040000@mpil-ploen.mpg.de> Message-ID: Gyrogy, If this is your main goal, then I think bioperl may be a little overkill. Have you considered the EMBOSS suite? http://www.emboss.org Particularly, the cpgreport tool http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Apps/cpgreport.html -r At 6:07 PM +0100 3/5/04, Gyoergy Abrusan wrote: >Dear All, > >I am a biologiist with quite "moderate" knowledge in bioinformatics. >I would like to ask whether a script for estimating CpG frequencies >(no. of CG pairs/no. of nucleotides) in files containing several DNA >sequences (fasta format) exist in the bioperl database. -- Richard Sucgang, PhD (713) 798 7657 Dictyostelium Genome Sequencing Project @ BCM http://www.dictygenome.org/ From brian_osborne at cognia.com Fri Mar 5 12:20:30 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Mar 5 12:26:26 2004 Subject: [Bioperl-l] CpG frequency In-Reply-To: <4048B3B6.3040000@mpil-ploen.mpg.de> Message-ID: Gyorgy, Yes, there's a script in the scripts/seqstats/ directory called gccalc.PLS that will do this. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Gyoergy Abrusan Sent: Friday, March 05, 2004 12:07 PM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] CpG frequency Dear All, I am a biologiist with quite "moderate" knowledge in bioinformatics. I would like to ask whether a script for estimating CpG frequencies (no. of CG pairs/no. of nucleotides) in files containing several DNA sequences (fasta format) exist in the bioperl database. Thanking you in advance. kind regards, Gyorgy Abrusan _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From kviel at emory.edu Fri Mar 5 12:44:44 2004 From: kviel at emory.edu (Kevin Roland Viel) Date: Fri Mar 5 12:50:30 2004 Subject: [Bioperl-l] CpG frequency In-Reply-To: References: Message-ID: I am a novice at perl, but it seems to me that, in general, you can compare the lengths of the original fasta to that with GC or CG pairs "cut" out. If you translate CpG to any other byte character then you will need to multiple by 2, unless you want the number of pairs. Regards, Kevin Kevin Viel Department of Epidemiology Rollins School of Public Health Emory University Atlanta, GA 30322 From laurichj at bioinfo.ucr.edu Fri Mar 5 13:45:10 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Fri Mar 5 13:50:57 2004 Subject: [Bioperl-l] Unusual behaviour of SeqIO::tigr In-Reply-To: <404751D7.6030406@binf.ku.dk> References: <404751D7.6030406@binf.ku.dk> Message-ID: <20040305184510.GB7843@batch107a> On Thu 03/04/04 16:57, Morten Lindow wrote: > I am trying to build a table of genomic features from the tigrxml-format > of a rice (pseudo)chromosome. > > However the tigr-parser seem to behave differently from genbank/embl: > tigr.pm considers every TU/etc an individual sequence, and hence resets > its coordinate system every time it starts on a new TU. > > My question is: > Is there a bioperl-way to get to the global coordinates, like when I am > parsing a genbankfile of a whole chromosome? Sure: my $tigrin = Bio::SeqIO->new( -format => 'tigr', -file => 'chr01.xml'); while (my $seq = $tigrin->next_seq){ my ($source) = grep { $_->primary_tag() eq "source" } $seq->get_SeqFeatures(); # These are the 5' and 3' ends of each TU my($end5) = $source->get_tag_values('end5'); my($end3) = $source->get_tag_values('end3'); my($strand) = $end3 <=> $end5; # Then foreach location just do: my $loc = get_some_location.... $start = $end5 + ($loc->start() - 1)*$strand; $end = $end5 + ($loc->end() - 1)*$strand; ... } This bit of code isn't tested, but I've been using these alot, so it is probably correct. -- ------------------------------------------------------ | Josh Lauricha | Ford, your turning into | | laurichj@bioinfo.ucr.edu | a penguin. Stop it. | | Bioinformatics, UCR | | |----------------------------------------------------| | OpenPG: | | 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8 | |----------------------------------------------------| From scooby21georgia at hotmail.com Fri Mar 5 18:08:11 2004 From: scooby21georgia at hotmail.com (lucas) Date: Fri Mar 5 18:14:11 2004 Subject: [Bioperl-l] Impressive new discovery: The Virility Patch Message-ID: <1078528091-18839@excite.com> Publications such as Maxim, GQ and Stuff have written about the all new Virility Patch RX which is the first high-tech patch designed to dramatically increase both penis size and male potency. No other male erectile growth formula works faster, is more effective or is easier to use than Virility Patch RX. Learn more about it here: http://drugsbusiness.com/pp/index.php?pid=eph9106 baskeT sarah1mission racerx kathy swimming sailor rufus sugar amanda1metallic dollars stingray tootsie cardinal cougars Get off this list by going here: http://drugsbusiness.com/pp/applepie.php From hlapp at gnf.org Fri Mar 5 20:05:54 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Mar 5 20:11:46 2004 Subject: [Bioperl-l] DB.t failures Message-ID: <6AF86968-6F0A-11D8-97AC-000A959EB4C4@gnf.org> The date range query on Onchocerca volvulus[Organism] is failing on both main trunk and stable branch for two reasons. First, NCBI either changed, or now enforces, the date syntax as YYYY/MM/DD. The MM/DD/YYYY format documented in Bio::DB::Query::GenBank (and possibly elsewhere) will not raise an exception; instead it just produces zero results. I changed the POD and the test to use the correct format. Second, after this correction some tests still fail because not really expectedly the query produces different results meanwhile as the default is to query by modification date, which at some point will get updated, thereby yielding a different query result. There are tests which test the first three sequences returned for an expected length. I changed those tests to use the new results, but this won't last long. Either, those tests need to be dropped, or maybe a safer query is to constrain by publication date if that's possible. Any opinions? Any takers? BTW I also fixed a couple of other errors and poor dealing with undefined values as the tests on the main trunk got way too noisy for my taste. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gnf.org Fri Mar 5 20:15:59 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Mar 5 20:21:50 2004 Subject: [Bioperl-l] DB.t failures In-Reply-To: <6AF86968-6F0A-11D8-97AC-000A959EB4C4@gnf.org> Message-ID: On Friday, March 5, 2004, at 05:05 PM, Hilmar Lapp wrote: > because not really expectedly that should have read 'not really unexpectedly' ... -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From cjm at fruitfly.org Fri Mar 5 20:52:31 2004 From: cjm at fruitfly.org (Chris Mungall) Date: Fri Mar 5 20:58:18 2004 Subject: [Bioperl-l] new GFF3 support methods added Message-ID: I have committed some new stuff to bioperl-live: the script seq/unflatten_seq will now generate GFF3 - the unflattener module is used to build the 'feature graph' connecting genes, transcripts, exons and CDSs together. This means we can have GFF3 for anything in genbank! As far as I'm aware, the only other sensible output formats to use here (ie formats that support feature graphs/containment hierarchies) are: chado, chaos, and the write-only asciitree. This feature graph is written out in the GFF3 using the ID and Parent tags. To do this there is an extra intermediate step - the bioperl FeatureHolderI hierarchy is traversed and ID/Parent tags are generated. Here is a description of the changes I have made: [unless you're a bioperl hacker you don't really need to read the rest of this] You can get the context of what I'm on about from this thread: http://bioperl.org/pipermail/bioperl-l/2003-December/014150.html Two new public methods: FeatureHolderI->set_ParentIDs_from_hierarchy sets both ID and ParentID from FeatureHolder hierarchy SeqFeatureI->generate_unique_persistent_id this is required by the above method Lincoln wanted this to be private, but I think it has to be called from outside FeatureHolderI->create_hierarchy_from_ParentIDs the inverse of set_ParentIDs_from_hierarchy (note that I have put the implementation in the interface - in the absence of proper abstract classes, this was deemed the best thing to do in the previous discussion on this) Modifications: SeqFeatureI->primary_id This now maps to the tag_value 'ID' (ie the tag that GFF3 uses to uniquely identify a feature). Minor modification Bio::Tools::GFF now allows the -noparse=>1 option this is simply to stop the module waiting on input from STDIN when used in write-mode (maybe there's a better way of doing this but I didn't want to mess with this module) Proto-test t/FeatureHolder.x This unflattens a genbank sequences and roundtrips it to chadoxml via GFF3 This doesn't work yet - if you dump a splitfeature as GFF3 and re-import it, it becomes two features. Any volunteers to help fix this? Unique IDs in bioperl: In the discussion that preceeded this, it seemed that people liked the idea of persistent unique IDs, but there was no suggestions as to how to go about it. This is inherently difficult with objects, but I borrowed a solution from relational modeling. A persistent unique ID is generated using seq_id primary_tag start end It is assumed that these are all set and comprise a "unique key" over features. Of course, there's no way to enforce this with objects. The generated ID is simply these values concatenated with : delimiters. You can think of this is a skolem function if you're that way inclined. Another assumption is that seq_id is unique and persistent. Of course, if you're dealing with data that changes with time, then changing the coordinates of a feature will change it's id. This is fine. If you want to use your own IDs rather than the generated ones, you can simply set the primary_id() field - or if you are using genbank files, add something like this /ID=CG12345-RA to the feature. Stuff still to do: * fix GFF3 to deal with roundtripping splitlocations * A nest_features() method, as discussed in the previous email. This is the opposite of set_ParentIDs_from_hierarchy(), for reading in GFF3 (and then writing to a feature-graph compatible format, or to a database such as biosql or chado). * Bio::SeqIO::GFF3 I know a lot of us would like this a lot - is there any plans to implement this yet? * A GeneModel factory This would take the output of the unflattener (a set of feature graphs typed to SO) and make SeqFeature::Gene objects Cheers Chris From hlapp at gmx.net Sat Mar 6 00:33:15 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat Mar 6 00:39:02 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: Message-ID: Nice work Chris. I don't have very many comments. On Friday, March 5, 2004, at 05:52 PM, Chris Mungall wrote: > FeatureHolderI->set_ParentIDs_from_hierarchy > > sets both ID and ParentID from FeatureHolder hierarchy > > FeatureHolderI->create_hierarchy_from_ParentIDs > > the inverse of set_ParentIDs_from_hierarchy > Hmm - is this unique to feature graphs or to GFF3? > SeqFeatureI->generate_unique_persistent_id > > this is required by the above method > > Lincoln wanted this to be private, but I think it has > to be called from outside I wouldn't want it to be private, but I'd rather make this a property representing a generator (with a single required method $generator->generate_id($feature)), or alternatively - and also simpler - a closure, than a method. The reason is that if you wanted to change the way the ID is generated you'd have to subclass an entire SeqFeatureI implementation instead of just setting the property to some anonymous method you whip up. > > Unique IDs in bioperl: > > In the discussion that preceeded this, it seemed that people liked the > idea of persistent unique IDs, but there was no suggestions as to how > to > go about it. This is inherently difficult with objects, but I borrowed > a > solution from relational modeling. > > A persistent unique ID is generated using > > seq_id > primary_tag > start > end > > It is assumed that these are all set and comprise a "unique key" over > features. Hmm. Wouldn't you need to include source_tag()? (Source_tag is part of the unique key in biosql.) Without the source_tag being part of this, wouldn't that mean you cannot have the exact (start+end) same segment predicted as exon by different methods and have those different predictions co-exist as separate features in the graph? (Presumably those would only differ in source_tag) > > Another assumption is that seq_id is unique and persistent. > I don't think that's going to be a very safe assumption. > > * A GeneModel factory > > This would take the output of the unflattener (a set of feature graphs > typed to SO) and make SeqFeature::Gene objects > Yeah, that'd be cool ... -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From paula21arizona at hotmail.com Sat Mar 6 04:09:40 2004 From: paula21arizona at hotmail.com (stacey) Date: Sat Mar 6 04:19:50 2004 Subject: [Bioperl-l] V-1-A-G-R-A 70% off!!! Message-ID: <1078564180-10997@excite.com> The lowest price on V I A G R A on the 'net!! Click here: http://royaldrugs.com/sv/index.php?pid=eph9106 benoit percyelectric politics scooby tracy looney genius cesar sugarproperty charlott velvet gray apple1 diane To get off this list, go to http://drugsbusiness.com/gv/applepie.php From scannedr at tcd.ie Sat Mar 6 15:55:21 2004 From: scannedr at tcd.ie (Devin Scannell) Date: Sat Mar 6 16:01:06 2004 Subject: [Bioperl-l] getting a subtree In-Reply-To: Message-ID: <951230CC-6FB0-11D8-960E-000393B293CE@tcd.ie> Hi Jason and Deng, I suspect Jasons solution was the required one but I have been getting a lot of use out of the method below which does something similar - return a branch as a new tree object but also remove it from the original tree. I have been using it to split trees into well supported clades according to certain criteria. if its useful and the caveats (1. only works for bifurcating nodes and 2. does not correct branch lengths (it was written for use with phylip trees)) are not too problematic, I would be happy to have it added to the Tree::FunctionsI module. Failing this, if I get an interested reply, I'll correct these problems when less busy and resubmit. best, Devin =head2 remove_branch Title : remove_branch Usage : $tree->remove_branch($first_node_on_branch_to_be_removed) Function: At a bifurcating node removes one descendant branch and replaces the ancestral branch with the other descendant branch. As a bonus the removed node is used to root and return a new tree. This function therefore effectively makes two trees from the original. This method DOES NOT work at trifurcating nodes and DOES NOT correct branch lengths. Returns : New tree object corresponding to removed branch. Args : Bio::Tree::NodeI object or node id Added : Devin Scannell Wed Feb 11 22:09:28 GMT 2004 =cut sub remove_branch { # if b is a bifurcating node # where a->b is the ancestral branch # and b->c, b->d are descendent branches # then # 1) destroy central_node (b) # 2) make retain_node (c) a descendent of attach_node (a) # 3) return remove_node (d) as a new tree object my $self = shift; my $remove_node = shift; $remove_node = $self->find_node($remove_node) unless ref($remove_node); # some light checking unless ($remove_node) { $self->warn("Requires Bio::Tree::NodeI object or node id as an argument"); return undef; } unless (scalar($remove_node->ancestor->each_Descendent) == 2 ) { $self->warn("Tree not bifurcating"); return undef; } # get attach_node && central_node my $central_node = $remove_node->ancestor; my $attach_node = $central_node->ancestor; # get retain_node my $retain_node = ''; foreach ($remove_node->ancestor->each_Descendent) { $retain_node = $_; last if $retain_node ne $remove_node; } # destroy central_node $self->remove_Node($central_node); # if no attach_node, tree is bisected # ie remove_node and retain_node are immediate descendants of the root node # therefore just reroot current tree at retain_node if ($attach_node) { $attach_node->add_Descendent($retain_node, 1); } else { $retain_node->ancestor(undef); $self->set_root_node($retain_node); } # make new tree from removed branch and return $remove_node->ancestor(undef); return(Bio::Tree::Tree->new(-root => $remove_node)); } On Thursday, Mar 4, 2004, at 21:15 Europe/Dublin, Jason Stajich wrote: > Deng - here is some code to answer your question. > > use Bio::Tree::Tree; > use Bio::TreeIO; > > # get a tree somehow > # choose the subnodes for finding the lca somehow > > # get the least common ancestor > my $node = $tree->get_lca( -nodes => \@nodes ); > > # build a new tree with its root at $node > my $subtree = Bio::Tree::Tree->new(-root => $node, -nodelete => 1); > > my $out = Bio::TreeIO->new(-format=>'newick'); > $out->write_tree($subtree); > > -jason > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > ----------------- Devin Scannell, Wolfe Lab, TCD, Ireland 00353-1-6081288 ----------------- From adejo1nge at hotmail.com Sat Mar 6 16:57:51 2004 From: adejo1nge at hotmail.com (jesse) Date: Sat Mar 6 17:03:34 2004 Subject: [Bioperl-l] Save up to 80% on your medications! 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sjames Get off this list by writing to getmeoff731@excitemail.com From Steven.Roels at mpi.com Sat Mar 6 17:00:33 2004 From: Steven.Roels at mpi.com (Roels, Steven) Date: Sat Mar 6 17:07:13 2004 Subject: [Bioperl-l] DB.t failures Message-ID: Hilmar, See bugs #1594 (which describes the problem below) and #1595, which mentions a $NUMTESTS problem with the penultimate tests in DB.t. You may have seen them already, but if not - you just fixed at least one :) Thanks, -Steve ***************************************************************** Steve Roels, Ph.D. Senior Scientist I - Computational Biology Phone: (617) 761-6820 Millennium Pharmaceuticals, Inc. FAX: (617) 577-3555 640 Memorial Drive Email: roels@mpi.com Cambridge, MA 02139-4853 ***************************************************************** >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf >Of Hilmar Lapp >Sent: Friday, March 05, 2004 8:06 PM >To: Bioperl >Subject: [Bioperl-l] DB.t failures > >The date range query on Onchocerca volvulus[Organism] is failing on >both main trunk and stable branch for two reasons. > >First, NCBI either changed, or now enforces, the date syntax as >YYYY/MM/DD. The MM/DD/YYYY format documented in Bio::DB::Query::GenBank >(and possibly elsewhere) will not raise an exception; instead it just >produces zero results. I changed the POD and the test to use the >correct format. > >Second, after this correction some tests still fail because not really >expectedly the query produces different results meanwhile as the >default is to query by modification date, which at some point will get >updated, thereby yielding a different query result. There are tests >which test the first three sequences returned for an expected length. > >I changed those tests to use the new results, but this won't last long. >Either, those tests need to be dropped, or maybe a safer query is to >constrain by publication date if that's possible. > >Any opinions? Any takers? > >BTW I also fixed a couple of other errors and poor dealing with >undefined values as the tests on the main trunk got way too noisy for >my taste. > > -hilmar >-- >------------------------------------------------------------- >Hilmar Lapp email: lapp at gnf.org >GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >------------------------------------------------------------- > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. 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Message-ID: <1078692632-26932@excite.com> The lowest price on V I A G R A on the 'net!! Click here: http://sally.royaldrugs.com/gv/index.php?pid=eph9106 shawn wondercorrado master1 kenneth lady safety fountain hazel gordonjazz fiona fozzie olivier sapphire saskia To get off this list, go to http://velvet.royaldrugs.com/gv/applepie.php From ericbrown99 at yahoo.com.au Sun Mar 7 20:39:06 2004 From: ericbrown99 at yahoo.com.au (=?iso-8859-1?q?Eric=20Brown?=) Date: Sun Mar 7 20:44:47 2004 Subject: [Bioperl-l] Why Perl Message-ID: <20040308013906.78435.qmail@web41205.mail.yahoo.com> Dear All, I am new to the discussion group.I am student in comparative genomics and know bit of python and java. Would anybody advise me about making choice between Perl and Python for bioinformatic applications. I guess userbase, resorce richness, job perspective and language stregnth are issues with me to compare and start one. With thanks and regards, Eric Find local movie times and trailers on Yahoo! Movies. http://au.movies.yahoo.com From joel21sbdc at hotmail.com Mon Mar 8 03:08:54 2004 From: joel21sbdc at hotmail.com (darnell) Date: Mon Mar 8 03:14:39 2004 Subject: [Bioperl-l] sugper viagrga Message-ID: <1078733334-9608@excite.com> Did you know That the normal cost for Super V i a g r a is $20, per dose? We are running a hot special!! T0DAY Its only an amazing $3.00 Shipped world wide! DISC0UNT 0RDER: http://baskeT.royaldrugs.com/sv/index.php?pid=eph9106 christop publicaliens first spitfire sasha concept ladybug fireball orchidobiwan turbo deutsch spain mailer dundee Get off this list by going to http://e-mail.royaldrugs.com/sv/applepie.php From pvh at egenetics.com Mon Mar 8 03:50:13 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Mon Mar 8 03:56:01 2004 Subject: [Bioperl-l] Testing BioPerl objects for equality In-Reply-To: <200402031137.34626.lstein@cshl.edu> References: <401E1528.5060309@biomax.de> <200402031137.34626.lstein@cshl.edu> Message-ID: <404C33C5.6000208@egenetics.com> Lincoln Stein wrote: >I think that's a great idea. I hadn't known about test_deeply(). >There's also a Test::Differences module, that does something similar. > > > The problem with doing a data structure level comparison is that you might now want to test the data structures for literal equality - equality != equivalence. That's why the equals() methods that I've been adding to various classes try to be smart about how Bioperl objects actually work. Having said that, I must still think about how to make diff'ing work... it is frustrating to simply have equals / doesn't equal, but no details. I'll look into that after I've finished the initial code. Peter >Lincoln > >On Monday 02 February 2004 11:15 am, Bernhard Schmalhofer wrote: > > >>Ewan Birney wrote: >> >> >>>On Thu, 29 Jan 2004, Peter van Heusden wrote: >>> >>> >>>>I've got an idea for testing where I'd like to 'round-trip' >>>>through SeqIO: read in from a file on disk, write out again with >>>>write_seq() and then read in the file written by write_seq() and >>>>compare the two sequence objects. If they aren't equal, it means >>>>we've got a problem. >>>> >>>> >>>That sounds like a great idea... we've always had problems with >>>diff'ing the files because of whitespace issues, but diff'ing the >>>objects sounds great. >>> >>> >>> >>>>To make this work requires some kind of equals() method on Seq, >>>>SeqFeature, etc. This doesn't seem to be there at the moment - or >>>>am I missing something? Maybe there should probably be some kind >>>>of Bio::ComparableI interface which provides an equals() >>>>abstract method. >>>> >>>> >>If the roundtrip is starting from a file is a specific format, >>shouldn't it be possiple to compare the data structures of the >>sequence object directly? >>I was think of using something like Test::More::is_deeply(), which >>tells you where the data structures start to become different. >> >>CU, Bernhard >> >> > > > From Richard.Adams at ed.ac.uk Mon Mar 8 04:31:03 2004 From: Richard.Adams at ed.ac.uk (Richard Adams) Date: Mon Mar 8 04:36:44 2004 Subject: [Bioperl-l] protein networks Message-ID: <404C3D57.2050600@ed.ac.uk> Hi, I've been writing some modules to apply Nathan Goodman's "SimpleGraph.pm" module to protein interaction networks. He has written this as a replacement for the the broken CPAN graph modules. The aim of these modules is 1. To convert protein interaction data between differentet formats 2. To be able to link protein interaction data to protein sequence data. 3. To be able to read in interaction data from separate sources, and make a merged graph with duplicate interactions flagged or removed. Could some core person give some idea for namespace to put these in CVS? The modules are : 1. Nathan's modules SimpleGraph.pm - a generic graph module with methods to build and represent a graph SimpleGraph::Traversal.pm - generic methods to navigate a graph. 2. My modules a. An I/O system analagous to SeqIO that lazyloads the correct modules for a particular format ProteinGraphIO.pm - with next_graph, write_graph methods ProteinGraphIO::dip.pm - parser for DIP format interactions ProteinGraphIO::xml.pm - to read in PSI_XML formatted records (still being worked on). b. Modules to represent a protein network: PrimaryProteinGraph.pm - subclass of SimpleGraph.pm. This will be made from a dip record, analagous to PrimarySeq FullProteinGraph .pm - subclas of SimpleGraph.pm, contains PrimaryProteinGraph and metadata of graph, will be made from an XML file, analagous to RichSeq. c. Classes to represent nodes/ edges. NodeI.pm - interface describing methods that all nodes should have ProteinNode.pm - implements NodeI, currently has methods primary_id(), seq(), secondary_id() InteractionI.pm - interface describing methods all edges should have ProteinInteraction.pm - implements InteractionI, currently has methods weight(), interactors(), id(). Cheers Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk From Mailer-Daemon at eff.org Mon Mar 8 11:07:45 2004 From: Mailer-Daemon at eff.org (Mail Delivery System) Date: Mon Mar 8 11:13:27 2004 Subject: [Bioperl-l] Mail delivery failed: returning message to sender Message-ID: This message was created automatically by mail delivery software. A message that you sent could not be delivered to one or more of its recipients. This is a permanent error. The following address(es) failed: selena@eff.org Unrouteable address ------ This is a copy of the message, including all the headers. ------ ------ The body of the message is 24043 characters long; only the first ------ 8192 or so are included here. 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CORrQlXb6L9rQq3Y6lGydhhgGy1UNarlimuVVTqKQv1VrRUkRdYiHphy0WWijssLCEbBuKZe mWJ4WeI2mcUZqWdbyoQrqghR5pYo4qSFGur From barry.moore at genetics.utah.edu Fri Mar 5 09:26:47 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Mon Mar 8 11:20:20 2004 Subject: [Bioperl-l] Getting values from a GenBank File In-Reply-To: <200403051039.45640.heikki@ebi.ac.uk> References: <404791F9.2030103@genetics.utah.edu> <200403051039.45640.heikki@ebi.ac.uk> Message-ID: <40488E27.8010002@genetics.utah.edu> Heikki- Sure, but I've got to figure out DocBook first - never used it. I've got the web site, and downloaded the book. I'll get to that as soon as I can. Barry Heikki Lehvaslaiho wrote: >Barry, > >I like your RichSeq breakdown! It would make a great addition into BioPerl >howtos. Would you be interested in converting it into DocBook yourself? > > -Heikki > >On Thursday 04 Mar 2004 20:30, Barry Moore wrote: > > >>While learning BioPerl, I've spent a good bit of time trying to figure >>out where some bit of information in a GenBank file might be tucked away >>in that RichSeq object, and how the hell to get at it. I finally >>decided it was time to sift through that object and find out what's in >>there and where it is. Along the way I wrote down what I found, and >>then added a bit to it to try and turn it into something that I would >>like to have found when I first started learning Bioperl. The result is >>a "GeneBank-file-centric" crib sheet for Bioperl. The document is >>centered around a "standard" GenBank file where each seperate item of >>information is marked-up with numbers and codes that refer to >>information later in the document about how to get at that particular >>value in using BioPerl. It also includes a script at the end that can >>be modified easily to get at all the major stuff in the GenBank file. >>This document is aimed at beginners to BioPerl, but assumes a working >>knowledge of Perl. The file is, of course, free to be used by anyone in >>anyway that they wish. I'd appreciate any corrections or improvements >>if you find errors or shortcomings. >> >>Barry >> >> > > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From bsman at tom.com Sat Mar 6 14:00:34 2004 From: bsman at tom.com (=?gb2312?B?zfXqySwgU2FuIFdhbmc=?=) Date: Mon Mar 8 11:20:38 2004 Subject: [Bioperl-l] Can't locate object method "start" via package "Bio::Seq::RichSeq" Message-ID: <200403061906.i26J6I9Q010205@portal.open-bio.org> Dear bioperl-l: The code ------ #!/usr/bin/perl use Bio::Tools::SiRNA; use Bio::Seq::RichSeq; use strict; my $seq='ATGGGGGTGGTGGTACCCTTTATCGGAAATTTACCTGCTGCACAGGAATGTTTTCTGGTGT'; #$seq=~s/T/U/; my $bio_rich_seq = Bio::Seq::RichSeq->new( -seq =>$seq , -start=>1, -end => 100); $bio_rich_seq->molecule('mRNA'); my $sirna_designer = Bio::Tools::SiRNA->new( -target => $bio_rich_seq ); my @pairs = $sirna_designer->design; foreach my $pair (@pairs) { my $sense_oligo_sequence = $pair->sense->seq; print $sense_oligo_sequence; my $antisense_oligo_sequence = $pair->antisense->seq; # print out results #print join ("\t", $pair->start, $pair->end, $pair->rank, $sense_oligo_sequence, $antisense_oligo_sequence), "\n"; } ---- Can't locate object method "start" via package "Bio::Seq::RichSeq" (perhaps you forgot to load "Bio::Seq::RichSeq"?) at D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263. Best Regards! Yours sincerely ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman@tom.com ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-07 ,-,-. ,-,-. ,-,-. ,-,-. ,- / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / `-'-' `-'-' `-'-' `-'-' San Wang Dr. Student Bioinformatics and Gene Network Research Group Zhejiang University P.R.China Address: Room 415# ,Bio-technology Institute, Zhejiang University, Kaixuan Road 268# Hangzhou Zhejiang, P.R.China 310027 Tel: 0086-571-86892051 Fax: 0086-571-86961525 E-mail: bsman@163.com Website: http://www.estarray.org £­£­£­£­£­£­£­£­£­£­ Innovation is everything. When you are on the forefront, you can see what the next innovation needs to be? --- from Robert Noyce, Founder of Intel The more things change, the more they stay the same! The more things seem to be complicated ,the more they are simple in fact! From bsman at tom.com Sat Mar 6 14:08:11 2004 From: bsman at tom.com (=?gb2312?B?zfXqySwgU2FuIFdhbmc=?=) Date: Mon Mar 8 11:20:40 2004 Subject: [Bioperl-l] modules for siRNA design Message-ID: <200403061913.i26JDq9Q010414@portal.open-bio.org> Dear bioperl-l: I have report a bug for it. "Can't locate object method "start" via package "Bio::Seq::RichSeq" (perhaps you forgot to load "Bio::Seq::RichSeq"?) at D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263." Best Regards! Yours sincerely ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman@tom.com ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-07 ,-,-. ,-,-. ,-,-. ,-,-. ,- / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / `-'-' `-'-' `-'-' `-'-' San Wang Dr. Student Bioinformatics and Gene Network Research Group Zhejiang University P.R.China Address: Room 415# ,Bio-technology Institute, Zhejiang University, Kaixuan Road 268# Hangzhou Zhejiang, P.R.China 310027 Tel: 0086-571-86892051 Fax: 0086-571-86961525 E-mail: bsman@163.com Website: http://www.estarray.org £­£­£­£­£­£­£­£­£­£­ Innovation is everything. When you are on the forefront, you can see what the next innovation needs to be? --- from Robert Noyce, Founder of Intel The more things change, the more they stay the same! The more things seem to be complicated ,the more they are simple in fact! From morten at binf.ku.dk Mon Mar 8 05:48:51 2004 From: morten at binf.ku.dk (Morten Lindow) Date: Mon Mar 8 11:25:39 2004 Subject: [Bioperl-l] Unusual behaviour of SeqIO::tigr In-Reply-To: <20040305184510.GB7843@batch107a> References: <404751D7.6030406@binf.ku.dk> <20040305184510.GB7843@batch107a> Message-ID: <404C4F93.1010606@binf.ku.dk> Thanks Josh that helped, In case somebody else can use it I am pasting the complete code to get the coordinates of all locations on one line each. But another thing: When parsing rice-pseudochromosome files I get a few warnings like this(from around 20-30 sequences per chromosome): From chr01.xml -------------------- WARNING --------------------- MSG: Seq [8350.t06547]: Not using a valid terminator codon! --------------------------------------------------- -------------------- WARNING --------------------- MSG: Seq [8350.t06547]: Terminator codon inside CDS! --------------------------------------------------- -------------------- WARNING --------------------- MSG: Seq [8350.t06547]: Not using a valid initiator codon! --------------------------------------------------- since the problem is only with a small fraction of the TUs I guess it is not a bioperl problem, but rather a TIGR problem? Any comments? - Morten ----BEGIN code to get featuretable from tigrxml. #!/usr/bin/perl use warnings; use strict; use lib "$ENV{HOME}/bioperl/bioperl-live"; use Bio::SeqIO; my $file = shift; my $tigrin = Bio::SeqIO->new( -format => 'tigr', -file => $file); while (my $seq = $tigrin->next_seq){ #Get global start and end coordinates for this sequence my ($source) = grep { $_->primary_tag() eq "source" } $seq->get_SeqFeatures(); my($end5) = $source->get_tag_values('end5'); my($end3) = $source->get_tag_values('end3'); my($strand) = $end3 <=> $end5; foreach my $feat($seq->get_all_SeqFeatures){ next if $feat->primary_tag eq 'source'; foreach my $location ($feat->location->each_Location){ print $feat->primary_tag, "\t"; my $start = $end5 + ($location->start() - 1)*$strand; my $end = $end5 + ($location->end() - 1)*$strand; print join "\t", ($feat->primary_tag, $seq->id, $start, $end, $strand); print "\n"; } } # if ($seq->id eq '8350.t06547'){ # print $seq->seq; # die $! # } } Josh Lauricha wrote: >On Thu 03/04/04 16:57, Morten Lindow wrote: > > >>I am trying to build a table of genomic features from the tigrxml-format >>of a rice (pseudo)chromosome. >> >>However the tigr-parser seem to behave differently from genbank/embl: >>tigr.pm considers every TU/etc an individual sequence, and hence resets >>its coordinate system every time it starts on a new TU. >> >>My question is: >>Is there a bioperl-way to get to the global coordinates, like when I am >>parsing a genbankfile of a whole chromosome? >> >> > >Sure: > >my $tigrin = Bio::SeqIO->new( -format => 'tigr', -file => 'chr01.xml'); > >while (my $seq = $tigrin->next_seq){ > my ($source) = grep { $_->primary_tag() eq "source" } > $seq->get_SeqFeatures(); > > # These are the 5' and 3' ends of each TU > my($end5) = $source->get_tag_values('end5'); > my($end3) = $source->get_tag_values('end3'); > my($strand) = $end3 <=> $end5; > > # Then foreach location just do: > my $loc = get_some_location.... > $start = $end5 + ($loc->start() - 1)*$strand; > $end = $end5 + ($loc->end() - 1)*$strand; > ... >} > >This bit of code isn't tested, but I've been using these alot, so it is >probably correct. > > > From bioperl-guts-l-bounces at portal.open-bio.org Mon Mar 8 11:43:20 2004 From: bioperl-guts-l-bounces at portal.open-bio.org (bioperl-guts-l-bounces@portal.open-bio.org) Date: Mon Mar 8 11:43:33 2004 Subject: [Bioperl-l] Forward of moderated message Message-ID: An embedded message was scrubbed... From: Ruifang Subject: a problem of RestrictionEnzyme Date: Mon, 08 Mar 2004 15:28:13 +0800 Size: 1941 Url: http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040308/b9b3c189/attachment.eml From iain.wallace at ucd.ie Mon Mar 8 11:57:34 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Mon Mar 8 12:03:15 2004 Subject: [Bioperl-l] Locatable sequence with numbers Message-ID: <1078765054.4741.7.camel@bioinf10> Hi I am trying to create a file for clustalw that is of that includes the secondary structure mask !GM_id 1111144444411 id GVPINVSCTGSPQ My problem is that the code below doesn't work as $gap_mask is a string of numbers, and not a proper sequence. my $newseq1 = new Bio::LocatableSeq(-seq => $gap_mask, -id => "!GM_".$seq->id, -start => 1, -end => $seq->length()); print "adding id:\t",$seq->id,"\n"; $Align->add_seq($newseq1); The error that gets generated is -------------------- WARNING --------------------- MSG: seq doesn't validate, mismatch is 1 --------------------------------------------------- ------------- EXCEPTION ------------- MSG: Attempting to set the sequence to [12211111114444444444412222222112222221] which does not look healthy STACK Bio::PrimarySeq::seq /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:268 STACK Bio::PrimarySeq::new /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:217 STACK Bio::LocatableSeq::new /usr/lib/perl5/site_perl/5.8.0/Bio/LocatableSeq.pm:100 STACK toplevel ./dssp.pl:61 -------------------------------------- Does anyone know how I could get around this ? Thanks Iain From heikki at ebi.ac.uk Mon Mar 8 12:03:40 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Mar 8 12:09:21 2004 Subject: [Bioperl-l] modules for siRNA design In-Reply-To: <200403061913.i26JDq9Q010414@portal.open-bio.org> References: <200403061913.i26JDq9Q010414@portal.open-bio.org> Message-ID: <200403081703.40515.heikki@ebi.ac.uk> San Wang, The code in SiRNA.pm around line 263 looks like this: if ($cds) { $left = $cds->start + $self->end_pad; $right = $cds->end - $self->start_pad; } else { $left = $target->start + $self->end_pad; # line #263 $right = $target->end - $self->start_pad; } Start and end calls are fine on a SeqFeature object like a CDS, but are not defined for a sequence. These lines should be replaced by something like the following: $left = 1 + $self->end_pad; $right = $target->length - $self->start_pad; Your example sequence is not too realistic, so you'll get an other error caused by the shortness of the sequece. Call $sirna_designer->start_pad(0); $sirna_designer->end_pad(0); before calling design(). Yours, -Heikki On Saturday 06 Mar 2004 19:08, ÍõêÉ, San Wang wrote: > Dear bioperl-l: > > I have report a bug for it. > "Can't locate object method "start" via package "Bio::Seq::RichSeq" > (perhaps you forgot to load "Bio::Seq::RichSeq"?) at > D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263." > > Best Regards! > > Yours sincerely > ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang > ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman@tom.com > ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-07 > ,-,-. ,-,-. ,-,-. ,-,-. ,- > / / \ \ / / \ \ / / \ \ / / \ \ / / > \ \ / / \ \ / / \ \ / / \ \ / / > `-'-' `-'-' `-'-' `-'-' > > > San Wang > Dr. Student > Bioinformatics and Gene Network Research Group > Zhejiang University > P.R.China > > Address: > Room 415# ,Bio-technology Institute, > Zhejiang University, > Kaixuan Road 268# Hangzhou > Zhejiang, P.R.China > 310027 > > Tel: > 0086-571-86892051 > Fax: > 0086-571-86961525 > E-mail: > bsman@163.com > Website: > http://www.estarray.org > > £­£­£­£­£­£­£­£­£­£­ > Innovation is everything. When you are on the forefront, you can see what > the next innovation needs to be? --- from Robert Noyce, Founder of Intel > The more things change, the more they stay the same! > The more things seem to be complicated ,the more they are simple in fact! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From redwards at utmem.edu Mon Mar 8 12:09:02 2004 From: redwards at utmem.edu (Rob Edwards) Date: Mon Mar 8 12:14:57 2004 Subject: [Bioperl-l] Forward of moderated message In-Reply-To: References: Message-ID: <4C3BE857-7123-11D8-8461-000A959E1622@utmem.edu> Are you sure that you are using the right module. This has been fixed in Bio::Restriction (ver. 1.4) e.g. use Bio::Seq; use Bio::Restriction::Enzyme; use Bio::Restriction::Analysis; use strict; my $seq=Bio::Seq->new(-seq=>'GTACTTTTAGAGGATGAAACCT'); my $renz=Bio::Restriction::Enzyme->new(-enzyme=>'MnII', -seq=>'^CCTC'); my $ranal=Bio::Restriction::Analysis->new(-seq=>$seq, -enzymes=>$renz); my $enz='MnII'; my @frags=$ranal->fragments($enz); print join "\n", @frags, "\n"; gives GTACTTTTA GAGGATGAAACCT Rob On Mar 8, 2004, at 10:43 AM, bioperl-guts-l-bounces@portal.open-bio.org wrote: > > From: Ruifang > Date: March 8, 2004 1:28:13 AM CST > To: bioperl-guts-l@portal.open-bio.org > Subject: a problem of RestrictionEnzyme > > > Dear, > > I am a graduate student in National Lab of Medical Genetics of China. > > I am using Bioperl Module: RestrictionEnzyme.pm and I have encountered > a question about this code. > > I found the restriction enzymes could not recognize the DAN sequence > which is reverse complement to the enzymes sequence. > For example, the enzyme: MnlI, the recognize sequence :CCTC, the DNA > sequence: GTACTTTTAGAGGATGAAACCT > the DAN sequence include GAGG , which is reverse complement to CCTC, > and the MnlI should cut this sequence, but the code could not give > this result. > > May I could have answer from you soon! > > Thanks! > Best Wishes! > > Ruifang > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From heikki at ebi.ac.uk Mon Mar 8 12:21:59 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Mar 8 12:27:42 2004 Subject: [Bioperl-l] Forward of moderated message In-Reply-To: References: Message-ID: <200403081721.59780.heikki@ebi.ac.uk> Ruifang, The code works. See this example: ###################################### use Bio::Tools::RestrictionEnzyme; use Bio::PrimarySeq; $seqobj = new Bio::PrimarySeq(-seq=>'GTACTTTTAGAGGATGAAACCT'); $re2 = new Bio::Tools::RestrictionEnzyme(-NAME =>'MnlI--CC^TC', -MAKE =>'custom'); @fragments = $re2->cut_seq($seqobj); print scalar @fragments, "\n"; ###################################### However, you should notice that Bio:Tools::RestrictionEnzyme class is deprecated and not really supported any more. You should have a look at Bio::Restriction classes. Yours, -Heikki On Monday 08 Mar 2004 16:43, bioperl-guts-l-bounces@portal.open-bio.org wrote: > Dear, > > I am a graduate student in National Lab of Medical Genetics of China. > > I am using Bioperl Module: RestrictionEnzyme.pm and I have encountered a > question about this code. > > I found the restriction enzymes could not recognize the DAN sequence > which is reverse complement to the enzymes sequence. > For example, the enzyme: MnlI, the recognize sequence :CCTC, the DNA > sequence: GTACTTTTAGAGGATGAAACCT > the DAN sequence include GAGG , which is reverse complement to CCTC, > and the MnlI should cut this sequence, but the code could not give this > result. > > May I could have answer from you soon! > > Thanks! > Best Wishes! > > Ruifang -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From heikki at ebi.ac.uk Mon Mar 8 12:30:34 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Mar 8 12:36:15 2004 Subject: [Bioperl-l] Locatable sequence with numbers In-Reply-To: <1078765054.4741.7.camel@bioinf10> References: <1078765054.4741.7.camel@bioinf10> Message-ID: <200403081730.34719.heikki@ebi.ac.uk> Ian, You could use Bio::Seq::Meta to store the mask, but Bio::Tools::Run::Alignment::Clustalw would not know about your mask encoded into the sequence object, so you'd have to modify its code to actually pass the mask to clustalw. -Heikki On Monday 08 Mar 2004 16:57, Iain Wallace wrote: > Hi > > I am trying to create a file for clustalw that is of that includes the > secondary structure mask > > !GM_id 1111144444411 > id GVPINVSCTGSPQ > > My problem is that the code below doesn't work as $gap_mask is a string > of numbers, and not a proper sequence. > > my $newseq1 = new Bio::LocatableSeq(-seq => $gap_mask, > -id => "!GM_".$seq->id, > -start => 1, > -end => $seq->length()); > print "adding id:\t",$seq->id,"\n"; > $Align->add_seq($newseq1); > > The error that gets generated is > > -------------------- WARNING --------------------- > MSG: seq doesn't validate, mismatch is 1 > --------------------------------------------------- > > ------------- EXCEPTION ------------- > MSG: Attempting to set the sequence to > [12211111114444444444412222222112222221] which does not look healthy > STACK Bio::PrimarySeq::seq > /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:268 > STACK Bio::PrimarySeq::new > /usr/lib/perl5/site_perl/5.8.0/Bio/PrimarySeq.pm:217 > STACK Bio::LocatableSeq::new > /usr/lib/perl5/site_perl/5.8.0/Bio/LocatableSeq.pm:100 > STACK toplevel ./dssp.pl:61 > > -------------------------------------- > > > Does anyone know how I could get around this ? > > Thanks > > Iain > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From lstein at cshl.edu Mon Mar 8 13:01:11 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Mar 8 13:07:15 2004 Subject: [Bioperl-l] Bio::Graphics::Glyph::translation.pm In-Reply-To: <1078347825.4592.39.camel@gentiBk> References: <1078347825.4592.39.camel@gentiBk> Message-ID: <200403081301.17539.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 You need to attach a Bio::PrimarySeqI to the Bio::SeqFeature::Generic, not a Bio::SeqI. I know this is confusing, but I think that you can get the effect you want by changing this line to read: $feature->attach_seq($seq_object->seq); Lincoln On Wednesday 03 March 2004 04:03 pm, Dr. Todd Naumann wrote: > Hi, > > I am trying to use the translation glyph and I am running into > problems. When I run the program below with glyph=>'dna' I get a > picture of double stranded DNA sequence as I expected. When I try > to use > glyph=>'translation' I get the following error message: > > Can't locate object method "translate" via package > "Bio::SeqFeature::Generic" at > /usr/lib/perl5/site_perl/5.8.2/Bio/Graphics/Glyph/translation.pm > line 134, line 118. > > I tried to find another SeqFeature object that has a translate > method but did not have any luck. If someone could point me in the > right direction I would really appreciate it. > > -Todd > > #!/usr/bin/perl > > use strict; > use warnings; > > use Bio::Graphics; > use Bio::SeqFeature::Generic; > use Bio::SeqIO; > > # initialize the graphics panel > my $panel = Bio::Graphics::Panel->new(-length => 80, > -width => 800, > -pad_left => 10, > -pad_right => 10, > ); > > # make the feature object > my $feature = Bio::SeqFeature::Generic->new(-start=>1, > -end=>60, > ); > > # create a sequence object > my $seqIO_object = Bio::SeqIO->new(-file => 'test_sequence.gb', > -format => 'genbank', > ); > > my $seq_object = $seqIO_object->next_seq(); > > # attach sequence object to feature > $feature->attach_seq($seq_object); > > # add track to panel > $panel->add_track($feature, > -glyph => 'translation', > -fgcolor => 'black', > ); > > print $panel->png; > > exit; > ============================ > Todd Naumann > Dept. of Chemistry > Penn State University > University Park, PA 16802 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATLTt0CIvUP7P+AkRAgrqAJ9YLCuetr50r704+MyFo1+H7Py+4wCeOXeM YiFetRZeCf+misFV4omy+f0= =sLUm -----END PGP SIGNATURE----- From jason at cgt.duhs.duke.edu Mon Mar 8 13:12:30 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Mar 8 13:18:21 2004 Subject: [Bioperl-l] Bio::Graphics::Glyph::translation.pm In-Reply-To: <200403081301.17539.lstein@cshl.edu> References: <1078347825.4592.39.camel@gentiBk> <200403081301.17539.lstein@cshl.edu> Message-ID: err - I don't think you should be calling attach_seq really, but rather add_feature on the seq object $seq_object->add_SeqFeature($feature); This is really the right way to do this - it will properly update the seqfeature and call attach_feature for you. -jason On Mon, 8 Mar 2004, Lincoln Stein wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > You need to attach a Bio::PrimarySeqI to the Bio::SeqFeature::Generic, > not a Bio::SeqI. I know this is confusing, but I think that you can > get the effect you want by changing this line to read: > > $feature->attach_seq($seq_object->seq); > > Lincoln > > On Wednesday 03 March 2004 04:03 pm, Dr. Todd Naumann wrote: > > Hi, > > > > I am trying to use the translation glyph and I am running into > > problems. When I run the program below with glyph=>'dna' I get a > > picture of double stranded DNA sequence as I expected. When I try > > to use > > glyph=>'translation' I get the following error message: > > > > Can't locate object method "translate" via package > > "Bio::SeqFeature::Generic" at > > /usr/lib/perl5/site_perl/5.8.2/Bio/Graphics/Glyph/translation.pm > > line 134, line 118. > > > > I tried to find another SeqFeature object that has a translate > > method but did not have any luck. If someone could point me in the > > right direction I would really appreciate it. > > > > -Todd > > > > #!/usr/bin/perl > > > > use strict; > > use warnings; > > > > use Bio::Graphics; > > use Bio::SeqFeature::Generic; > > use Bio::SeqIO; > > > > # initialize the graphics panel > > my $panel = Bio::Graphics::Panel->new(-length => 80, > > -width => 800, > > -pad_left => 10, > > -pad_right => 10, > > ); > > > > # make the feature object > > my $feature = Bio::SeqFeature::Generic->new(-start=>1, > > -end=>60, > > ); > > > > # create a sequence object > > my $seqIO_object = Bio::SeqIO->new(-file => 'test_sequence.gb', > > -format => 'genbank', > > ); > > > > my $seq_object = $seqIO_object->next_seq(); > > > > # attach sequence object to feature > > $feature->attach_seq($seq_object); > > > > # add track to panel > > $panel->add_track($feature, > > -glyph => 'translation', > > -fgcolor => 'black', > > ); > > > > print $panel->png; > > > > exit; > > ============================ > > Todd Naumann > > Dept. of Chemistry > > Penn State University > > University Park, PA 16802 > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > - -- > Lincoln D. Stein > Cold Spring Harbor Laboratory > 1 Bungtown Road > Cold Spring Harbor, NY 11724 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.2.1 (GNU/Linux) > > iD8DBQFATLTt0CIvUP7P+AkRAgrqAJ9YLCuetr50r704+MyFo1+H7Py+4wCeOXeM > YiFetRZeCf+misFV4omy+f0= > =sLUm > -----END PGP SIGNATURE----- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From lstein at cshl.edu Mon Mar 8 13:17:26 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Mar 8 13:23:15 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: References: Message-ID: <200403081317.26261.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Chris, Nice job. My only comment is that there's been a great deal of consternation over the role of whitespace in GFF3 recently and I am thinking changing the column delimiter back to strict tabs and allowing spaces (but no tabs or other unescaped whitespace) in the fields. I don't think this will affect your methods at all, but just a heads up. Lincoln On Friday 05 March 2004 08:52 pm, Chris Mungall wrote: > I have committed some new stuff to bioperl-live: > > the script seq/unflatten_seq will now generate GFF3 - the > unflattener module is used to build the 'feature graph' connecting > genes, transcripts, exons and CDSs together. This means we can have > GFF3 for anything in genbank! > > As far as I'm aware, the only other sensible output formats to use > here (ie formats that support feature graphs/containment > hierarchies) are: chado, chaos, and the write-only asciitree. > > This feature graph is written out in the GFF3 using the ID and > Parent tags. To do this there is an extra intermediate step - the > bioperl FeatureHolderI hierarchy is traversed and ID/Parent tags > are generated. > > Here is a description of the changes I have made: > > [unless you're a bioperl hacker you don't really need to read the > rest of this] > > You can get the context of what I'm on about from this thread: > http://bioperl.org/pipermail/bioperl-l/2003-December/014150.html > > Two new public methods: > > FeatureHolderI->set_ParentIDs_from_hierarchy > > sets both ID and ParentID from FeatureHolder hierarchy > > SeqFeatureI->generate_unique_persistent_id > > this is required by the above method > > Lincoln wanted this to be private, but I think it has > to be called from outside > > FeatureHolderI->create_hierarchy_from_ParentIDs > > the inverse of set_ParentIDs_from_hierarchy > > (note that I have put the implementation in the interface - in the > absence of proper abstract classes, this was deemed the best thing > to do in the previous discussion on this) > > Modifications: > > SeqFeatureI->primary_id > > This now maps to the tag_value 'ID' (ie the tag that GFF3 uses to > uniquely identify a feature). > > Minor modification > > Bio::Tools::GFF now allows the -noparse=>1 option > > this is simply to stop the module waiting on input from STDIN > when used in write-mode (maybe there's a better way of doing this > but I didn't want to mess with this module) > > Proto-test > > t/FeatureHolder.x > > This unflattens a genbank sequences and roundtrips it to chadoxml > via GFF3 > > This doesn't work yet - if you dump a splitfeature as GFF3 and > re-import it, it becomes two features. Any volunteers to help > fix this? > > Unique IDs in bioperl: > > In the discussion that preceeded this, it seemed that people liked > the idea of persistent unique IDs, but there was no suggestions as > to how to go about it. This is inherently difficult with objects, > but I borrowed a solution from relational modeling. > > A persistent unique ID is generated using > > seq_id > primary_tag > start > end > > It is assumed that these are all set and comprise a "unique key" > over features. Of course, there's no way to enforce this with > objects. The generated ID is simply these values concatenated with > : delimiters. You can think of this is a skolem function if you're > that way inclined. > > Another assumption is that seq_id is unique and persistent. > > Of course, if you're dealing with data that changes with time, then > changing the coordinates of a feature will change it's id. This is > fine. If you want to use your own IDs rather than the generated > ones, you can simply set the primary_id() field - or if you are > using genbank files, add something like this > > /ID=CG12345-RA > > to the feature. > > Stuff still to do: > > * fix GFF3 to deal with roundtripping splitlocations > > * A nest_features() method, as discussed in the previous email. > This is the opposite of set_ParentIDs_from_hierarchy(), for reading > in GFF3 (and then writing to a feature-graph compatible format, or > to a database such as biosql or chado). > > * Bio::SeqIO::GFF3 > > I know a lot of us would like this a lot - is there any plans to > implement this yet? > > * A GeneModel factory > > This would take the output of the unflattener (a set of feature > graphs typed to SO) and make SeqFeature::Gene objects > > Cheers > Chris > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATLi20CIvUP7P+AkRAuErAKCc4iNS3cnVLpbkLAfpba176o29aQCgndia SZzP/ANnxz7kvKmg+5Ovq9c= =FM1X -----END PGP SIGNATURE----- From birney at ebi.ac.uk Mon Mar 8 13:17:50 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Mon Mar 8 13:23:45 2004 Subject: [Bioperl-l] Bio::Graphics::Glyph::translation.pm In-Reply-To: <200403081301.17539.lstein@cshl.edu> Message-ID: On Mon, 8 Mar 2004, Lincoln Stein wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > You need to attach a Bio::PrimarySeqI to the Bio::SeqFeature::Generic, > not a Bio::SeqI. I know this is confusing, but I think that you can > get the effect you want by changing this line to read: > > $feature->attach_seq($seq_object->seq); > We should probably get $feature->attach_seq(xxx) to do something magical with Bio::SeqI's... This has always been unsatisfactory, but roll on parrot with its mark-and-sweep style GC so we can do something more sensible here (circular references...) From lstein at cshl.edu Mon Mar 8 13:47:13 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Mon Mar 8 13:53:03 2004 Subject: [Bioperl-l] Bio::Graphics::Glyph::translation.pm In-Reply-To: References: <1078347825.4592.39.camel@gentiBk> <200403081301.17539.lstein@cshl.edu> Message-ID: <200403081347.13182.lstein@cshl.edu> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Todd, Maybe I've made a mistake. Let me know which way works. Lincoln On Monday 08 March 2004 01:12 pm, Jason Stajich wrote: > err - I don't think you should be calling attach_seq really, but > rather add_feature on the seq object > > $seq_object->add_SeqFeature($feature); > > This is really the right way to do this - it will properly update > the seqfeature and call attach_feature for you. > > -jason > > On Mon, 8 Mar 2004, Lincoln Stein wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA1 > > > > You need to attach a Bio::PrimarySeqI to the > > Bio::SeqFeature::Generic, not a Bio::SeqI. I know this is > > confusing, but I think that you can get the effect you want by > > changing this line to read: > > > > $feature->attach_seq($seq_object->seq); > > > > Lincoln > > > > On Wednesday 03 March 2004 04:03 pm, Dr. Todd Naumann wrote: > > > Hi, > > > > > > I am trying to use the translation glyph and I am running into > > > problems. When I run the program below with glyph=>'dna' I get > > > a picture of double stranded DNA sequence as I expected. When I > > > try to use > > > glyph=>'translation' I get the following error message: > > > > > > Can't locate object method "translate" via package > > > "Bio::SeqFeature::Generic" at > > > /usr/lib/perl5/site_perl/5.8.2/Bio/Graphics/Glyph/translation.p > > >m line 134, line 118. > > > > > > I tried to find another SeqFeature object that has a translate > > > method but did not have any luck. If someone could point me in > > > the right direction I would really appreciate it. > > > > > > -Todd > > > > > > #!/usr/bin/perl > > > > > > use strict; > > > use warnings; > > > > > > use Bio::Graphics; > > > use Bio::SeqFeature::Generic; > > > use Bio::SeqIO; > > > > > > # initialize the graphics panel > > > my $panel = Bio::Graphics::Panel->new(-length => 80, > > > -width => 800, > > > -pad_left => 10, > > > -pad_right => 10, > > > ); > > > > > > # make the feature object > > > my $feature = Bio::SeqFeature::Generic->new(-start=>1, > > > -end=>60, > > > ); > > > > > > # create a sequence object > > > my $seqIO_object = Bio::SeqIO->new(-file => 'test_sequence.gb', > > > -format => 'genbank', > > > ); > > > > > > my $seq_object = $seqIO_object->next_seq(); > > > > > > # attach sequence object to feature > > > $feature->attach_seq($seq_object); > > > > > > # add track to panel > > > $panel->add_track($feature, > > > -glyph => 'translation', > > > -fgcolor => 'black', > > > ); > > > > > > print $panel->png; > > > > > > exit; > > > ============================ > > > Todd Naumann > > > Dept. of Chemistry > > > Penn State University > > > University Park, PA 16802 > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > - -- > > Lincoln D. Stein > > Cold Spring Harbor Laboratory > > 1 Bungtown Road > > Cold Spring Harbor, NY 11724 > > -----BEGIN PGP SIGNATURE----- > > Version: GnuPG v1.2.1 (GNU/Linux) > > > > iD8DBQFATLTt0CIvUP7P+AkRAgrqAJ9YLCuetr50r704+MyFo1+H7Py+4wCeOXeM > > YiFetRZeCf+misFV4omy+f0= > > =sLUm > > -----END PGP SIGNATURE----- > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l - -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) iD8DBQFATL+x0CIvUP7P+AkRAh2bAJwIEXstWUJYdwAYuJ/O0nG87I7hyACfZWxR mGai9ckUJFQb6sAozxuxJBk= =OPAW -----END PGP SIGNATURE----- From adegjp at hotmail.com Mon Mar 8 14:26:48 2004 From: adegjp at hotmail.com (marlin) Date: Mon Mar 8 14:32:29 2004 Subject: [Bioperl-l] Use offshore phar-macies to save $$$ on your meds! Message-ID: <1078774008-32193@excite.com> We created an online medical consultation to get you the medications you need without the hassle, embarrassment, and cost of the doctor's office and pharmacy. When you need them fast: X a n a x - S o m a - V a l i u m - V i a g r a - M e r i d i a - MORE! We don't require any prescriptions. Because you can add more to your life. Shop Now. http://selcydc.com/s95/index.php?id=s95 brooks
  • ssurdi nlee zgao mekdecic nnguyen marrowmontreal a1b2c3 mulcahy   Bigdog vandam foster dmiller1 jcheydwe parrot stan mahartna Get off this list by writing to getmeoff731@excitemail.com From mcipriano at mbl.edu Mon Mar 8 14:48:54 2004 From: mcipriano at mbl.edu (Michael Cipriano) Date: Mon Mar 8 14:54:35 2004 Subject: [Bioperl-l] phd 2 abi file Message-ID: <000801c40546$6371f9c0$8fae8080@Ripley> Is there a way to create an abi sequence file(abi, ab1) from a phred (phd) file within bioperl? If not within bioperl, does anyone know of any way to do this? Thanks in advance Michael Cipriano (mcipriano@mbl.edu) Research Assistant I, Global Infectious Diseases Josephine Bay Paul Center, Marine Biological Laboratory 7 MBL Street, Woods Hole, MA 02543-1015 From cjm at fruitfly.org Mon Mar 8 16:07:16 2004 From: cjm at fruitfly.org (Chris Mungall) Date: Mon Mar 8 16:12:58 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: Message-ID: On Fri, 5 Mar 2004, Hilmar Lapp wrote: > Nice work Chris. I don't have very many comments. > > On Friday, March 5, 2004, at 05:52 PM, Chris Mungall wrote: > > > FeatureHolderI->set_ParentIDs_from_hierarchy > > > > sets both ID and ParentID from FeatureHolder hierarchy > > > > FeatureHolderI->create_hierarchy_from_ParentIDs > > > > the inverse of set_ParentIDs_from_hierarchy > > > > Hmm - is this unique to feature graphs or to GFF3? I think it's useful for any time you want to capture the hierarchical knowledge from the bioperl FeatureHolder hierarchy in any kind of format that does not explicitly capture this kind of info. You could use this with any flavour of GFF - the difference with GFF3 is that the ID and Parent tags are part of the format specification If you wanted to persist your bioperl data through genbank files, this would also be useful, as features could use /ID and /Parent tags (although this is actually an extension of the genbank format) It is useful in a variety of contexts, but it does 'clutter up' FeatureHolder a little > > SeqFeatureI->generate_unique_persistent_id > > > > this is required by the above method > > > > Lincoln wanted this to be private, but I think it has > > to be called from outside > > I wouldn't want it to be private, but I'd rather make this a property > representing a generator (with a single required method > $generator->generate_id($feature)), or alternatively - and also simpler > - a closure, than a method. The reason is that if you wanted to change > the way the ID is generated you'd have to subclass an entire > SeqFeatureI implementation instead of just setting the property to some > anonymous method you whip up. Much as I like closures, I think there should be a standard sanctioned way of generating unique/persistent IDs > > Unique IDs in bioperl: > > > > In the discussion that preceeded this, it seemed that people liked the > > idea of persistent unique IDs, but there was no suggestions as to how > > to > > go about it. This is inherently difficult with objects, but I borrowed > > a > > solution from relational modeling. > > > > A persistent unique ID is generated using > > > > seq_id > > primary_tag > > start > > end > > > > It is assumed that these are all set and comprise a "unique key" over > > features. > > Hmm. Wouldn't you need to include source_tag()? (Source_tag is part of > the unique key in biosql.) Without the source_tag being part of this, > wouldn't that mean you cannot have the exact (start+end) same segment > predicted as exon by different methods and have those different > predictions co-exist as separate features in the graph? (Presumably > those would only differ in source_tag) Good point! I've added this Ok, so are you saying that some of these methods don't really belong in the class-interfaces they are in? Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler class? This would contain methods generate_unique_persistent_id($feat) # uses $feat->seq_id generate_unique_persistent_id($feat, $seq_id) create_hierarchy_from_ParentIDs($featholder); set_ParentIDs_from_hierarchy($featholder); Any preference? I'm leaving them as is for now if that's ok, but I have no objections to moving everything to a seperate class if that's prefered. > > > > Another assumption is that seq_id is unique and persistent. > > > > I don't think that's going to be a very safe assumption. Fair enough, but I think this is the responsibility of the user. This is also partially the fault of the bioperl model - $feat->seq_id() generally refers to the versionless accession no. There isn't really a way to get to the versioned seq_id from the feature. I think it would cause too much churn to add at this late stage... > > > > * A GeneModel factory > > > > This would take the output of the unflattener (a set of feature graphs > > typed to SO) and make SeqFeature::Gene objects > > > > Yeah, that'd be cool ... Sometime.. > -hilmar > > From stefan.weckx at ua.ac.be Mon Mar 8 17:26:56 2004 From: stefan.weckx at ua.ac.be (Stefan Weckx) Date: Mon Mar 8 17:32:21 2004 Subject: [Bioperl-l] phd 2 abi file References: <000801c40546$6371f9c0$8fae8080@Ripley> Message-ID: <001d01c4055c$8cd5f9e0$df8f0b51@desktop> Michael, have look at http://bioperl.org/pipermail/bioperl-l/2001-August/006176.html, You can also try this: translate your phd file to a fasta using phd2fasta, then run mktrace. This will create an scf file. mktrace comes with Consed (http://www.phrap.org/consed/distributions/README.13.0.txt). other possibility: try "sudophred" which comes with the newest release of PolyPhred (see at http://droog.mbt.washington.edu/poly_doc.html). Stefan -- Stefan Weckx Bioinformatics Unit Department of Molecular Genetics VIB8 University of Antwerp Belgium ----- Original Message ----- From: "Michael Cipriano" To: Sent: Monday, March 08, 2004 8:48 PM Subject: [Bioperl-l] phd 2 abi file > Is there a way to create an abi sequence file(abi, ab1) from a phred > (phd) file within bioperl? If not within bioperl, does anyone know of > any way to do this? > > Thanks in advance > > Michael Cipriano (mcipriano@mbl.edu) > Research Assistant I, Global Infectious Diseases > Josephine Bay Paul Center, Marine Biological Laboratory > 7 MBL Street, Woods Hole, MA 02543-1015 > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From mcipriano at mbl.edu Mon Mar 8 17:29:34 2004 From: mcipriano at mbl.edu (Michael Cipriano) Date: Mon Mar 8 17:35:14 2004 Subject: [Bioperl-l] phd 2 abi file In-Reply-To: <001d01c4055c$8cd5f9e0$df8f0b51@desktop> Message-ID: <000d01c4055c$d58352a0$8fae8080@Ripley> Thank you, I will look into those solutions. Michael Cipriano (mcipriano@mbl.edu) Research Assistant I, Global Infectious Diseases Josephine Bay Paul Center, Marine Biological Laboratory 7 MBL Street, Woods Hole, MA 02543-1015 > -----Original Message----- > From: Stefan Weckx [mailto:stefan.weckx@ua.ac.be] > Sent: Monday, March 08, 2004 5:27 PM > To: Michael Cipriano > Cc: bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] phd 2 abi file > > Michael, > > have look at http://bioperl.org/pipermail/bioperl-l/2001- > August/006176.html, > You can also try this: translate your phd file to a fasta using phd2fasta, > then run mktrace. This will create an scf file. mktrace comes with Consed > (http://www.phrap.org/consed/distributions/README.13.0.txt). > other possibility: try "sudophred" which comes with the newest release of > PolyPhred (see at http://droog.mbt.washington.edu/poly_doc.html). > > Stefan > > -- > Stefan Weckx > Bioinformatics Unit > Department of Molecular Genetics VIB8 > University of Antwerp > Belgium > > ----- Original Message ----- > From: "Michael Cipriano" > To: > Sent: Monday, March 08, 2004 8:48 PM > Subject: [Bioperl-l] phd 2 abi file > > > > Is there a way to create an abi sequence file(abi, ab1) from a phred > > (phd) file within bioperl? If not within bioperl, does anyone know of > > any way to do this? > > > > Thanks in advance > > > > Michael Cipriano (mcipriano@mbl.edu) > > Research Assistant I, Global Infectious Diseases > > Josephine Bay Paul Center, Marine Biological Laboratory > > 7 MBL Street, Woods Hole, MA 02543-1015 > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > From hz5 at njit.edu Mon Mar 8 17:48:57 2004 From: hz5 at njit.edu (hz5@njit.edu) Date: Mon Mar 8 17:54:39 2004 Subject: [Bioperl-l] GD::SVG In-Reply-To: <200403081347.13182.lstein@cshl.edu> References: <1078347825.4592.39.camel@gentiBk> <200403081301.17539.lstein@cshl.edu> <200403081347.13182.lstein@cshl.edu> Message-ID: <1078786137.404cf859816f7@webmail.njit.edu> Dear friends, I've successfully rendered multiple panels into png image using GD module and bioperl panel object. Now I am trying to make the picture quality higher. So I tried to use GD::SVG like this: my $panel = Bio::Graphics::Panel->new( #-segment => $whole_seq, -start => $s-1000, -end => $t+1000, #-grid => 'true', -key_style => 'bottom', -key_font => GD::Font->Large(), -width => $width, -pad_left => 10, -pad_right => 10, -pad_bottom => 10, -image_class=> 'GD::SVG', -spacing => 1*$ratio, ); ...... open (OUT, ">my.svg"); binmode OUT; print OUT $panel->svg(); Now I get the following message: Can't locate object method "formatting" via package "GD::Font" (perhaps you forgot to load "GD::Font"?) at /usr/lib/perl5/site_perl/5.6.1/GD/SVG.pm line 702, line 191. don't know why, thanks in advance for your help! haibo From harris at cshl.edu Mon Mar 8 20:14:54 2004 From: harris at cshl.edu (Todd Harris) Date: Mon Mar 8 20:21:46 2004 Subject: [Bioperl-l] GD::SVG In-Reply-To: <1078786137.404cf859816f7@webmail.njit.edu> Message-ID: Hi Haibo - The problem you are seeing is due to how GD::SVG mimics the interface of GD in order to generate SVG. The "Can't locate object method "formatting" via package "GD::Font" (perhaps you..." error is because you aren't working with GD (or GD::Font) objects anymore. Instead, try passing a string for your key_font: -key_font => 'gdLargeFont', It's admittedly not an ideal solution, but GD::SVG will know what to do. Thanks for bringing this up, and I'll make a note in the documentation to address this issue. Todd > On 3/8/04 4:48 PM, hz5@njit.edu wrote: > Dear friends, > > I've successfully rendered multiple panels into png image using GD module and > bioperl panel object. Now I am trying to make the picture quality higher. So I > tried to use GD::SVG like this: > > my $panel = Bio::Graphics::Panel->new( > #-segment => $whole_seq, > -start => $s-1000, > -end => $t+1000, > #-grid => 'true', > -key_style => 'bottom', > -key_font => GD::Font->Large(), > -width => $width, > -pad_left => 10, > -pad_right => 10, > -pad_bottom => 10, > -image_class=> 'GD::SVG', > -spacing => 1*$ratio, > ); > > ...... > > open (OUT, ">my.svg"); > binmode OUT; > print OUT $panel->svg(); > > Now I get the following message: > Can't locate object method "formatting" via package "GD::Font" (perhaps you > forgot to load "GD::Font"?) at /usr/lib/perl5/site_perl/5.6.1/GD/SVG.pm line > 702, line 191. > > don't know why, thanks in advance for your help! > haibo > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From donald.jackson at bms.com Mon Mar 8 21:46:19 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Mon Mar 8 21:51:58 2004 Subject: [Bioperl-l] modules for siRNA design Message-ID: <8a74589334.893348a745@bms.com> San and Heikki, I've modified the SiRNA.pm module to fixed the bug per Heikki's suggestion. I also added a sanity check in case the sequence is so short that the start_pad and end_pad values don't leave room for an oligo, and I added a feature to allow oligo design in the 3 prime UTR. The mods just went into CVS as version 1.7 San - I strongly suggest that you give the module a longer target sequence if at all possible! Don Jackson ----- Original Message ----- From: Heikki Lehvaslaiho Date: Monday, March 8, 2004 12:03 pm Subject: Re: [Bioperl-l] modules for siRNA design > San Wang, > > The code in SiRNA.pm around line 263 looks like this: > > if ($cds) { > $left = $cds->start + $self->end_pad; > $right = $cds->end - $self->start_pad; > } > else { > $left = $target->start + $self->end_pad; # line #263 > $right = $target->end - $self->start_pad; > } > > Start and end calls are fine on a SeqFeature object like a CDS, but > are not > defined for a sequence. These lines should be replaced by > something like the > following: > > $left = 1 + $self->end_pad; > $right = $target->length - $self->start_pad; > > Your example sequence is not too realistic, so you'll get an other > error > caused by the shortness of the sequece. Call > > $sirna_designer->start_pad(0); > $sirna_designer->end_pad(0); > > before calling design(). > > Yours, > -Heikki > > On Saturday 06 Mar 2004 19:08, ??, San Wang wrote: > > Dear bioperl-l: > > > > I have report a bug for it. > > "Can't locate object method "start" via package "Bio::Seq::RichSeq" > > (perhaps you forgot to load "Bio::Seq::RichSeq"?) at > > D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263." > > > > Best Regards! > > > > Yours sincerely > > ??????????, San Wang > > ????????bsman@tom.com > > ??????????2004-03-07 > > ,-,-. ,-,-. ,-,-. ,-,-. ,- > > / / \ \ / / \ \ / / \ \ / / \ \ / / > > \ \ / / \ \ / / \ \ / / \ \ / / > > `-'-' `-'-' `-'-' `-'-' > > > > > > San Wang > > Dr. Student > > Bioinformatics and Gene Network Research Group > > Zhejiang University > > P.R.China > > > > Address: > > Room 415# ,Bio-technology Institute, > > Zhejiang University, > > Kaixuan Road 268# Hangzhou > > Zhejiang, P.R.China > > 310027 > > > > Tel: > > 0086-571-86892051 > > Fax: > > 0086-571-86961525 > > E-mail: > > bsman@163.com > > Website: > > http://www.estarray.org > > > > ?????????? > > Innovation is everything. When you are on the forefront, you > can see what > > the next innovation needs to be? --- from Robert Noyce, Founder > of Intel > > The more things change, the more they stay the same! > > The more things seem to be complicated ,the more they are > simple in fact! > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- > ______ _/ _/_____________________________________________________ > _/ _/ http://www.ebi.ac.uk/mutations/ > _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk > _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute > _/ _/ _/ Wellcome Trust Genome Campus, Hinxton > _/ _/ _/ Cambs. CB10 1SD, United Kingdom > _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 > ___ _/_/_/_/_/________________________________________________________ > From donald.jackson at bms.com Mon Mar 8 15:10:35 2004 From: donald.jackson at bms.com (Donald Jackson) Date: Mon Mar 8 22:03:10 2004 Subject: [Bioperl-l] modules for siRNA design In-Reply-To: <200403081703.40515.heikki@ebi.ac.uk> References: <200403061913.i26JDq9Q010414@portal.open-bio.org> <200403081703.40515.heikki@ebi.ac.uk> Message-ID: <404CD33B.2080405@bms.com> Thanks Heikki, I thought I'd fixed all my code to handle that change from 1.0 to 1.2, but clearly I messed one. I'll get a patch into CVS later today and will also try to get some better error checking on sequence lengths and start/end pad. Don Heikki Lehvaslaiho wrote: >San Wang, > >The code in SiRNA.pm around line 263 looks like this: > > if ($cds) { > $left = $cds->start + $self->end_pad; > $right = $cds->end - $self->start_pad; > } > else { > $left = $target->start + $self->end_pad; # line #263 > $right = $target->end - $self->start_pad; > } > >Start and end calls are fine on a SeqFeature object like a CDS, but are not >defined for a sequence. These lines should be replaced by something like the >following: > > $left = 1 + $self->end_pad; > $right = $target->length - $self->start_pad; > >Your example sequence is not too realistic, so you'll get an other error >caused by the shortness of the sequece. Call > >$sirna_designer->start_pad(0); >$sirna_designer->end_pad(0); > >before calling design(). > >Yours, > -Heikki > >On Saturday 06 Mar 2004 19:08, ÍõêÉ, San Wang wrote: > > >>Dear bioperl-l: >> >> I have report a bug for it. >>"Can't locate object method "start" via package "Bio::Seq::RichSeq" >>(perhaps you forgot to load "Bio::Seq::RichSeq"?) at >>D:/Tools/perl/site/lib/Bio/Tools/SiRNA.pm line 263." >> >> Best Regards! >> >> Yours sincerely >>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang >>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman@tom.com >>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-07 >> ,-,-. ,-,-. ,-,-. ,-,-. ,- >>/ / \ \ / / \ \ / / \ \ / / \ \ / / >> \ \ / / \ \ / / \ \ / / \ \ / / >> `-'-' `-'-' `-'-' `-'-' >> >> >>San Wang >>Dr. Student >>Bioinformatics and Gene Network Research Group >>Zhejiang University >>P.R.China >> >>Address: >>Room 415# ,Bio-technology Institute, >>Zhejiang University, >>Kaixuan Road 268# Hangzhou >>Zhejiang, P.R.China >>310027 >> >>Tel: >>0086-571-86892051 >>Fax: >>0086-571-86961525 >>E-mail: >>bsman@163.com >>Website: >>http://www.estarray.org >> >>£­£­£­£­£­£­£­£­£­£­ >> Innovation is everything. When you are on the forefront, you can see what >>the next innovation needs to be? --- from Robert Noyce, Founder of Intel >> The more things change, the more they stay the same! >> The more things seem to be complicated ,the more they are simple in fact! >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > > From laurichj at bioinfo.ucr.edu Mon Mar 8 14:38:33 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Mon Mar 8 22:03:17 2004 Subject: [Bioperl-l] Unusual behaviour of SeqIO::tigr In-Reply-To: <404C4F93.1010606@binf.ku.dk> References: <404751D7.6030406@binf.ku.dk> <20040305184510.GB7843@batch107a> <404C4F93.1010606@binf.ku.dk> Message-ID: <20040308193832.GA10347@batch107a> On Mon 03/08/04 11:48, Morten Lindow wrote: > Thanks Josh that helped, > > In case somebody else can use it I am pasting the complete code to get > the coordinates of all locations on one line each. > > But another thing: When parsing rice-pseudochromosome files I get a few > warnings like this(from around 20-30 sequences per chromosome): Thats because not all of the proteins annotated are valid proteins. > since the problem is only with a small fraction of the TUs I guess it is > not a bioperl problem, but rather a TIGR problem? Any comments? TIGRs rice publications have some flaws that are slowly getting worked out. The invalid proteins are one and there are still some examples where the exon's are annotated to be outside of the TU their enclosed in. -- ------------------------------------------------------ | Josh Lauricha | Ford, your turning into | | laurichj@bioinfo.ucr.edu | a penguin. Stop it. | | Bioinformatics, UCR | | |----------------------------------------------------| | OpenPG: | | 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8 | |----------------------------------------------------| -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 197 bytes Desc: Digital signature Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040308/7e9f40d8/attachment.bin From hlapp at gmx.net Tue Mar 9 02:51:57 2004 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue Mar 9 02:57:35 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: Message-ID: On Monday, March 8, 2004, at 01:07 PM, Chris Mungall wrote: > Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler > class? This would contain methods > > generate_unique_persistent_id($feat) # uses $feat->seq_id > generate_unique_persistent_id($feat, $seq_id) > > create_hierarchy_from_ParentIDs($featholder); > set_ParentIDs_from_hierarchy($featholder); > > Any preference? I'm leaving them as is for now if that's ok, but I > have no > objections to moving everything to a seperate class if that's prefered. > I like your suggestion. Keeps FeatureHolderI lighter, and is easier to change behaviour. But maybe it's just me who likes this better. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From allenday at ucla.edu Tue Mar 9 04:04:52 2004 From: allenday at ucla.edu (Allen Day) Date: Tue Mar 9 04:10:36 2004 Subject: [Bioperl-l] Unique IDs in bioperl (Was: new GFF3 support methods added) In-Reply-To: Message-ID: I'd be interested in having this discussion and/or method documented as a set of guidelines or rules for creating unique IDs. We've had to deal with a similar problem to generate unique IDs for our chado GFF3 loader and UCSC datafile parsers and the solutions are essentially bad hacks. -allen > Much as I like closures, I think there should be a standard sanctioned way > of generating unique/persistent IDs > > > > Unique IDs in bioperl: > > > > > > In the discussion that preceeded this, it seemed that people liked the > > > idea of persistent unique IDs, but there was no suggestions as to how > > > to > > > go about it. This is inherently difficult with objects, but I borrowed > > > a > > > solution from relational modeling. > > > > > > A persistent unique ID is generated using > > > > > > seq_id > > > primary_tag > > > start > > > end > > > > > > It is assumed that these are all set and comprise a "unique key" over > > > features. > > > > Hmm. Wouldn't you need to include source_tag()? (Source_tag is part of > > the unique key in biosql.) Without the source_tag being part of this, > > wouldn't that mean you cannot have the exact (start+end) same segment > > predicted as exon by different methods and have those different > > predictions co-exist as separate features in the graph? (Presumably > > those would only differ in source_tag) > > Good point! I've added this > > Ok, so are you saying that some of these methods don't really belong in > the class-interfaces they are in? > > Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler > class? This would contain methods > > generate_unique_persistent_id($feat) # uses $feat->seq_id > generate_unique_persistent_id($feat, $seq_id) > > create_hierarchy_from_ParentIDs($featholder); > set_ParentIDs_from_hierarchy($featholder); > > Any preference? I'm leaving them as is for now if that's ok, but I have no > objections to moving everything to a seperate class if that's prefered. 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    whatever
    },$result->algorithm); } If I try this I get back the html returned from the method 'default_start_report'??? Specifically I want to add some js links(head) and a logo(body) to the HTML report for blast. Charles From mbatealann at netscape.net Tue Mar 9 11:23:25 2004 From: mbatealann at netscape.net (mbatealann@netscape.net) Date: Tue Mar 9 11:25:32 2004 Subject: [Bioperl-l] REPLY SOON Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From barry.moore at genetics.utah.edu Tue Mar 9 13:17:39 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Tue Mar 9 13:23:37 2004 Subject: [Bioperl-l] Bio::Annotation::Reference Message-ID: <404E0A43.3000303@genetics.utah.edu> The value for the PUBMED line of a GenBank file seems to be ending up in the wrong place. When I call $ref->location on a Bio::Annotation::Reference object, I get a line such as, "Mol. Biol. Cell 12 (12), 3839-3851 (2001) PUBMED 11739784". When I call $ref->pubmed on the same object it returns undefined. It seems to me that $ref->location should return "Mol. Biol. Cell 12 (12), 3839-3851 (2001)" and $ref->pubmed should return "11739784". Is this a bug or is this the intended behaviour? I didn't put this in Bugzilla since I wasn't entirely sure it was really a bug, should it go there? Here's a bit of code that should repeat this situation. It does the same thing for me on half a dozen different RefSeq accessions that I have tried. use Bio::DB::GenBank; use Bio::SeqIO; my @ids = (NM_013366); my $gb = new Bio::DB::GenBank(); my $seqio = $gb->get_Stream_by_id(@ids); while (my $seq = $seqio->next_seq) { my $ann = $seq->annotation(); my @refs = ($ann->get_Annotations('reference')); my $ref = shift @refs; print "LOCATION:\t",$ref->location, "\n"; print "PUBMED:\t", $ref->pubmed, "\n"; } I am running BioPerl 1.4 and ActiveState Perl 5.8 on Windows XP. Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From jason at cgt.duhs.duke.edu Tue Mar 9 13:39:59 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 9 13:45:41 2004 Subject: [Bioperl-l] Bio::Annotation::Reference In-Reply-To: <404E0A43.3000303@genetics.utah.edu> References: <404E0A43.3000303@genetics.utah.edu> Message-ID: I think I may have already fixed this since the 1.4 release. I'll test it out when I get a chance or you can test on the CVS version of the code. I don't remember if I migrated the fix to the 1.4 branch yet though. -jason On Tue, 9 Mar 2004, Barry Moore wrote: > The value for the PUBMED line of a GenBank file seems to be ending up in > the wrong place. When I call $ref->location on a > Bio::Annotation::Reference object, I get a line such as, "Mol. Biol. > Cell 12 (12), 3839-3851 (2001) PUBMED 11739784". When I call > $ref->pubmed on the same object it returns undefined. It seems to me > that $ref->location should return "Mol. Biol. Cell 12 (12), 3839-3851 > (2001)" and $ref->pubmed should return "11739784". Is this a bug or is > this the intended behaviour? I didn't put this in Bugzilla since I > wasn't entirely sure it was really a bug, should it go there? > > Here's a bit of code that should repeat this situation. It does the > same thing for me on half a dozen different RefSeq accessions that I > have tried. > > use Bio::DB::GenBank; > use Bio::SeqIO; > > my @ids = (NM_013366); > my $gb = new Bio::DB::GenBank(); > my $seqio = $gb->get_Stream_by_id(@ids); > > while (my $seq = $seqio->next_seq) { > my $ann = $seq->annotation(); > my @refs = ($ann->get_Annotations('reference')); > my $ref = shift @refs; > print "LOCATION:\t",$ref->location, "\n"; > print "PUBMED:\t", $ref->pubmed, "\n"; > } > > I am running BioPerl 1.4 and ActiveState Perl 5.8 on Windows XP. > > Barry > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From ksdoctor at burnham.org Tue Mar 9 13:46:12 2004 From: ksdoctor at burnham.org (Kutbuddin Doctor) Date: Tue Mar 9 14:03:16 2004 Subject: [Bioperl-l] Bioperl 1.4 on Debian Message-ID: <404E10F4.5010300@burnham.org> I am about to switch a debian machine from the stable debian package "bioperl 1.0-1". The test package "bioperl 1.2.1-2" is listed as unstable. Why is this ~1yr old source still listed as "unstable"? I wish to go directly to bioperl 1.4 . I see my options as CPAN for 1.4 or the test debian package "bioperl 1.2.1-2". Our happy-go-lucky system admin prefers debian packages :) Are there any plans for updating the debian packages in the near future? thanks. -- -<>--<>--<>--<>--<>--<>--<>--<>- Kutbuddin S. Doctor, PhD Informatics & Data Management, The Burnham Institute, La Jolla, CA 92037 ksdoctor (AT)burnham.org http://burnham.org/ -<>--<>--<>--<>--<>--<>--<>--<>- From laurichj at bioinfo.ucr.edu Tue Mar 9 14:06:12 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Tue Mar 9 14:11:50 2004 Subject: [Bioperl-l] Bioperl 1.4 on Debian In-Reply-To: <404E10F4.5010300@burnham.org> References: <404E10F4.5010300@burnham.org> Message-ID: <20040309190612.GB9004@bioinfo.ucr.edu> On Tue 03/09/04 10:46, Kutbuddin Doctor wrote: > > I am about to switch a debian machine from the stable debian package > "bioperl 1.0-1". > The test package "bioperl 1.2.1-2" is listed as unstable. > > Why is this ~1yr old source still listed as "unstable"? The package is not unstable, it is in the unstable distro. If I recall correctly, its also in testing. This just means that it was released after woody was. When sarge is released, it will be in stable. > I wish to go directly to bioperl 1.4 . I see my options as CPAN for 1.4 > or the test debian package "bioperl 1.2.1-2". Our happy-go-lucky system > admin prefers debian packages :) I've got an unofficial 1.4 package that I could make availible, but its not likely to ever get into debian (I'm not a maintainer) and when 1.4 is in, its not likely to be structured like mine (which isn't really a big deal.) -- ------------------------------------------------------ | Josh Lauricha | Ford, your turning into | | laurichj@bioinfo.ucr.edu | a penguin. Stop it. | | Bioinformatics, UCR | | |----------------------------------------------------| | OpenPG: | | 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8 | |----------------------------------------------------| From jhpark98 at dreamwiz.com Mon Mar 8 23:40:37 2004 From: jhpark98 at dreamwiz.com (=?ks_c_5601-1987?B?udrB2Mf8?=) Date: Tue Mar 9 14:23:34 2004 Subject: [Bioperl-l] biosql error Message-ID: Dear Bioperl Experts I have some problem to perform biosql database update like this. Until upgrade perl 5.8.3, I had been used load_seqdatabase.pl script to update genbank file into biosql database. I don?t know what is the problem. Is there some method to fix these bugs? ------------- EXCEPTION ------------- MSG: failed to open connection: STACK Bio::DB::DBI::base::new_connection /usr/local/lib/perl5/site_perl/5.8. 3//Bio/DB/DBI/base.pm:249 STACK Bio::DB::DBI::base::get_connection /usr/local/lib/perl5/site_perl/5.8. 3//Bio/DB/DBI/base.pm:209 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/BasePersistenceAdaptor.p m:1443 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::rollback /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/BasePersistenceAdaptor.p m:1362 STACK toplevel load_seqdatabase.pl:515 From hlapp at gnf.org Tue Mar 9 15:05:44 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Mar 9 15:11:24 2004 Subject: [Bioperl-l] biosql error In-Reply-To: Message-ID: <25C41E56-7205-11D8-A93D-000A959EB4C4@gnf.org> If you upgraded perl you will need to recompile and re-install DBI as well as your DBD driver(s) of choice. What you're seeing is most likely not due to a bug - it rather looks like an installation issue on your machine. Also, to see the DBI error messages, which in this case I'm pretty sure will conclusively point at the problem, supply --printerror to the script. (If your version doesn't recognize that option, you need to update from bioperl-db cvs.) -hilmar On Monday, March 8, 2004, at 08:40 PM, ??? wrote: > Dear Bioperl Experts > > I have some problem to perform biosql database update like this. > > Until upgrade perl 5.8.3, I had been used load_seqdatabase.pl script to > update genbank file into biosql database. > > I don?t know what is the problem. > > Is there some method to fix these bugs? > > > > ------------- EXCEPTION ------------- > > MSG: failed to open connection: > > STACK Bio::DB::DBI::base::new_connection > /usr/local/lib/perl5/site_perl/5.8. > 3//Bio/DB/DBI/base.pm:249 > > STACK Bio::DB::DBI::base::get_connection > /usr/local/lib/perl5/site_perl/5.8. > 3//Bio/DB/DBI/base.pm:209 > > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::dbh > /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/ > BasePersistenceAdaptor.p > m:1443 > > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::rollback > /usr/local/lib/perl5/site_perl/5.8.3//Bio/DB/BioSQL/ > BasePersistenceAdaptor.p > m:1362 > > STACK toplevel load_seqdatabase.pl:515 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From cjm at fruitfly.org Tue Mar 9 20:54:30 2004 From: cjm at fruitfly.org (Chris Mungall) Date: Tue Mar 9 21:00:13 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: Message-ID: On Mon, 8 Mar 2004, Hilmar Lapp wrote: > > On Monday, March 8, 2004, at 01:07 PM, Chris Mungall wrote: > > > Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler > > class? This would contain methods > > > > generate_unique_persistent_id($feat) # uses $feat->seq_id > > generate_unique_persistent_id($feat, $seq_id) > > > > create_hierarchy_from_ParentIDs($featholder); > > set_ParentIDs_from_hierarchy($featholder); > > > > Any preference? I'm leaving them as is for now if that's ok, but I > > have no > > objections to moving everything to a seperate class if that's prefered. > > > > I like your suggestion. Keeps FeatureHolderI lighter, and is easier to > change behaviour. But maybe it's just me who likes this better. Ok, I'll go ahead and add this We will now have 3 classes in Bio::SeqFeature::Tools Unflattener TypeMapper IDHandler Personally I like this pattern, whereby the object model is kept simple and lightweight, and complex behaviour is punted to seperate classes. It does force the question - how do we decide which methods goes in the model class and which goes in a behaviour class? Is it just an intuitive thing? I'm happy for the bioperl czar to weigh in (who is that these days?) and make individual judgement calls, I just want what I'm doing to be consistent with some overall plan. Cheers Chris > -hilmar > > From jason at cgt.duhs.duke.edu Tue Mar 9 21:25:53 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 9 21:31:33 2004 Subject: [Bioperl-l] OSX, NCBI blast 2.2.8, blast parsers Message-ID: Strict BLAST parsers are going to fall over on ncbi blast 2.2.8 produced reports. You can see what happens on you system by doing this is the bioperl directory: $ blastpgp -d $BLASTDB/swissprot -i t/data/amino.fa -j 2 | grep "total letters" U79 sequences; E27 total letters $ blastall -p blastn -i t/data/test.txt -d $BLASTDB/ecoli.nt | grep "total letters" 400 sequences; N39 total letters The parser expects numbers in those spots not a combination. This is using ftp://ftp.ncbi.nih.gov/blast/executables/blast-2.2.8-powerpc-macosx.tar.gz This does not appear on linux ia32 distribution so I assume it is an OSX specific issue or compilation related issue. This was found per bug #1598 http://bugzilla.open-bio.org/show_bug.cgi?id=1598 -jason -- Jason Stajich Duke University jason at cgt.mc.duke.edu From skchan at cs.usask.ca Wed Mar 10 00:56:24 2004 From: skchan at cs.usask.ca (Simon K. Chan) Date: Wed Mar 10 01:02:46 2004 Subject: [Bioperl-l] TreeIO question/problem Message-ID: <1078898184.404eae08173ae@webmail.usask.ca> Hi, I wish to parse a tree in newick format. I attempted to use the TreeIO module to do so: My problem is that $treeio->next_tree does not return anything, thus I cannot call the get_nodes method to get all the nodes in my tree. My code follows. Many thanks for your time. use lib '/home/skchan/bioperl/bioperl-1.4'; use Bio::Tree::Node; use Bio::TreeIO; use Bio::Tree::Tree; use Bio::Tree::TreeI; # obtained code from bioperl documentation: my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree"); my $tree = $treeio->next_tree; print "tree: $tree\n"; my @nodes = $treeIO->get_nodes; print "nodes: @nodes\n"; From skchan at cs.usask.ca Wed Mar 10 01:05:03 2004 From: skchan at cs.usask.ca (Simon K. Chan) Date: Wed Mar 10 01:10:54 2004 Subject: Part 2: [Bioperl-l] TreeIO question/problem Message-ID: <1078898703.404eb00f5833d@webmail.usask.ca> My apologies, but there was a mistake in my first email. My code is actually the following: use lib '/home/skchan/bioperl/bioperl-1.4'; use Bio::Tree::Node; use Bio::TreeIO; use Bio::Tree::Tree; use Bio::Tree::TreeI; # obtained code from bioperl documentation: my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree"); my $tree = $treeio->next_tree; print "tree: $tree\n"; $treeio->next_tree does not return anything, thus, I cannot run get_nodes. Many thanks again. Simon ----- Forwarded message from "Simon K. Chan" ----- Date: Tue, 09 Mar 2004 23:56:24 -0600 From: "Simon K. Chan" Reply-To: "Simon K. Chan" Subject: [Bioperl-l] TreeIO question/problem To: bioperl-l@bioperl.org Hi, I wish to parse a tree in newick format. I attempted to use the TreeIO module to do so: My problem is that $treeio->next_tree does not return anything, thus I cannot call the get_nodes method to get all the nodes in my tree. My code follows. Many thanks for your time. use lib '/home/skchan/bioperl/bioperl-1.4'; use Bio::Tree::Node; use Bio::TreeIO; use Bio::Tree::Tree; use Bio::Tree::TreeI; # obtained code from bioperl documentation: my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree"); my $tree = $treeio->next_tree; print "tree: $tree\n"; my @nodes = $treeIO->get_nodes; print "nodes: @nodes\n"; _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l ----- End forwarded message ----- From abrusan at mpil-ploen.mpg.de Wed Mar 10 07:32:25 2004 From: abrusan at mpil-ploen.mpg.de (Gyoergy Abrusan) Date: Wed Mar 10 07:36:53 2004 Subject: [Bioperl-l] Printing string fragments? Message-ID: <404F0AD9.2040809@mpil-ploen.mpg.de> Dear All, I would like to ask how can I print out certain fragments of strings. my data are in the format: >seqname1#uninteresting_information ATCGTACGTGCGAGACGT...... >seqname2#..... ATGTCATG.... I wrote a script that makes some statistics on the nucleotide sequences. I would like to print the results out as: seqname1 results seqname2 results at the moment I can print them out only as: >seqname1#uninteresting_information results >seqname2#uninteresting_information results Because the scriprt prints out the entire seqname-sting. How can I print out parts of a string, say from symbol '>' to symbol '#'? Thanking you in advance. Kind regards, Gyorgy Abrusan, Max-Planck Institute for Limnology, Ploen, Germany From ak at ebi.ac.uk Wed Mar 10 07:52:04 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Wed Mar 10 07:57:42 2004 Subject: [Bioperl-l] Printing string fragments? In-Reply-To: <404F0AD9.2040809@mpil-ploen.mpg.de> References: <404F0AD9.2040809@mpil-ploen.mpg.de> Message-ID: <20040310125204.GA27239@ebi.ac.uk> On Wed, Mar 10, 2004 at 01:32:25PM +0100, Gyoergy Abrusan wrote: > Dear All, > > I would like to ask how can I print out certain fragments of strings. > my data are in the format: > > >seqname1#uninteresting_information > ATCGTACGTGCGAGACGT...... > >seqname2#..... > ATGTCATG.... > > I wrote a script that makes some statistics on the nucleotide sequences. > I would like to print the results out as: > > seqname1 results > seqname2 results > > at the moment I can print them out only as: > > >seqname1#uninteresting_information results > >seqname2#uninteresting_information results > > Because the scriprt prints out the entire seqname-sting. > How can I print out parts of a string, say from symbol '>' to > symbol '#'? my $result = 'some result'; my $string = '>seqname1#uninteresting_information'; $string =~ /^>([^#]+)#/; # See the perlre manual ("perldoc perlre") my $seqname = $1; print "$seqname\t$result\n"; Cheers, Andreas -- | {} | Andreas K?h?ri |][][| |{}{}| EMBL, European Bioinformatics Institute |[][]| | {} | Wellcome Trust Genome Campus |][][| |{}{}| Hinxton, Cambridgeshire, CB10 1SD |[][]| | {} | United Kingdom |][][| From brian_osborne at cognia.com Wed Mar 10 08:35:21 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Mar 10 08:41:02 2004 Subject: [Bioperl-l] Web site notes Message-ID: Bioperl-l, Just writing to tell you that over the past few weeks I've been editing many of the Web pages. Changes include: - standardizing font sizes and faces over the pages - removing links to outdated pages - editing outdated text - making the "highlights" in the left navigation bar work on every page, giving every page a navigation bar - fixing some broken links Much of this work is returning the site to its initial "graphic" state, as it existed before it was editable in CVS. Brian O. From brian_osborne at cognia.com Wed Mar 10 09:02:06 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Mar 10 09:07:50 2004 Subject: [Bioperl-l] Printing string fragments? In-Reply-To: <404F0AD9.2040809@mpil-ploen.mpg.de> Message-ID: Gyoergy, If you are actually creating this fasta file yourself then you could change the format of the header a bit by adding a space, to: >seqname1 #uninteresting_information Then, $seq_obj->display_id will give "seqname1", not "seqname1#uninteresting_information". Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Gyoergy Abrusan Sent: Wednesday, March 10, 2004 7:32 AM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Printing string fragments? Dear All, I would like to ask how can I print out certain fragments of strings. my data are in the format: >seqname1#uninteresting_information ATCGTACGTGCGAGACGT...... >seqname2#..... ATGTCATG.... I wrote a script that makes some statistics on the nucleotide sequences. I would like to print the results out as: seqname1 results seqname2 results at the moment I can print them out only as: >seqname1#uninteresting_information results >seqname2#uninteresting_information results Because the scriprt prints out the entire seqname-sting. How can I print out parts of a string, say from symbol '>' to symbol '#'? Thanking you in advance. Kind regards, Gyorgy Abrusan, Max-Planck Institute for Limnology, Ploen, Germany _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason at cgt.duhs.duke.edu Wed Mar 10 09:17:36 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 10 09:23:15 2004 Subject: Part 2: [Bioperl-l] TreeIO question/problem In-Reply-To: <1078898703.404eb00f5833d@webmail.usask.ca> References: <1078898703.404eb00f5833d@webmail.usask.ca> Message-ID: Did you try other tree files like the examples in t/data? I cannot do much to help without a copy of the offending tree file in newick_tree. -jason On Wed, 10 Mar 2004, Simon K. Chan wrote: > My apologies, but there was a mistake in my first email. My code is actually > the following: > > > use lib '/home/skchan/bioperl/bioperl-1.4'; > use Bio::Tree::Node; > use Bio::TreeIO; > use Bio::Tree::Tree; > use Bio::Tree::TreeI; > > # obtained code from bioperl documentation: > > my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree"); > my $tree = $treeio->next_tree; > > print "tree: $tree\n"; > > $treeio->next_tree does not return anything, thus, I cannot run get_nodes. > > Many thanks again. > > Simon > > > ----- Forwarded message from "Simon K. Chan" ----- > Date: Tue, 09 Mar 2004 23:56:24 -0600 > From: "Simon K. Chan" > Reply-To: "Simon K. Chan" > Subject: [Bioperl-l] TreeIO question/problem > To: bioperl-l@bioperl.org > > Hi, > > I wish to parse a tree in newick format. > > I attempted to use the TreeIO module to do so: > > My problem is that $treeio->next_tree does not return anything, thus I cannot > call the get_nodes method to get all the nodes in my tree. > > My code follows. Many thanks for your time. > > use lib '/home/skchan/bioperl/bioperl-1.4'; > use Bio::Tree::Node; > use Bio::TreeIO; > use Bio::Tree::Tree; > use Bio::Tree::TreeI; > > # obtained code from bioperl documentation: > > my $treeio = new Bio::TreeIO(-format=>"newick", -file=>"./newick_tree"); > my $tree = $treeio->next_tree; > > print "tree: $tree\n"; > > my @nodes = $treeIO->get_nodes; > > print "nodes: @nodes\n"; > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > ----- End forwarded message ----- > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From dlondon at ebi.ac.uk Wed Mar 10 09:35:02 2004 From: dlondon at ebi.ac.uk (Darin London) Date: Wed Mar 10 09:40:40 2004 Subject: [Bioperl-l] BOSC 2004 Announcement and Call for Papers (fwd) Message-ID: {Please pass the word!} MEETING ANNOUNCEMENT & CALL FOR SPEAKERS The 5th annual Bioinformatics Open Source Conference (BOSC'2004) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place July 29-30, 2004 in Glasgow, Scotland, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 12th International Conference on Intelligent Systems for Molecular Biology. see http://www.iscb.org/ismb2004/ for more information. The focus of the meeting will be on current and emerging Open Source** informatics tools and toolkits. BOSC provides a forum for developers, project groups, users and interested parties to meet personally, exchange ideas and collaborate together. In addition, keynote speeches from well known Open Source Bioinformatics leaders are being planned. BOSC PROGRAM & CONTACT INFO * Web: http://www.open-bio.org/bosc2004/ * Email: bosc@open-bio.org * Online registration: https://www.cteusa.com/iscb3/ FEES * Corporate :GBP ?165.00 british pounds sterling * Academic : GBP ?120.00 british pounds sterling * Student : GBP ?90.00 british pounds sterling A 17.5% Valued Added Tax(VAT) will be added to all fees. Note: We have tried to set our fees as low as possible without risking the chance that the foundation will lose money on the event. We budget with the goal of breaking even on costs or realizing a small profit. REGISTER ONLINE FOR BOSC'2004 & ISMB AT: https://www.cteusa.com/iscb3/ SPEAKERS & ABSTRACTS WANTED The program committee is currently seeking abstracts for talks at BOSC 2004. BOSC is a great opportunity for you to tell the community about your use, development, or philosophy of open source software development in bioinformatics. The committee will select several submitted abstracts for 25-minute talks and others for shorter "lightning" talks. Accepted abstracts will be published on the BOSC web site. If you are interested in speaking at BOSC 2004, please send us: * an abstract (no more than a few paragraphs) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. LIGHTNING-TALK SPEAKERS WANTED! The program committee is currently seeking speakers for the lightning talks at BOSC 2004. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. If you are interested in giving a lightning talk at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * information about the open source license used for your software or your release plans. We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.
    SOFTWARE DEMONSTRATIONS WANTED! If you are involved in the development of Open Source Bioinformatics Software, you are invited to provide a short demonstration to attendees of BOSC 2004. If you are interested in giving a software demonstration at BOSC 2004, please send us: * a brief title and summary (one or two lines) * a URL for the project page, if applicable * Internet connectivity requirements (e.g. website Application served on the world wide web, or web based client application). We will accept entries on-line until the BOSC starts, but space for demos and lightning talks is limited. ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy. See the following websites for further details: href="http://www.opensource.org/licenses/ href="http://www.opensource.org/docs/definition.php From nathanhaigh at ukonline.co.uk Wed Mar 10 13:17:39 2004 From: nathanhaigh at ukonline.co.uk (Nathan Haigh) Date: Wed Mar 10 13:23:19 2004 Subject: [Bioperl-l] fasta3 program support Message-ID: Does the standalonefasta module support any other version that fasta3, I have fasta34 and am running into problems! If it only runs with fasta3, does anyone know where I can download the correct version to run with bioperl, and what the differences between fasta3 and fasta34 are? Regards Nathan From Cariaso at yahoo.com Wed Mar 10 13:59:52 2004 From: Cariaso at yahoo.com (Michael Cariaso) Date: Wed Mar 10 14:05:30 2004 Subject: [Bioperl-l] seeking advice about setting up a local GenBank mirror In-Reply-To: References: Message-ID: <404F65A8.3040806@yahoo.com> This is not a strictly bioperl question so I'll take non-bioperl related answers offline. I need to setup a local mirror of most of GenBank (I don't need the ESTs or indexes). There seems to be several ways to achieve this, but no single definitive solution. I'd like to keep the files in their gzipped form. And my copies don't need to be too fresh, up to a week old should be acceptable. Can anyone recommend, or warn me away from *ANY* of these approaches. Is there a suitable part of bioperl? Has anyone used BioMirror.pm? http://www.bio-mirror.net/biomirror/software/biomirror/biomir-help.txt What about ftpmirror? http://noc.intec.co.jp/ftpmirror.html What about mirror? (It's hard to find a current copy, the word is too common. Is anyone still using this?) http://www.etsimo.uniovi.es/mirror/mirror.html I'm about 10 miles away from the NIH, and not connected to the I2 network. Is there any reason to prefer mirroring off of ftp://bio-mirror.net/biomirror//genbank/ versus ftp://ftp.ncbi.nih.gov/genbank/ -- Michael Cariaso http://www.cariaso.com From sdavis2 at mail.nih.gov Wed Mar 10 14:20:14 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed Mar 10 14:24:19 2004 Subject: [Bioperl-l] bio::tools::run::blat? Message-ID: Just a quick question: Has anyone considered (or achieved) the blat equivalent of standaloneblast? Thanks, Sean From jason at cgt.duhs.duke.edu Wed Mar 10 14:39:16 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 10 14:44:54 2004 Subject: [Bioperl-l] bio::tools::run::blat? In-Reply-To: References: Message-ID: Bio::Tools::Run::Alignment::Blat In the bioperl-run CVS repository and in the bioperl-run distro. Any new "standalone-xxx" should be written in the bioperl runnable way. StandAloneBlast is legacy code in many ways and pretty hard to manage. Will Spooner at Ensembl has written some very nice generic pairwise alignment search interfaces that allow dispatching of Fasta,SSAHA, Blast, etc. One day we may be able to import some more of his nice design into the system. -jason On Wed, 10 Mar 2004, Sean Davis wrote: > Just a quick question: Has anyone considered (or achieved) the blat > equivalent of standaloneblast? > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From shawnh at stanford.edu Wed Mar 10 14:46:13 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Wed Mar 10 14:51:53 2004 Subject: [Bioperl-l] bio::tools::run::blat? In-Reply-To: References: Message-ID: <9661DDC0-72CB-11D8-8DA3-000A95783436@stanford.edu> yes, its implemented. Bio::Tools::Run::Alignment::Blat shawn On Mar 10, 2004, at 11:20 AM, Sean Davis wrote: > Just a quick question: Has anyone considered (or achieved) the blat > equivalent of standaloneblast? > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From lstein at cshl.edu Wed Mar 10 16:27:21 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Wed Mar 10 16:32:58 2004 Subject: use of seq_id. was: [Bioperl-l] Bio::Tools::GFF use of seqname In-Reply-To: References: Message-ID: <200403101627.21642.lstein@cshl.edu> Bio::Graphics doesn't depend on a seq_id as far as I know. Please let me know if you have evidence otherwise. Lincoln On Tuesday 24 February 2004 10:28 pm, Hilmar Lapp wrote: > On Tuesday, February 24, 2004, at 01:55 AM, Dave Howorth wrote: > > Hilmar Lapp wrote: > >> Actually, $feat->can('seq_id') must be true at all times iff > >> $feat->isa("Bio::SeqFeatureI"), so it's kind of superfluous to test > >> for it. > > > > Where does this come from, please? In the SeqFeatureI documentation > > it says seq_id 'is an attribute such that you *can* store the ID' (my > > emphasis). You seem to be saying that if I'm creating a bunch of > > (sub) features just so I can use Bio::Graphics, I must attach a seq_id > > to each and every one. > > I'm not saying anything about the value of the attribute. > $feat->can('seq_id') will be true if you can call $feat->seq_id(), > which you will always be able to since it's defined in > Bio::SeqFeatureI. Whether that method returns garbage or something > useful is another story. I'm not sure whether you have to set seq_id() > to something meaningful in order to remain compatible with > Bio::Graphics, but I'd guess you do. Lincoln? > > > I have an inverse question that I haven't managed to find an answer to > > yet. If I'm displaying these sub-features as segments, how can I > > attach some text to the feature that will be displayed alongside each > > individual segment? > > This one is for Lincoln ... > > -hilmar > > > Thanks, Dave > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From dag at sonsorol.org Wed Mar 10 21:30:13 2004 From: dag at sonsorol.org (Chris Dagdigian) Date: Wed Mar 10 21:35:57 2004 Subject: [Bioperl-l] O|B|F mail update -- making progress on anti-spam issues with our mailing lists Message-ID: <404FCF35.5010705@sonsorol.org> Hi folks, Apologies for the cross-posting but I just wanted to give our list members and admins an update on some new anti-spam measures we have (re)enabled. Good news to report basically... The most annoying spams recently have been the simple plain text messages without any HTML, attachments or mime-encoding that just slip right by our filters. Some lists have been forced to switch over to "only members can post" while other lists (like bioperl) have consistantly voted to stay as open as possible. I'll update you on our current efforts as well as a new effort that is about 24 hours old but already working really well so far. Until yesterday we had three main lines of defense against spam: 1. The mailserver itself (rejects mail from nonexistant domains, etc.) 2. The sendmail Mail::Milter extention (MIMEDefang+SpamAssassin are used to scan all incoming messages. Anything that scores higher than 8.0 is simply discarded automatically. MIMEDefang also strips dangerous attachments like .exe and .pif) 3. Our mailing list moderation queue (emails with attachments, odd MIME encodings and spamassassin scores from 0.0 - 7.9 are held in a moderator queue for a human to make an accept/discard decision) Here are some stats on how this system worked over the past few days: o 138 attempts to relay mail through our server blocked o 192 emails blocked due to forged or unresolvable sender domain o 577 emails discarded automatically by SpamAssassin+MIMEDefang This system worked *ok* but put a lot of work onto the shoulders of our list admins who constantly had to weed out the spam caught up in the mailing list moderator system. Yesterday I brought online another system that seems to be already working really well. It catches spam before we even accept it on our server which makes the load easier on both our scanning software and our human list moderators. The system is the RBL+ blackhole list from http://www.mail-abuse.org and the way it works is that we now query (via DNS) the RBL+ database each time someone connects to our mail server. If the RBL check against the sender IP address comes back as "positive" we reject the incoming email. RBL+ is a combination of four constantly updated databases: 1. RBL -- IP addresses of known, documented spammers and spam machines 2. RSS -- IP addresses of documented/tested unsecured email relays 3. OPS -- IP addresses of documented open proxy servers w/ spam history 3. DUL -- IP addresses belonging to ISP dialup and DHCP customers We have already blocked 137 email attempts in the last 24 hours from machines that were listed in one or more of the RBL databases. It is too soon to tell but if the RBL+ system plus our existing anti-spam measures work well enough we may be in a position where our "closed" mailing lists could revert back to being 'anyone can post'. Feedback appreciated. Especially if you get a "reject" message from us saying that you are listed in the RBL+ blackhole database! Regards, Chris O|B|F From MAILER-DAEMON at xmegs.com Thu Mar 11 05:40:54 2004 From: MAILER-DAEMON at xmegs.com (MAILER-DAEMON@xmegs.com) Date: Thu Mar 11 05:36:22 2004 Subject: [Bioperl-l] failure notice Message-ID: <200403111036.i2BAaEtl017063@portal.open-bio.org> Hi. This is the qmail-send program at xmegs.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. <.skedo@kspc.com.my>: vdeliver: Invalid or unknown virtual user '.skedo' --- Below this line is a copy of the message. Return-Path: Received: (qmail 22341 invoked from network); 11 Mar 2004 10:40:51 -0000 Received: from unknown (HELO kspc.com.my) (218.208.34.66) by 202.157.185.141 with SMTP; 11 Mar 2004 10:40:51 -0000 From: bioperl-l@bioperl.org To: .skedo@kspc.com.my Subject: hello Date: Thu, 11 Mar 2004 18:30:48 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="70606400" --70606400 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit my hero --70606400 Content-Type: application/octet-stream; name="information.scr" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="information.scr" TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAgAAAAA4fug4AtAnNIbgBTM0hVGhpcyBwcm9ncmFtIGNhbm5vdCBiZSBydW4gaW4g RE9TIG1vZGUuDQ0KJAAAAAAAAABQRQAATAEDAFn0MEAAAAAAAAAAAOAADwILAQI4AFAAAAAQ AAAAQAEA0JABAABQAQAAoAEAAABAAAAQAAAAAgAABAAAAAAAAAAEAAAAAAAAAACwAQAAEAAA AAAAAAIAAAAAABAAABAAAAAAEAAAEAAAAAAAABAAAAAAAAAAAAAAAGStAQCAAQAAAKABAGQN 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From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Mar 11 08:22:26 2004 Subject: [Bioperl-l] protein networks In-Reply-To: <404C3D57.2050600@ed.ac.uk> Message-ID: Richard, You may want to reconsider the name "ProteinGraphIO::xml.pm" since other pathway databases (BIND certainly, KEGG perhaps) also export to XML. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Richard Adams Sent: Monday, March 08, 2004 4:31 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] protein networks Hi, I've been writing some modules to apply Nathan Goodman's "SimpleGraph.pm" module to protein interaction networks. He has written this as a replacement for the the broken CPAN graph modules. The aim of these modules is 1. To convert protein interaction data between differentet formats 2. To be able to link protein interaction data to protein sequence data. 3. To be able to read in interaction data from separate sources, and make a merged graph with duplicate interactions flagged or removed. Could some core person give some idea for namespace to put these in CVS? The modules are : 1. Nathan's modules SimpleGraph.pm - a generic graph module with methods to build and represent a graph SimpleGraph::Traversal.pm - generic methods to navigate a graph. 2. My modules a. An I/O system analagous to SeqIO that lazyloads the correct modules for a particular format ProteinGraphIO.pm - with next_graph, write_graph methods ProteinGraphIO::dip.pm - parser for DIP format interactions - to read in PSI_XML formatted records (still being worked on). b. Modules to represent a protein network: PrimaryProteinGraph.pm - subclass of SimpleGraph.pm. This will be made from a dip record, analagous to PrimarySeq FullProteinGraph .pm - subclas of SimpleGraph.pm, contains PrimaryProteinGraph and metadata of graph, will be made from an XML file, analagous to RichSeq. c. Classes to represent nodes/ edges. NodeI.pm - interface describing methods that all nodes should have ProteinNode.pm - implements NodeI, currently has methods primary_id(), seq(), secondary_id() InteractionI.pm - interface describing methods all edges should have ProteinInteraction.pm - implements InteractionI, currently has methods weight(), interactors(), id(). Cheers Richard -- Dr Richard Adams Psychiatric Genetics Group, Medical Genetics, Molecular Medicine Centre, Western General Hospital, Crewe Rd West, Edinburgh UK EH4 2XU Tel: 44 131 651 1084 richard.adams@ed.ac.uk _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From baber at mrtcbko.org Thu Mar 11 09:46:47 2004 From: baber at mrtcbko.org (Ibrahima BABER) Date: Thu Mar 11 10:01:49 2004 Subject: [Bioperl-l] how to set up bioperl cygwin Message-ID: <3FE6D6566E4FD511B54A009027EEADE71BE649@MRTCBKO> Dear I have installed Cygwin successfully, and I would like to know how to set up bioperl with cygwin? Thanks Ibrahima Mali - west-Africa From heikki at ebi.ac.uk Thu Mar 11 10:06:10 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Thu Mar 11 10:11:47 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid In-Reply-To: <40507A3C.6090208@ed.ac.uk> References: <40507A3C.6090208@ed.ac.uk> Message-ID: <200403111506.10392.heikki@ebi.ac.uk> James, I think you are on the right track here. Getting the taxid and the higher taxa is more important than the lack of binomial name. I am moving this discussion from guts into bioperl-l list where it belongs. Thank your your contribution. Putting a patch into bugzilla as an attachment is exactly the right thing to do. -Heikki On Thursday 11 Mar 2004 14:39, James Wasmuth wrote: > Brian and all at bioperl-guts, > > > below is the comment I've added to the bug[1600]. I think it may need > some discussion, but the patch I've added works to the extent that it > allows creation of a Bio::Species object but the subsequent genus, > species, subspecies calls will be 'wrong'. Personally I'm more > concerned with the taxid, which I think will be sufficient. > > If you want to see the size of this problem go to NCBI taxonomy and > enter the term identified as a token set! I think that maintaining the > taxid is enough, otherwise the artifical split of terms such as > **unidentified diatom endosymbiont of Peridinium foliaceum* > 7&lvl=3&lin=f&keep=1&srchmode=3&unlock>* may be a problem, though some of > them are intuitive. > > One last question, I've never tried to fix a bug before, so I've > commited a patch as an attachment to Bugzilla for the bug. Do others > check this and if okay place it in the code... > apologies for the newbie bit... > > -james > > > > genbank.pm > > line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; > > a number of species are described as Unknown blah blah blah. > > The NCBI taxid assigned to unknown taxa is 32644 and has a number of > synonyms, none of which are 'unknown'. > > The list includes: other, unknown organism, not specified, not shown, > unspecified, Unknown, None, unclassified , unidentified organism > > I've changed the _read_GenBank_Species subroutine to allow organism > names such as 'unknown marine gamma proteobacterium NOR5'. This will > create a Bio::Species object, but the genus=unknown species=marine > subspecies=gamma. > > There is a whole host of species names that ignore the nice rules in > _read_GenBank_Species! However this fix will allow the correct taxid to > be provided which I think is more than the name! > > > > sub _read_GenBank_Species { > my( $self,$buffer) = @_; > my @organell_names = ("chloroplast", "mitochondr"); > # only those carrying DNA, apart from the nucleus > > #CHANGE > my @unkn_names=("other", 'unknown organism', 'not specified', 'not > shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified > organism'); > > $_ = $$buffer; > > my( $sub_species, $species, $genus, $common, $organelle, @class, > $ns_name ); > # upon first entering the loop, we must not read a new line -- the > SOURCE > # line is already in the buffer (HL 05/10/2000) > while (defined($_) || defined($_ = $self->_readline())) { > # de-HTMLify (links that may be encountered here don't contain > # escaped '>', so a simple-minded approach suffices) > s/<[^>]+>//g; > if (/^SOURCE\s+(.*)/o) { > # FIXME this is probably mostly wrong (e.g., it yields things like > # Homo sapiens adult placenta cDNA to mRNA > # which is certainly not what you want) > $common = $1; > $common =~ s/\.$//; # remove trailing dot > } elsif (/^\s{2}ORGANISM/o) { > my @spflds = split(' ', $_); > ($ns_name) = $_ =~ /\w+\s+(.*)/o; > shift(@spflds); # ORGANISM > > if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { > $organelle = shift(@spflds); > } > $genus = shift(@spflds); > if(@spflds) { > $species = shift(@spflds); > } elsif ( grep { $genus } @unkn_names){ > $species = ''; > } else {$species='sp.';} #there's no species name but it > isn't unclassified > $sub_species = shift(@spflds) if(@spflds); > } elsif (/^\s+(.+)/o) { > # only split on ';' or '.' so that > # classification that is 2 words will > # still get matched > # use map to remove trailing/leading spaces > push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, > $1); > } else { > last; > } > > $_ = undef; # Empty $_ to trigger read of next line > } > > $$buffer = $_; > > # Don't make a species object if it's empty or "Unknown" or "None" > my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; > > return unless $genus and $unkn==0; > > # Bio::Species array needs array in Species -> Kingdom direction > if ($class[0] eq 'Viruses') { > push( @class, $ns_name ); > } > elsif ($class[$#class] eq $genus) { > push( @class, $species ); > } else { > push( @class, $genus, $species ); > } > @class = reverse @class; > > my $make = Bio::Species->new(); > $make->classification( \@class, "FORCE" ); # no name validation please > $make->common_name( $common ) if $common; > unless ($class[-1] eq 'Viruses') { > $make->sub_species( $sub_species ) if $sub_species; > } > $make->organelle($organelle) if $organelle; > return $make; > } > > Brian Osborne wrote: > >James, > > > >Your guess is right, no Species is made because of the name. That's > > because genbank.pm normally looks at: > > > >ORGANISM Bos taurus > > > >And makes "Bos" the genus, and so on. > > > >If it sees: > > > >ORGANISM Unknown > > > >It refuses to make a Species object, and it's interpreting your ORGANISM > >line in the same way because it can't make a valid genus, that's the > > current rule. Personally I'd say that I agree with its principle - how > > can we make a Species object without genus and species? > > > >You can get the taxid from a SeqFeature object, you already knew that. > > > >Brian O. > > > > > >-----Original Message----- > >From: bioperl-guts-l-bounces@portal.open-bio.org > >[mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of > >bugzilla-daemon@portal.open-bio.org > >Sent: Thursday, March 11, 2004 4:21 AM > >To: bioperl-guts-l@bioperl.org > >Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > > > >http://bugzilla.bioperl.org/show_bug.cgi?id=1600 > > > > Summary: $gb->species->ncbi_taxid > > Product: Bioperl > > Version: unspecified > > Platform: PC > > OS/Version: Linux > > Status: NEW > > Severity: normal > > Priority: P2 > > Component: Bio::SeqIO > > AssignedTo: bioperl-guts-l@bioperl.org > > ReportedBy: james.wasmuth@ed.ac.uk > > > > > >I've included a genbank file for which I have been unable to extract the > >ncbi_taxid for using > > > >$gb->species->ncbi_taxid > > > >the error is: > >Can't call method "ncbi_taxid" on an undefined value > > > >infact I don't get a Bio::Species object. I'm sure its because of the > > name, which is correct. > > > >I've tried looking into it, but could not find which Seq object creates > > the Bio::Species object. > > > > > > > >LOCUS AY007676 1389 bp DNA linear BCT > >29-OCT-2001 > >DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA, > > partial sequence. > >ACCESSION AY007676 > >VERSION AY007676.1 GI:12000362 > >KEYWORDS . > >SOURCE unknown marine gamma proteobacterium NOR5 > > ORGANISM unknown marine gamma proteobacterium NOR5 > > Bacteria; Proteobacteria; Gammaproteobacteria. > >REFERENCE 1 (bases 1 to 1389) > > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. > >and > > Amann,R. > > TITLE Isolation of novel pelagic bacteria from the German bight and > >their > > seasonal contributions to surface picoplankton > > JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) > > MEDLINE 21536174 > > PUBMED 11679337 > >REFERENCE 2 (bases 1 to 1389) > > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., > > Gerdts,G., Schuett,C. and Amann,R. > > TITLE Identification and seasonal dominance of culturable marine > >bacteria > > JOURNAL Unpublished > >REFERENCE 3 (bases 1 to 1389) > > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., > > Gerdts,G., Schuett,C. and Amann,R. > > TITLE Direct Submission > > JOURNAL Submitted (29-AUG-2000) Molecular Ecology, > > Max-Planck-Institute, Celsiusstrasse 1, Bremen 28359, Germany > >FEATURES Location/Qualifiers > > source 1..1389 > > /organism="unknown marine gamma proteobacterium NOR5" > > /mol_type="genomic DNA" > > /db_xref="taxon:145658" > > rRNA <1..>1389 > > /product="16S ribosomal RNA" > >BASE COUNT 343 a 319 c 453 g 274 t > >ORIGIN > > 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt > > aggaatctat 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc > > ctaagggaga 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt > > agctagttgg 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg > > atcagccaca 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat > > attgcgcaat 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg > > ttgtaaagca 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat > > tacctttaga 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg > > agcgttaatc 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg > > aaagccccgg 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag > > ggaggtagaa 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc > > gaaggcggcc 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg > > attagatacc 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat > > ttcttggtgg 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta > > aaactcaaat 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg > > caacgcgaag 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg > > ccttcgggaa 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt > > gggttaagtc 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga > > actctaagga 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat > > ggcccttacg 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc > > gcgaggggga 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac > > tccgtgaagt 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg > > ggccttgtac 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct > > aaccttcggg 1381 agggcgatc > >// > > > > > > > >------- You are receiving this mail because: ------- > >You are the assignee for the bug, or are watching the assignee. > >_______________________________________________ > >Bioperl-guts-l mailing list > >Bioperl-guts-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From brian_osborne at cognia.com Thu Mar 11 10:16:12 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Mar 11 10:22:19 2004 Subject: [Bioperl-l] how to set up bioperl cygwin In-Reply-To: <3FE6D6566E4FD511B54A009027EEADE71BE649@MRTCBKO> Message-ID: Ibrahima, If you've installed Cygwin's Perl as well then you should be ready to install Bioperl. Download, gunzip, and untar the latest 1.4 package and take a look at the INSTALL document online (http://bioperl.org/Core/Latest/INSTALL), it's the most up-to-date. Choose one of the "easy" methods, either should work, and write back if there are any problems. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Ibrahima BABER Sent: Thursday, March 11, 2004 9:47 AM To: 'gillyfish@hotmail.com' Cc: 'bioperl-l@bioperl.org' Subject: [Bioperl-l] how to set up bioperl cygwin Dear I have installed Cygwin successfully, and I would like to know how to set up bioperl with cygwin? Thanks Ibrahima Mali - west-Africa _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Thu Mar 11 10:17:17 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Mar 11 10:23:06 2004 Subject: [Bioperl-l] RE: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid In-Reply-To: <40507A3C.6090208@ed.ac.uk> Message-ID: James, Right, some discussion is called for. What James is saying is that Genbank entries with ORGANISM lines like "Unknown marine bacterium" should have Species objects, although binomial() will return something like "unknown". This Species object will be useful to those who want to use classification() and ncbi_taxid(). Are there votes or comments? Brian O. -----Original Message----- From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] Sent: Thursday, March 11, 2004 9:40 AM To: Brian Osborne Cc: bioperl-guts-l@bioperl.org Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid Brian and all at bioperl-guts, below is the comment I've added to the bug[1600]. I think it may need some discussion, but the patch I've added works to the extent that it allows creation of a Bio::Species object but the subsequent genus, species, subspecies calls will be 'wrong'. Personally I'm more concerned with the taxid, which I think will be sufficient. If you want to see the size of this problem go to NCBI taxonomy and enter the term identified as a token set! I think that maintaining the taxid is enough, otherwise the artifical split of terms such as **unidentified diatom endosymbiont of Peridinium foliaceum* * may be a problem, though some of them are intuitive. One last question, I've never tried to fix a bug before, so I've commited a patch as an attachment to Bugzilla for the bug. Do others check this and if okay place it in the code... apologies for the newbie bit... -james genbank.pm line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; a number of species are described as Unknown blah blah blah. The NCBI taxid assigned to unknown taxa is 32644 and has a number of synonyms, none of which are 'unknown'. The list includes: other, unknown organism, not specified, not shown, unspecified, Unknown, None, unclassified , unidentified organism I've changed the _read_GenBank_Species subroutine to allow organism names such as 'unknown marine gamma proteobacterium NOR5'. This will create a Bio::Species object, but the genus=unknown species=marine subspecies=gamma. There is a whole host of species names that ignore the nice rules in _read_GenBank_Species! However this fix will allow the correct taxid to be provided which I think is more than the name! sub _read_GenBank_Species { my( $self,$buffer) = @_; my @organell_names = ("chloroplast", "mitochondr"); # only those carrying DNA, apart from the nucleus #CHANGE my @unkn_names=("other", 'unknown organism', 'not specified', 'not shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified organism'); $_ = $$buffer; my( $sub_species, $species, $genus, $common, $organelle, @class, $ns_name ); # upon first entering the loop, we must not read a new line -- the SOURCE # line is already in the buffer (HL 05/10/2000) while (defined($_) || defined($_ = $self->_readline())) { # de-HTMLify (links that may be encountered here don't contain # escaped '>', so a simple-minded approach suffices) s/<[^>]+>//g; if (/^SOURCE\s+(.*)/o) { # FIXME this is probably mostly wrong (e.g., it yields things like # Homo sapiens adult placenta cDNA to mRNA # which is certainly not what you want) $common = $1; $common =~ s/\.$//; # remove trailing dot } elsif (/^\s{2}ORGANISM/o) { my @spflds = split(' ', $_); ($ns_name) = $_ =~ /\w+\s+(.*)/o; shift(@spflds); # ORGANISM if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { $organelle = shift(@spflds); } $genus = shift(@spflds); if(@spflds) { $species = shift(@spflds); } elsif ( grep { $genus } @unkn_names){ $species = ''; } else {$species='sp.';} #there's no species name but it isn't unclassified $sub_species = shift(@spflds) if(@spflds); } elsif (/^\s+(.+)/o) { # only split on ';' or '.' so that # classification that is 2 words will # still get matched # use map to remove trailing/leading spaces push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, $1); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; # Don't make a species object if it's empty or "Unknown" or "None" my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; return unless $genus and $unkn==0; # Bio::Species array needs array in Species -> Kingdom direction if ($class[0] eq 'Viruses') { push( @class, $ns_name ); } elsif ($class[$#class] eq $genus) { push( @class, $species ); } else { push( @class, $genus, $species ); } @class = reverse @class; my $make = Bio::Species->new(); $make->classification( \@class, "FORCE" ); # no name validation please $make->common_name( $common ) if $common; unless ($class[-1] eq 'Viruses') { $make->sub_species( $sub_species ) if $sub_species; } $make->organelle($organelle) if $organelle; return $make; } Brian Osborne wrote: >James, > >Your guess is right, no Species is made because of the name. That's because >genbank.pm normally looks at: > >ORGANISM Bos taurus > >And makes "Bos" the genus, and so on. > >If it sees: > >ORGANISM Unknown > >It refuses to make a Species object, and it's interpreting your ORGANISM >line in the same way because it can't make a valid genus, that's the current >rule. Personally I'd say that I agree with its principle - how can we make a >Species object without genus and species? > >You can get the taxid from a SeqFeature object, you already knew that. > >Brian O. > > >-----Original Message----- >From: bioperl-guts-l-bounces@portal.open-bio.org >[mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of >bugzilla-daemon@portal.open-bio.org >Sent: Thursday, March 11, 2004 4:21 AM >To: bioperl-guts-l@bioperl.org >Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >http://bugzilla.bioperl.org/show_bug.cgi?id=1600 > > Summary: $gb->species->ncbi_taxid > Product: Bioperl > Version: unspecified > Platform: PC > OS/Version: Linux > Status: NEW > Severity: normal > Priority: P2 > Component: Bio::SeqIO > AssignedTo: bioperl-guts-l@bioperl.org > ReportedBy: james.wasmuth@ed.ac.uk > > >I've included a genbank file for which I have been unable to extract the >ncbi_taxid for using > >$gb->species->ncbi_taxid > >the error is: >Can't call method "ncbi_taxid" on an undefined value > >infact I don't get a Bio::Species object. I'm sure its because of the name, >which is correct. > >I've tried looking into it, but could not find which Seq object creates the >Bio::Species object. > > > >LOCUS AY007676 1389 bp DNA linear BCT >29-OCT-2001 >DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA, > partial sequence. >ACCESSION AY007676 >VERSION AY007676.1 GI:12000362 >KEYWORDS . >SOURCE unknown marine gamma proteobacterium NOR5 > ORGANISM unknown marine gamma proteobacterium NOR5 > Bacteria; Proteobacteria; Gammaproteobacteria. >REFERENCE 1 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. >and > Amann,R. > TITLE Isolation of novel pelagic bacteria from the German bight and >their > seasonal contributions to surface picoplankton > JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) > MEDLINE 21536174 > PUBMED 11679337 >REFERENCE 2 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G., > Schuett,C. and Amann,R. > TITLE Identification and seasonal dominance of culturable marine >bacteria > JOURNAL Unpublished >REFERENCE 3 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G., > Schuett,C. and Amann,R. > TITLE Direct Submission > JOURNAL Submitted (29-AUG-2000) Molecular Ecology, Max-Planck-Institute, > Celsiusstrasse 1, Bremen 28359, Germany >FEATURES Location/Qualifiers > source 1..1389 > /organism="unknown marine gamma proteobacterium NOR5" > /mol_type="genomic DNA" > /db_xref="taxon:145658" > rRNA <1..>1389 > /product="16S ribosomal RNA" >BASE COUNT 343 a 319 c 453 g 274 t >ORIGIN > 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt aggaatctat > 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc ctaagggaga > 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt agctagttgg > 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg atcagccaca > 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat attgcgcaat > 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg ttgtaaagca > 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat tacctttaga > 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg agcgttaatc > 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg aaagccccgg > 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag ggaggtagaa > 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc gaaggcggcc > 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg attagatacc > 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat ttcttggtgg > 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta aaactcaaat > 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg caacgcgaag > 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg ccttcgggaa > 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt gggttaagtc > 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga actctaagga > 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat ggcccttacg > 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc gcgaggggga > 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac tccgtgaagt > 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg ggccttgtac > 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct aaccttcggg > 1381 agggcgatc >// > > > >------- You are receiving this mail because: ------- >You are the assignee for the bug, or are watching the assignee. >_______________________________________________ >Bioperl-guts-l mailing list >Bioperl-guts-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > > > > -- "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison Nematode Bioinformatics || Blaxter Nematode Genomics Group || School of Biological Sciences || Ashworth Laboratories || King's Buildings || tel: +44 131 650 7403 University of Edinburgh || web: www.nematodes.org Edinburgh || EH9 3JT || UK || From boris.steipe at utoronto.ca Thu Mar 11 10:42:36 2004 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu Mar 11 10:48:12 2004 Subject: [Bioperl-l] protein networks In-Reply-To: Message-ID: Richard, Thanks for this initiative ! I might suggest including "interaction" in the package name rather than "protein" since this is what you are graphing. Also there are Protein-DNA and DNA-DNA interactions (and there will be many more) which are being stored by some. In terms of IO, I would like to suggest supporting the HUPO-PSI standard (which DIP supports) for consideration, and naming the module after the format, not the database. In terms of methods: again, I am not sure you *want* to restrict yourself to protein only. MolecularInteraction.pm would suggest itself. Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe/ > Richard, > > You may want to reconsider the name "ProteinGraphIO::xml.pm" since > other > pathway databases (BIND certainly, KEGG perhaps) also export to XML. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Richard > Adams > Sent: Monday, March 08, 2004 4:31 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] protein networks > > Hi, > I've been writing some modules to apply Nathan Goodman's > "SimpleGraph.pm" module to protein interaction networks. He has > written this as a replacement for the the broken CPAN graph modules. > The > aim of these modules is > > 1. To convert protein interaction data between differentet formats > 2. To be able to link protein interaction data to protein sequence > data. > 3. To be able to read in interaction data from separate sources, and > make a merged graph with duplicate interactions flagged or removed. > > > > Could some core person give some idea for namespace to put these in > CVS? > > The modules are : > 1. Nathan's modules > SimpleGraph.pm - a generic graph module with methods > to build and represent a graph > SimpleGraph::Traversal.pm - generic methods to navigate a graph. > > 2. My modules > > a. An I/O system analagous to SeqIO that lazyloads the correct modules > for a particular format > ProteinGraphIO.pm - with next_graph, write_graph methods > ProteinGraphIO::dip.pm - parser for DIP format interactions > - to read in PSI_XML formatted records > (still being worked on). > > b. Modules to represent a protein network: > PrimaryProteinGraph.pm - subclass of SimpleGraph.pm. This will be > made from a dip record, analagous to PrimarySeq > FullProteinGraph .pm - subclas of SimpleGraph.pm, contains > PrimaryProteinGraph and metadata of graph, will be made from an XML > file, analagous to RichSeq. > > c. Classes to represent nodes/ edges. > NodeI.pm - interface describing methods that all nodes should > have > ProteinNode.pm - implements NodeI, currently has methods > primary_id(), seq(), secondary_id() > InteractionI.pm - interface describing methods all edges > should have > ProteinInteraction.pm - implements InteractionI, currently has > methods weight(), interactors(), id(). > > Cheers Richard > > > -- > Dr Richard Adams > Psychiatric Genetics Group, > Medical Genetics, > Molecular Medicine Centre, > Western General Hospital, > Crewe Rd West, > Edinburgh UK > EH4 2XU > > Tel: 44 131 651 1084 > richard.adams@ed.ac.uk > From james.wasmuth at ed.ac.uk Thu Mar 11 10:40:37 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Thu Mar 11 10:53:17 2004 Subject: [Bioperl-l] RE: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid In-Reply-To: References: Message-ID: <40508875.5010904@ed.ac.uk> I feel there are just too many different permutations to deal with it clearly and robustly. If people did care to get the bionomial name then perhaps if the ORGANISM is not a synonym of unclassified, it gets all put into species and genus is left blank? I realise this may require relaxing some checks on Bio::Species. -james Brian Osborne wrote: >James, > >Right, some discussion is called for. What James is saying is that Genbank >entries with ORGANISM lines like "Unknown marine bacterium" should have >Species objects, although binomial() will return something like "unknown". >This Species object will be useful to those who want to use classification() >and ncbi_taxid(). Are there votes or comments? > >Brian O. > > >-----Original Message----- >From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] >Sent: Thursday, March 11, 2004 9:40 AM >To: Brian Osborne >Cc: bioperl-guts-l@bioperl.org >Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >Brian and all at bioperl-guts, > > >below is the comment I've added to the bug[1600]. I think it may need >some discussion, but the patch I've added works to the extent that it >allows creation of a Bio::Species object but the subsequent genus, >species, subspecies calls will be 'wrong'. Personally I'm more >concerned with the taxid, which I think will be sufficient. > >If you want to see the size of this problem go to NCBI taxonomy and >enter the term identified as a token set! I think that maintaining the >taxid is enough, otherwise the artifical split of terms such as >**unidentified diatom endosymbiont of Peridinium foliaceum* >&lvl=3&lin=f&keep=1&srchmode=3&unlock>* >may be a problem, though some of them are intuitive. > >One last question, I've never tried to fix a bug before, so I've >commited a patch as an attachment to Bugzilla for the bug. Do others >check this and if okay place it in the code... >apologies for the newbie bit... > >-james > > > >genbank.pm > >line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; > >a number of species are described as Unknown blah blah blah. > >The NCBI taxid assigned to unknown taxa is 32644 and has a number of >synonyms, none of which are 'unknown'. > >The list includes: other, unknown organism, not specified, not shown, >unspecified, Unknown, None, unclassified , unidentified organism > >I've changed the _read_GenBank_Species subroutine to allow organism >names such as 'unknown marine gamma proteobacterium NOR5'. This will >create a Bio::Species object, but the genus=unknown species=marine >subspecies=gamma. > >There is a whole host of species names that ignore the nice rules in >_read_GenBank_Species! However this fix will allow the correct taxid to >be provided which I think is more than the name! > > > >sub _read_GenBank_Species { > my( $self,$buffer) = @_; > my @organell_names = ("chloroplast", "mitochondr"); > # only those carrying DNA, apart from the nucleus > > #CHANGE > my @unkn_names=("other", 'unknown organism', 'not specified', 'not >shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified >organism'); > > $_ = $$buffer; > > my( $sub_species, $species, $genus, $common, $organelle, @class, >$ns_name ); > # upon first entering the loop, we must not read a new line -- the >SOURCE > # line is already in the buffer (HL 05/10/2000) > while (defined($_) || defined($_ = $self->_readline())) { > # de-HTMLify (links that may be encountered here don't contain > # escaped '>', so a simple-minded approach suffices) > s/<[^>]+>//g; > if (/^SOURCE\s+(.*)/o) { > # FIXME this is probably mostly wrong (e.g., it yields things like > # Homo sapiens adult placenta cDNA to mRNA > # which is certainly not what you want) > $common = $1; > $common =~ s/\.$//; # remove trailing dot > } elsif (/^\s{2}ORGANISM/o) { > my @spflds = split(' ', $_); > ($ns_name) = $_ =~ /\w+\s+(.*)/o; > shift(@spflds); # ORGANISM > > if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { > $organelle = shift(@spflds); > } > $genus = shift(@spflds); > if(@spflds) { > $species = shift(@spflds); > } elsif ( grep { $genus } @unkn_names){ > $species = ''; > } else {$species='sp.';} #there's no species name but it >isn't unclassified > $sub_species = shift(@spflds) if(@spflds); > } elsif (/^\s+(.+)/o) { > # only split on ';' or '.' so that > # classification that is 2 words will > # still get matched > # use map to remove trailing/leading spaces > push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, >$1); > } else { > last; > } > > $_ = undef; # Empty $_ to trigger read of next line > } > > $$buffer = $_; > > # Don't make a species object if it's empty or "Unknown" or "None" > my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; > > return unless $genus and $unkn==0; > > # Bio::Species array needs array in Species -> Kingdom direction > if ($class[0] eq 'Viruses') { > push( @class, $ns_name ); > } > elsif ($class[$#class] eq $genus) { > push( @class, $species ); > } else { > push( @class, $genus, $species ); > } > @class = reverse @class; > > my $make = Bio::Species->new(); > $make->classification( \@class, "FORCE" ); # no name validation please > $make->common_name( $common ) if $common; > unless ($class[-1] eq 'Viruses') { > $make->sub_species( $sub_species ) if $sub_species; > } > $make->organelle($organelle) if $organelle; > return $make; >} > > > > >Brian Osborne wrote: > > > >>James, >> >>Your guess is right, no Species is made because of the name. That's because >>genbank.pm normally looks at: >> >>ORGANISM Bos taurus >> >>And makes "Bos" the genus, and so on. >> >>If it sees: >> >>ORGANISM Unknown >> >>It refuses to make a Species object, and it's interpreting your ORGANISM >>line in the same way because it can't make a valid genus, that's the >> >> >current > > >>rule. Personally I'd say that I agree with its principle - how can we make >> >> >a > > >>Species object without genus and species? >> >>You can get the taxid from a SeqFeature object, you already knew that. >> >>Brian O. >> >> >>-----Original Message----- >>From: bioperl-guts-l-bounces@portal.open-bio.org >>[mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of >>bugzilla-daemon@portal.open-bio.org >>Sent: Thursday, March 11, 2004 4:21 AM >>To: bioperl-guts-l@bioperl.org >>Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid >> >>http://bugzilla.bioperl.org/show_bug.cgi?id=1600 >> >> Summary: $gb->species->ncbi_taxid >> Product: Bioperl >> Version: unspecified >> Platform: PC >> OS/Version: Linux >> Status: NEW >> Severity: normal >> Priority: P2 >> Component: Bio::SeqIO >> AssignedTo: bioperl-guts-l@bioperl.org >> ReportedBy: james.wasmuth@ed.ac.uk >> >> >>I've included a genbank file for which I have been unable to extract the >>ncbi_taxid for using >> >>$gb->species->ncbi_taxid >> >>the error is: >>Can't call method "ncbi_taxid" on an undefined value >> >>infact I don't get a Bio::Species object. I'm sure its because of the >> >> >name, > > >>which is correct. >> >>I've tried looking into it, but could not find which Seq object creates the >>Bio::Species object. >> >> >> >>LOCUS AY007676 1389 bp DNA linear BCT >>29-OCT-2001 >>DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA, >> partial sequence. >>ACCESSION AY007676 >>VERSION AY007676.1 GI:12000362 >>KEYWORDS . >>SOURCE unknown marine gamma proteobacterium NOR5 >> ORGANISM unknown marine gamma proteobacterium NOR5 >> Bacteria; Proteobacteria; Gammaproteobacteria. >>REFERENCE 1 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. >>and >> Amann,R. >> TITLE Isolation of novel pelagic bacteria from the German bight and >>their >> seasonal contributions to surface picoplankton >> JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) >> MEDLINE 21536174 >> PUBMED 11679337 >>REFERENCE 2 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >> >> >Gerdts,G., > > >> Schuett,C. and Amann,R. >> TITLE Identification and seasonal dominance of culturable marine >>bacteria >> JOURNAL Unpublished >>REFERENCE 3 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >> >> >Gerdts,G., > > >> Schuett,C. and Amann,R. >> TITLE Direct Submission >> JOURNAL Submitted (29-AUG-2000) Molecular Ecology, >> >> >Max-Planck-Institute, > > >> Celsiusstrasse 1, Bremen 28359, Germany >>FEATURES Location/Qualifiers >> source 1..1389 >> /organism="unknown marine gamma proteobacterium NOR5" >> /mol_type="genomic DNA" >> /db_xref="taxon:145658" >> rRNA <1..>1389 >> /product="16S ribosomal RNA" >>BASE COUNT 343 a 319 c 453 g 274 t >>ORIGIN >> 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt aggaatctat >> 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc ctaagggaga >> 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt agctagttgg >> 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg atcagccaca >> 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat attgcgcaat >> 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg ttgtaaagca >> 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat tacctttaga >> 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg agcgttaatc >> 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg aaagccccgg >> 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag ggaggtagaa >> 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc gaaggcggcc >> 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg attagatacc >> 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat ttcttggtgg >> 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta aaactcaaat >> 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg caacgcgaag >> 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg ccttcgggaa >> 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt gggttaagtc >> 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga actctaagga >> 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat ggcccttacg >> 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc gcgaggggga >> 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac tccgtgaagt >> 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg ggccttgtac >> 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct aaccttcggg >> 1381 agggcgatc >>// >> >> >> >>------- You are receiving this mail because: ------- >>You are the assignee for the bug, or are watching the assignee. >>_______________________________________________ >>Bioperl-guts-l mailing list >>Bioperl-guts-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> >> >> >> >> > >-- >"I have not failed. I've just found 10,000 ways that don't work." > --- Thomas Edison > >Nematode Bioinformatics || >Blaxter Nematode Genomics Group || >School of Biological Sciences || >Ashworth Laboratories || >King's Buildings || tel: +44 131 650 7403 >University of Edinburgh || web: www.nematodes.org >Edinburgh || >EH9 3JT || >UK || > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison Nematode Bioinformatics || Blaxter Nematode Genomics Group || School of Biological Sciences || Ashworth Laboratories || King's Buildings || tel: +44 131 650 7403 University of Edinburgh || web: www.nematodes.org Edinburgh || EH9 3JT || UK || From rus1 at duke.edu Thu Mar 11 12:21:48 2004 From: rus1 at duke.edu (Rhazes Spell) Date: Thu Mar 11 12:10:02 2004 Subject: [Bioperl-l] Bio::DB::GFF::Segment trouble Message-ID: <93F9BB66-7380-11D8-BE84-000393B65CBA@duke.edu> I am having trouble getting a list of features from a segment in my database. I can pull out all of the features, but I can not limit the features returned to a specific range. Following is a code excerpt and output. Any assistance that you can provide would be great! CODE: my @segment = $db->segment(-name => 'amata', -start => 1, -end => 40000); foreach my $segment (@segment) { my($start,$end) = ($segment->start,$segment->end); #Some debug info cuz I don't get it yet print "\n*** Segment= ",$segment->asString(); print " Seg Source= ",$segment->sourceseq,"\t"; print "Reference= ",$segment->ref,"\t"; print "Abs Start= ",$segment->abs_start," :: "; print "Abs End= ", $segment->abs_end,"\n"; #Change the coordinate system to absolute if necessary $segment->absolute(1) if (!($segment->sourceseq eq $segment->ref)); my @f = $segment->features(-types => ['similarity:blastn'], -rangetype => 'contained_in'); foreach my $feat (@f) { print "\n\t",$feat->gff_string(),"\n"; print "-Target == "; foreach ($feat->get_tag_values("Target")) { print $_; } print "\n-description == "; foreach ($feat->get_tag_values("description")) { print $_,"\n"; } } } OUTPUT:: (## = Added comment) *** Segment= amata:1,40000 Seg Source= amata Reference= amata Abs Start= 1 :: Abs End= 40000 ##This is the main segment and it should not have any blast similarities. *** Segment= amata:1,40000 Seg Source= amatalpha Reference= amata Abs Start= 14584 :: Abs End= 54583 ## These are blast hits that have a hit on my segment. I only want the hits that occur between 1 and 40000 on ## the segment, amata ## I have 2 questions: ## 1: Why are there any hits included with 'Target "Sequence:amata" start stop' where start or start is > 40000? ## 2: Why can't I access the members of the Target attribute tag as I can the description tag. ## Output follows amatalpha blastn similarity 14584 14713 0.832061 + . Target "Sequence:a mata" 41056 41186 ; description "upstream of CAP1 - downstream of CAP1" -Target == -description == upstream of CAP1 - downstream of CAP1 amatalpha blastn similarity 18722 18774 0.907407 + . Target "Sequence:a mata" 33568 33621 ; description "downstream of SPO14 - downstream of SPO14" -Target == -description == downstream of SPO14 - downstream of SPO14 amatalpha blastn similarity 19199 19283 0.905882 + . Target "Sequence:a mata" 34087 34171 ; description "downstream of SPO14 - downstream of SPO14" -Target == -description == downstream of SPO14 - downstream of SPO14 amatalpha blastn similarity 24823 24922 0.83 + . Target "Sequence:amata" 39 695 39794 ; description "upstream of RPL22 - downstream of CAP1" -Target == -description == upstream of RPL22 - downstream of CAP1 amatalpha blastn similarity 25099 25150 0.923077 + . Target "Sequence:a mata" 39971 40022 ; description "upstream of RPL22 - downstream of CAP1" -Target == -description == upstream of RPL22 - downstream of CAP1 Thanks, Rhazes ************************************** Duke University Department of Biomedical Engineering Duke University Medical Center, Center for Genome Technology 919.684.2720 (lab) *************************************** From Annie.Law at nrc-cnrc.gc.ca Thu Mar 11 15:32:38 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Thu Mar 11 15:45:15 2004 Subject: [Bioperl-l] Bioperl-db, bioperl schema, and load_seqdatabase.pl along with de l-assocs-sql.pl Message-ID: <10C94843061E094A98C02EB77CFC328722FE12@nrcmrdex1d.imsb.nrc.ca> Hi Hilmar, I would appreciate help with the following. 1. My problem is I am now unable to find the data in the database that I set it up for. It seems that I have successfully loaded NCBI taxonomy, GO information, locuslink (using LL_tmpl file) information and then unigene information. When I loaded the information in each case there seemed to be almost no problem in inserting the information into the database Ie. It seemed that all of the inserts worked properly. I would like to take clone ids (associated with a microarray associated with ESTs). I have matched the clone ids to GenBank accesion numbers form the IMAGE consortium. I wanted to check if the SQL statements that I was creating where giving me the desired result so I followed My statements through. If I were to do this by hand I would take the GenBank accession number and find out the Unigene identifier. I would then take the Unigene identifier and find the corresponding locuslink id. I would then take the locuslink ids and find the GO ids (from each category of go) My understanding of the the biosql schema is that as stated the bioentry table is the main table. From this you can perform some select statements to find out the other database references a bioentry has. For Example if we look at all of the fields in one entry of a Unigene database It has all of the fields that reference databases in the dbxref table. (I haven't figured out where all of the other data from this Entry goes or if it does get inserted in the database?) BX095770 --accession number Hs.2 --clusterid N-acetyltransferase 2 (arylamine N-acetyltransferase) --title NAT2 --gene_symbol 8p22 --cytoband liver--express S --gnm_terminus 10 --locuslink 8--chromosome ACC=G59899 UNISTS=137181--sts ORG=Escherischia coli; PROTGI=16129422; PROTID=ref:NP_415980.1; PCT=24; ALN=255--protsim sapiens--species Hs.2--diplay_id N-acetyltransferase 2 (arylamine N-acetyltransferase)--description 26--size Hs.2--object_id NCBI--authority UniGene--namespace Hs.2--display_name 26--scount The select statement I wrote to go from GenBank accession number to locuslink id was. Select dbxref.dbxref_id FROM dbxref WHERE dbxref.accession = 'H08278' With the dbxref_id that I got I was going to find out the corresponding bioentry_id (with biodatabase_id corresponding to Unigene) and then go back to the dbxref table to find the dbxref locuslink entry for the unigene bioentry (in the bioentry table). The problem is that for each Genbank accession number that I look up I get 0 rows returned using The select statement above (I don't think there is anyhing wrong with the SQL statement since I checked it With an unrelated GenBank accession number). This is true for all of the clones that I have followed through. I found that this GenBank accession number does exist in the Hs.data file I used as input. That entry is // ID Hs.478728 TITLE Homo sapiens transcribed sequences EXPRESS whole brain ; total brain CHROMOSOME 3 STS ACC=SHGC-77720 UNISTS=45248 SCOUNT 3 SEQUENCE ACC=R60728.1; NID=g831423; CLONE=IMAGE:42222; END=5'; LID=263; SEQTYPE=EST SEQUENCE ACC=Z42053.1; NID=g564288; CLONE=c-06h12; LID=186; SEQTYPE=EST SEQUENCE ACC=H08278.1; NID=g873100; CLONE=IMAGE:45161; END=5'; LID=263; SEQTYPE=EST // ????? Somehow this information is not getting entered in the database or I am trying to access the information in the wrong Manner? How can I resolve this problem? Is there some script that needs to be altered or some option used? Alternatively, I searched in the bioentry database for an entry with the GenBank accession number that I am looking for however I am unable to find the same bioentry_id in the bioentry_dbxref table. Sometimes I am not even able to find the Genbank accesion number I am looking for in the bioentry table. 2. My second question when hopefully I have sorted things out in the first question is. I am not exactly sure how to go about accessing the GO information corresponding to a locuslink id? Once I had found the bioentry_id of the relevant Locuslink bioentry and join with the bioentry table with the Bioentry relationship table and subsequently the term table. I would like to get the GO id and the category or ontology that The GO id is associated with be it molecular function, biological process or cellular component. It seems that most of the Entries in the term table are of Ontoloy Id = 1 (Gene ontology) and only around 200 entries molecular function, biological process, and cellular component put together when there are about 16000 entries in the term table. Shouldn't the total number of these three Types equal to the number of entries of Ontology Id = 1? How do I find out what GO category or rather ontology (molecular function, biological process, and cellular component) That a GO identifier belongs to? I am not sure that I understand what all 7 distinct Ontology Ids in the Ontology represent? (I understand the meaning of 3,4 and 5) 1 = Gene Ontology 2 = Annotation 3 = cellular 4 = molecular 5 = biological 6 = Object Slots 7 = Relationship 3. In a previous e-mail you were kind enough to mention that I could contact you once I had gotten to the point I would need to update the database. I have gotten to this point and would like to know how I can modify del-assocs-sql.pl to be used with MySQL for the --mergeobjs option It seems to me that the --lookup option in unlike the mergeobjs option ie. You would not enter something like --lookup=***.pl As an aside, I would like to know since locuslink, unigene takes around 2 days to load. What happens in between when a user is trying To access the database are there are deleterious effects? My guess is that the user will just get the data that is currently in the Database and that no harm will happen. Thanks very much, Annie. From sumit.kaur at sbri.org Thu Mar 11 16:36:43 2004 From: sumit.kaur at sbri.org (Sumit Kaur) Date: Thu Mar 11 16:42:24 2004 Subject: [Bioperl-l] (no subject) Message-ID: <9B09CC35724F4B4091625AD346E54D1BFE7631@exchange01.sbri.org> From sumit.kaur at sbri.org Thu Mar 11 16:36:45 2004 From: sumit.kaur at sbri.org (Sumit Kaur) Date: Thu Mar 11 16:42:26 2004 Subject: [Bioperl-l] (no subject) Message-ID: <9B09CC35724F4B4091625AD346E54D1BFE7632@exchange01.sbri.org> From lstein at cshl.edu Thu Mar 11 13:08:10 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu Mar 11 18:35:25 2004 Subject: [Bioperl-l] Bio::DB::GFF::Segment trouble In-Reply-To: <93F9BB66-7380-11D8-BE84-000393B65CBA@duke.edu> References: <93F9BB66-7380-11D8-BE84-000393B65CBA@duke.edu> Message-ID: <200403111308.11186.lstein@cshl.edu> Hi, This is a very slight misconception. You need to use the "contains" range type. The range type is relative to the viewpoint of the segment. You are looking for the features that the segment contains. The contained_in relationship works the other way around, and will find features that completely contain the segment. Looking at your output, the contained_in relationship doesn't appear to be working properly, however. I wonder which database adaptor you are using? The target information is a special method called target(). It is not treated as an ordinary tag. Lincoln On Thursday 11 March 2004 12:21 pm, Rhazes Spell wrote: > I am having trouble getting a list of features from a segment in my > database. I can pull out all of the features, but I can not limit > the features returned to a specific range. Following is a code > excerpt and output. Any assistance that you can provide would be > great! > > CODE: > my @segment = $db->segment(-name => 'amata', > -start => 1, > -end => 40000); > > foreach my $segment (@segment) { > my($start,$end) = ($segment->start,$segment->end); > > #Some debug info cuz I don't get it yet > > print "\n*** Segment= ",$segment->asString(); > print " Seg Source= ",$segment->sourceseq,"\t"; > print "Reference= ",$segment->ref,"\t"; > print "Abs Start= ",$segment->abs_start," :: "; > print "Abs End= ", $segment->abs_end,"\n"; > > #Change the coordinate system to absolute if necessary > $segment->absolute(1) if (!($segment->sourceseq eq > $segment->ref)); my @f = $segment->features(-types => > ['similarity:blastn'], -rangetype => 'contained_in'); > > foreach my $feat (@f) { > print "\n\t",$feat->gff_string(),"\n"; > print "-Target == "; > foreach ($feat->get_tag_values("Target")) { > print $_; > } > print "\n-description == "; > foreach ($feat->get_tag_values("description")) { > print $_,"\n"; > } > } > } > > OUTPUT:: (## = Added comment) > > *** Segment= amata:1,40000 Seg Source= amata Reference= amata > Abs Start= 1 :: Abs End= 40000 > ##This is the main segment and it should not have any blast > similarities. > > *** Segment= amata:1,40000 Seg Source= amatalpha Reference= > amata Abs Start= 14584 :: Abs End= 54583 > ## These are blast hits that have a hit on my segment. I only want > the hits that occur between 1 and 40000 on > ## the segment, amata > ## I have 2 questions: > ## 1: Why are there any hits included with 'Target "Sequence:amata" > start stop' where start or start is > 40000? > ## 2: Why can't I access the members of the Target attribute tag as > I can the description tag. > ## Output follows > > > amatalpha blastn similarity 14584 14713 > 0.832061 + . Target "Sequence:a > mata" 41056 41186 ; description "upstream of CAP1 - downstream of > CAP1" -Target == > -description == upstream of CAP1 - downstream of CAP1 > > amatalpha blastn similarity 18722 18774 > 0.907407 + . Target "Sequence:a > mata" 33568 33621 ; description "downstream of SPO14 - downstream > of SPO14" > -Target == > -description == downstream of SPO14 - downstream of SPO14 > > amatalpha blastn similarity 19199 19283 > 0.905882 + . Target "Sequence:a > mata" 34087 34171 ; description "downstream of SPO14 - downstream > of SPO14" > -Target == > -description == downstream of SPO14 - downstream of SPO14 > > amatalpha blastn similarity 24823 24922 > 0.83 + . Target "Sequence:amata" 39 > 695 39794 ; description "upstream of RPL22 - downstream of CAP1" > -Target == > -description == upstream of RPL22 - downstream of CAP1 > > amatalpha blastn similarity 25099 25150 > 0.923077 + . Target "Sequence:a > mata" 39971 40022 ; description "upstream of RPL22 - downstream of > CAP1" -Target == > -description == upstream of RPL22 - downstream of CAP1 > > > > Thanks, > Rhazes > > ************************************** > Duke University > Department of Biomedical Engineering > Duke University Medical Center, > Center for Genome Technology > > 919.684.2720 (lab) > *************************************** > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: signature Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040311/b4ca293d/attachment.bin From bsman at tom.com Thu Mar 11 15:33:14 2004 From: bsman at tom.com (=?gb2312?B?zfXqySwgU2FuIFdhbmc=?=) Date: Thu Mar 11 18:36:07 2004 Subject: [Bioperl-l] Anybody use 3'UTR for siRNA design? Message-ID: <200403112038.i2BKcetk021732@portal.open-bio.org> Dear bioperl-l: Anybody use 3'UTR for siRNA design? Best Regards! Yours sincerely ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ÍõêÉ, San Wang ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡bsman@tom.com ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-03-12 http://www.estarray.org ,-,-. ,-,-. ,-,-. ,-,-. ,- / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / \ \ / / `-'-' `-'-' `-'-' `-'-' San Wang Dr. Student Bioinformatics and Gene Network Research Group Zhejiang University P.R.China Address: Room 415# ,Bio-technology Institute, Zhejiang University, Kaixuan Road 268# Hangzhou Zhejiang, P.R.China 310027 Tel: 0086-571-86892051 Fax: 0086-571-86961525 E-mail: bsman@163.com Website: http://www.estarray.org £­£­£­£­£­£­£­£­£­£­ Innovation is everything. When you are on the forefront, you can see what the next innovation needs to be? --- from Robert Noyce, Founder of Intel The more things change, the more they stay the same! The more things seem to be complicated ,the more they are simple in fact! From confirm-s2-Ci_AjA_jwvYcCcj8Reh9HC1iG1A-bioperl-l=bioperl.org at yahoogroups.com Thu Mar 11 20:00:37 2004 From: confirm-s2-Ci_AjA_jwvYcCcj8Reh9HC1iG1A-bioperl-l=bioperl.org at yahoogroups.com (Yahoo! Groups) Date: Thu Mar 11 20:06:11 2004 Subject: [Bioperl-l] Please confirm your request to join kammi_dalnet Message-ID: <1079053237.107.93134.m19@yahoogroups.com> Hello bioperl-l@bioperl.org, We have received your request to join the kammi_dalnet group hosted by Yahoo! Groups, a free, easy-to-use community service. This request will expire in 7 days. TO BECOME A MEMBER OF THE GROUP: 1) Go to the Yahoo! Groups site by clicking on this link: http://groups.yahoo.com/i?i=Ci_AjA_jwvYcCcj8Reh9HC1iG1A&e=bioperl-l%40bioperl%2Eorg (If clicking doesn't work, "Cut" and "Paste" the line above into your Web browser's address bar.) -OR- 2) REPLY to this email by clicking "Reply" and then "Send" in your email program If you did not request, or do not want, a membership in the kammi_dalnet group, please accept our apologies and ignore this message. Regards, Yahoo! Groups Customer Care Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/ From JLJMJPLFIFG at hotmail.com Thu Mar 11 21:28:16 2004 From: JLJMJPLFIFG at hotmail.com (Heidi Wright) Date: Thu Mar 11 21:37:49 2004 Subject: [Bioperl-l] RE:[2] removal Message-ID: <200403035370.q9Q9PBt217715@gateway4.wongfaye.com> We offer a large selection of both domestic and international brand cheap cigarettes online at rock bottom prices! We carry Marlboros, Winstons, Camels, Salems, Parliaments, Kents, Dunhills, davidoffs and many, many more brands and flavors of Cheap Cigarettes Online. more information here: http://autobiography.cigaretesstore.biz/il/?reproach ______________________ Un_subscr1ber$ go here: http://riven.cigaretesstore.biz/pizdec.php?96555 ----396921786406309320-- From mgear911 at yahoo.com Thu Mar 11 21:49:41 2004 From: mgear911 at yahoo.com (=?iso-8859-1?q?Yuhui?=) Date: Thu Mar 11 21:55:18 2004 Subject: [Bioperl-l] How to display newick tree in graphics? Message-ID: <20040312024941.17553.qmail@web13303.mail.yahoo.com> hi, a newbie to perl here, can someone teach me how to output a newick file in the form of a image on a webpage. Thanks. __________________________________________________ Do You Yahoo!? Stand a chance to win a dream date, join the Dream Guy Contest! http://sg.yahoo.com/dreamguy From jonathon at mgcheo3.med.uottawa.ca Fri Mar 12 09:08:43 2004 From: jonathon at mgcheo3.med.uottawa.ca (Jonathon Greenwood) Date: Fri Mar 12 09:19:15 2004 Subject: [Bioperl-l] Parsing features Message-ID: Hi all! I'm wondering if it is possible to extract the features from a Genbank file and print out the feature information within a text box (I'm dealing with the text of the feature I don't want to display them as a glyph). I tried this already using the Dumper method...but it spews out too much information. I also get the errors when I run the code(which is for this feature): Bio::SeqFeature::Generic=HASH(0x654788) a bunch of times... and (in cleanup) Undefined subroutine Fh:flush at /usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 519 Thanks for any help that can be given... Jonathan Greenwood Co-op student, email: jonathon@mgcheo.med.uottawa.ca CODE: #! /usr/local/bin/perl -w use strict; use CGI qw / :standard /; use CGI::Pretty; use Bio::SeqFeature::Generic; use Bio::SeqIO; use Bio::Root::IO; use File::Temp; my @features = read_file(param('file')); print header, start_html('Plasmid Feature Editor'); print start_multipart_form (), table ({-cellpadding => 10}, TR({-class => 'resultsbody'}, td (textarea(-name => 'editarea', -values => "@features", -rows => 20, -cols => 70, -override => (@features) || (param('clear')), ), ), ), TR({-class => 'resultstitle'}, td (filefield(-name => 'file', -length => 40), ), td(submit(-name => 'submit_button', -value => 'Click to display features'), ), ), TR({-class => 'resultstitle'}, td(submit(-name => 'save_button', -value => 'Click here to save your work'), ), td(reset(), ), ), ), end_form; print end_html; exit 0; sub read_file { my $fh = param('file'); my $gb_parser = Bio::SeqIO->new(-fh=>$fh,-format=>'Genbank'); my @features; while (my $seq = $gb_parser-> next_seq) { push @features, $seq->get_SeqFeatures(); } return @features; } From jason at cgt.duhs.duke.edu Fri Mar 12 09:24:27 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 12 09:30:11 2004 Subject: [Bioperl-l] Parsing features In-Reply-To: References: Message-ID: Did you try some of the code in the Feature-Annotation HOWTO? http://bioperl.org/HOWTOs/ -jason On Fri, 12 Mar 2004, Jonathon Greenwood wrote: > Hi all! > > I'm wondering if it is possible to extract the features from a Genbank > file and print out the feature information within a text box (I'm dealing > with the text of the feature I don't want to display them as a glyph). I > tried this already using the Dumper method...but it spews out too much > information. I also get the errors when I run the code(which is for this > feature): > Bio::SeqFeature::Generic=HASH(0x654788) a bunch of times... and > (in cleanup) Undefined subroutine Fh:flush at > /usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 519 > > Thanks for any help that can be given... > > Jonathan Greenwood > Co-op student, > email: jonathon@mgcheo.med.uottawa.ca > > CODE: > > #! /usr/local/bin/perl -w > > use strict; > use CGI qw / :standard /; > use CGI::Pretty; > use Bio::SeqFeature::Generic; > use Bio::SeqIO; > use Bio::Root::IO; > use File::Temp; > > my @features = read_file(param('file')); > > print header, start_html('Plasmid Feature Editor'); > > print start_multipart_form (), > table ({-cellpadding => 10}, > TR({-class => 'resultsbody'}, > td (textarea(-name => 'editarea', > -values => "@features", > -rows => 20, > -cols => 70, > -override => (@features) || (param('clear')), > ), > ), > ), > TR({-class => 'resultstitle'}, > td (filefield(-name => 'file', > -length => 40), > ), > > td(submit(-name => 'submit_button', > -value => 'Click to display features'), > ), > ), > TR({-class => 'resultstitle'}, > td(submit(-name => 'save_button', > -value => 'Click here to save your work'), > ), > td(reset(), > ), > ), > ), > end_form; > > print end_html; > > exit 0; > > sub read_file { > > my $fh = param('file'); > my $gb_parser = Bio::SeqIO->new(-fh=>$fh,-format=>'Genbank'); > my @features; > > while (my $seq = $gb_parser-> next_seq) { > push @features, $seq->get_SeqFeatures(); > } > return @features; > } > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From Jan.Aerts at wur.nl Fri Mar 12 09:36:13 2004 From: Jan.Aerts at wur.nl (Aerts, Jan) Date: Fri Mar 12 09:41:50 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Message-ID: <7D030487F1A3D143A76F2A1E91F57035EF3D8F@scomp0010> Hi all, Has anyone encountered the following errors when trying to load a gff file into a PostgresQL database? The bioperl version is 1.4. The gff file looks like this: [start gff file] GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene VIM ; Accession NM_003380.1 GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene GTF2E1 ; Accession NM_005513.1 [stop gff file] [start error] ... psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/ftype.30284:3: invalid command \. psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fgroup.30284:13694: invalid command \. psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute.30284:3: invalid command \. psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error at or near "1" [stop error] Any help appreciated. Thanks, Jan Aerts From jonathon at mgcheo3.med.uottawa.ca Fri Mar 12 09:32:37 2004 From: jonathon at mgcheo3.med.uottawa.ca (Jonathon Greenwood) Date: Fri Mar 12 09:43:13 2004 Subject: [Bioperl-l] Parsing features In-Reply-To: Message-ID: I tried some of the code in the Feature Annotation HOWTO but it wouldn't display anything within the text box. Jonathan On Fri, 12 Mar 2004, Jason Stajich wrote: > Did you try some of the code in the Feature-Annotation HOWTO? > http://bioperl.org/HOWTOs/ > > -jason > On Fri, 12 Mar 2004, Jonathon Greenwood wrote: > > > Hi all! > > > > I'm wondering if it is possible to extract the features from a Genbank > > file and print out the feature information within a text box (I'm dealing > > with the text of the feature I don't want to display them as a glyph). I > > tried this already using the Dumper method...but it spews out too much > > information. I also get the errors when I run the code(which is for this > > feature): > > Bio::SeqFeature::Generic=HASH(0x654788) a bunch of times... and > > (in cleanup) Undefined subroutine Fh:flush at > > /usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 519 > > > > Thanks for any help that can be given... > > > > Jonathan Greenwood > > Co-op student, > > email: jonathon@mgcheo.med.uottawa.ca > > > > CODE: > > > > #! /usr/local/bin/perl -w > > > > use strict; > > use CGI qw / :standard /; > > use CGI::Pretty; > > use Bio::SeqFeature::Generic; > > use Bio::SeqIO; > > use Bio::Root::IO; > > use File::Temp; > > > > my @features = read_file(param('file')); > > > > print header, start_html('Plasmid Feature Editor'); > > > > print start_multipart_form (), > > table ({-cellpadding => 10}, > > TR({-class => 'resultsbody'}, > > td (textarea(-name => 'editarea', > > -values => "@features", > > -rows => 20, > > -cols => 70, > > -override => (@features) || (param('clear')), > > ), > > ), > > ), > > TR({-class => 'resultstitle'}, > > td (filefield(-name => 'file', > > -length => 40), > > ), > > > > td(submit(-name => 'submit_button', > > -value => 'Click to display features'), > > ), > > ), > > TR({-class => 'resultstitle'}, > > td(submit(-name => 'save_button', > > -value => 'Click here to save your work'), > > ), > > td(reset(), > > ), > > ), > > ), > > end_form; > > > > print end_html; > > > > exit 0; > > > > sub read_file { > > > > my $fh = param('file'); > > my $gb_parser = Bio::SeqIO->new(-fh=>$fh,-format=>'Genbank'); > > my @features; > > > > while (my $seq = $gb_parser-> next_seq) { > > push @features, $seq->get_SeqFeatures(); > > } > > return @features; > > } > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > From Jan.Aerts at wur.nl Fri Mar 12 10:00:27 2004 From: Jan.Aerts at wur.nl (Aerts, Jan) Date: Fri Mar 12 10:06:02 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Message-ID: <7D030487F1A3D143A76F2A1E91F57035EF3D90@scomp0010> I forgot to say: the command used was this: bp_pg_bulk_load_gff.pl -d my_db file.gff Jan -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org on behalf of Aerts, Jan Sent: Fri 12-Mar-04 15:36 To: bioperl-l@bioperl.org Cc: Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Hi all, Has anyone encountered the following errors when trying to load a gff file into a PostgresQL database? The bioperl version is 1.4. The gff file looks like this: [start gff file] GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene VIM ; Accession NM_003380.1 GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene GTF2E1 ; Accession NM_005513.1 [stop gff file] [start error] ... psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/ftype.30284:3: invalid command \. psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fgroup.30284:13694: invalid command \. psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute.30284:3: invalid command \. psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error at or near "1" [stop error] Any help appreciated. Thanks, Jan Aerts _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Jan.Aerts at wur.nl Fri Mar 12 10:44:24 2004 From: Jan.Aerts at wur.nl (Aerts, Jan) Date: Fri Mar 12 10:50:10 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Message-ID: <7D030487F1A3D143A76F2A1E91F57035EF3D92@scomp0010> Thanks Sean, I did try bp_load_gff.pl, and that one works. But the gff file I want to upload is almost 140,000 lines big, so it would take more than a day to get that into Postgres. I did use bp_pg_bulk_load_gff.pl before (must have been another version), and it worked then. So I'm afraid I'm still stuck here. Jan -----Original Message----- From: Sean Davis [mailto:sdavis2@mail.nih.gov] Sent: Fri 12-Mar-04 16:39 To: Aerts, Jan Cc: Subject: Re: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N I have had problems using the bp_bulk_load scripts for mysql on macos. I ended up solving the problem by using the bp_load script instead. If there is one for postgresql, you might try it, as I think the functionality is the same. Sean On 3/12/04 10:00 AM, "Aerts, Jan" wrote: > I forgot to say: the command used was this: bp_pg_bulk_load_gff.pl -d my_db > file.gff > > Jan > > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org on behalf of Aerts, Jan > Sent: Fri 12-Mar-04 15:36 > To: bioperl-l@bioperl.org > Cc: > Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N > Hi all, > > Has anyone encountered the following errors when trying to load a gff file > into a PostgresQL database? The bioperl version is 1.4. The gff file looks > like this: > > [start gff file] > GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene > VIM ; Accession NM_003380.1 > GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene > GTF2E1 ; Accession NM_005513.1 > [stop gff file] > > [start error] > ... > psql:/usr/tmp/fdata.30284:85393: invalid command \N > psql:/usr/tmp/fdata.30284:85393: invalid command \N > psql:/usr/tmp/fdata.30284:85394: invalid command \N > psql:/usr/tmp/fdata.30284:85394: invalid command \N > psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" > psql:/usr/tmp/ftype.30284:3: invalid command \. > psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" > psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" > psql:/usr/tmp/fgroup.30284:13694: invalid command \. > psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" > psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" > psql:/usr/tmp/fattribute.30284:3: invalid command \. > psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" > psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or > near "(" > psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. > psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error > at or near "1" > [stop error] > > Any help appreciated. > Thanks, > Jan Aerts > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From amackey at pcbi.upenn.edu Fri Mar 12 10:57:38 2004 From: amackey at pcbi.upenn.edu (Aaron J Mackey) Date: Fri Mar 12 11:03:11 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N In-Reply-To: <7D030487F1A3D143A76F2A1E91F57035EF3D92@scomp0010> Message-ID: The bulk loaders work by writing the data to files that are read by Pg/MySQL directly into the tables in a single operation; the \N's are the NULL entries for your GFF fields with "." in them. I would look through the documentation of your version of Pg to find out what the NULL encoding should be for your version; perhaps there was a change? -Aaron On Fri, 12 Mar 2004, Aerts, Jan wrote: > Thanks Sean, > > I did try bp_load_gff.pl, and that one works. But the gff file I want to upload is almost 140,000 lines big, so it would take more than a day to get that into Postgres. I did use bp_pg_bulk_load_gff.pl before (must have been another version), and it worked then. > > So I'm afraid I'm still stuck here. > Jan > > > -----Original Message----- > From: Sean Davis [mailto:sdavis2@mail.nih.gov] > Sent: Fri 12-Mar-04 16:39 > To: Aerts, Jan > Cc: > Subject: Re: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N > I have had problems using the bp_bulk_load scripts for mysql on macos. I > ended up solving the problem by using the bp_load script instead. If there > is one for postgresql, you might try it, as I think the functionality is the > same. > > Sean > > On 3/12/04 10:00 AM, "Aerts, Jan" wrote: > > > I forgot to say: the command used was this: bp_pg_bulk_load_gff.pl -d my_db > > file.gff > > > > Jan > > > > > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org on behalf of Aerts, Jan > > Sent: Fri 12-Mar-04 15:36 > > To: bioperl-l@bioperl.org > > Cc: > > Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N > > Hi all, > > > > Has anyone encountered the following errors when trying to load a gff file > > into a PostgresQL database? The bioperl version is 1.4. The gff file looks > > like this: > > > > [start gff file] > > GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene > > VIM ; Accession NM_003380.1 > > GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene > > GTF2E1 ; Accession NM_005513.1 > > [stop gff file] > > > > [start error] > > ... > > psql:/usr/tmp/fdata.30284:85393: invalid command \N > > psql:/usr/tmp/fdata.30284:85393: invalid command \N > > psql:/usr/tmp/fdata.30284:85394: invalid command \N > > psql:/usr/tmp/fdata.30284:85394: invalid command \N > > psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" > > psql:/usr/tmp/ftype.30284:3: invalid command \. > > psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" > > psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" > > psql:/usr/tmp/fgroup.30284:13694: invalid command \. > > psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" > > psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" > > psql:/usr/tmp/fattribute.30284:3: invalid command \. > > psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" > > psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or > > near "(" > > psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. > > psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error > > at or near "1" > > [stop error] > > > > Any help appreciated. > > Thanks, > > Jan Aerts > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From cain at cshl.org Fri Mar 12 11:19:48 2004 From: cain at cshl.org (Scott Cain) Date: Fri Mar 12 11:25:21 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N In-Reply-To: <200403121442.i2CEgVtl028921@portal.open-bio.org> References: <200403121442.i2CEgVtl028921@portal.open-bio.org> Message-ID: <1079108387.1491.54.camel@localhost.localdomain> Hi Jan, What version of Postgres are you using? At some point, the bulk loading format for Postgres changed, and bp_pg_bulk_load_gff.pl only supports the newer format. I believe that this change occurred between 7.2->7.3. If you are using an older Postgres, you should be able to still use bp_load_gff.pl, though it will be slower. Scott --------------Original Message--------------- Hi all, Has anyone encountered the following errors when trying to load a gff file into a PostgresQL database? The bioperl version is 1.4. The gff file looks like this: [start gff file] GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene VIM ; Accession NM_003380.1 GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene GTF2E1 ; Accession NM_005513.1 [stop gff file] [start error] ... psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/ftype.30284:3: invalid command \. psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fgroup.30284:13694: invalid command \. psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute.30284:3: invalid command \. psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error at or near "1" [stop error] Any help appreciated. Thanks, Jan Aerts -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From Jan.Aerts at wur.nl Fri Mar 12 11:23:35 2004 From: Jan.Aerts at wur.nl (Aerts, Jan) Date: Fri Mar 12 11:29:11 2004 Subject: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Message-ID: <7D030487F1A3D143A76F2A1E91F57035EF3D93@scomp0010> I just found out that it _is_ working with 7.3.4, but not with 7.2.2. Seems like I will have to update that postgres server... Thanks to all, jan. -----Original Message----- From: Scott Cain [mailto:cain@cshl.org] Sent: Fri 12-Mar-04 17:19 To: Bioperl list; Aerts, Jan Cc: Subject: Re: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N Hi Jan, What version of Postgres are you using? At some point, the bulk loading format for Postgres changed, and bp_pg_bulk_load_gff.pl only supports the newer format. I believe that this change occurred between 7.2->7.3. If you are using an older Postgres, you should be able to still use bp_load_gff.pl, though it will be slower. Scott --------------Original Message--------------- Hi all, Has anyone encountered the following errors when trying to load a gff file into a PostgresQL database? The bioperl version is 1.4. The gff file looks like this: [start gff file] GGA10_random Blast Gene 1906433 1908278 1e-102 + . Gene VIM ; Accession NM_003380.1 GGA10_random Blast Gene 1539573 1542536 0.0 + . Gene GTF2E1 ; Accession NM_005513.1 [stop gff file] [start error] ... psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85393: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/usr/tmp/fdata.30284:85394: invalid command \N psql:/upsql:/usr/tmp/ftype.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/ftype.30284:3: invalid command \. psql:/usr/tmp/ftype.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fgroup.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fgroup.30284:13694: invalid command \. psql:/usr/tmp/fgroup.30284:13695: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute.30284:3: invalid command \. psql:/usr/tmp/fattribute.30284:4: ERROR: parser: parse error at or near "1" psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR: parser: parse error at or near "(" psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \. psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR: parser: parse error at or near "1" [stop error] Any help appreciated. Thanks, Jan Aerts -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@cshl.org GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory From laurichj at bioinfo.ucr.edu Fri Mar 12 12:41:50 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Fri Mar 12 12:47:24 2004 Subject: [Bioperl-l] How to display newick tree in graphics? In-Reply-To: <20040312024941.17553.qmail@web13303.mail.yahoo.com> References: <20040312024941.17553.qmail@web13303.mail.yahoo.com> Message-ID: <20040312174150.GA5204@batch107a> On Fri 03/12/04 10:49, Yuhui wrote: > hi, > a newbie to perl here, can someone teach me how to > output a newick file in the form of a image on a > webpage. The sort version is, right now you can't, but I've got some code that will let you, its not to well documented now and is probably buggy, but seems to be working for me. The problem is, Bio::Graphics is geared towards sequence objects, so drawing a tree won't work to well. Since there was some interest in generalizing Bio::Graphics, I've added Bio::Graphics::Image (basically just a wraper around GD::Image (contains one, not inherits)) and Bio::Graphics::Widget{.pm,::Tree.pm} which aims to be a generic "here's a chunk of space, draw something" object. But neither of these have been added to bioperl, but I've been planning on making them availible for critique for a while, just been a little to busy to get around to it. -- ------------------------------------------------------ | Josh Lauricha | Ford, your turning into | | laurichj@bioinfo.ucr.edu | a penguin. Stop it. | | Bioinformatics, UCR | | |----------------------------------------------------| From brian_osborne at cognia.com Fri Mar 12 14:49:17 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Fri Mar 12 14:55:29 2004 Subject: [Bioperl-l] RE: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid In-Reply-To: <40507A3C.6090208@ed.ac.uk> Message-ID: James, Yes, I could read your patch but I'm lazy. You said: >> create a Bio::Species object, but the genus=unknown species=marine subspecies=gamma. Shouldn't the values be the same for all these "species" for which the genus is not known? Like: Genus=unknown, species=unknown, subspecies=unknown That way you can check, since one can no longer use "unless defined $species_object" to see if real species information is lacking or not. Have I missed something here? Brian O. -----Original Message----- From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] Sent: Thursday, March 11, 2004 9:40 AM To: Brian Osborne Cc: bioperl-guts-l@bioperl.org Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid Brian and all at bioperl-guts, below is the comment I've added to the bug[1600]. I think it may need some discussion, but the patch I've added works to the extent that it allows creation of a Bio::Species object but the subsequent genus, species, subspecies calls will be 'wrong'. Personally I'm more concerned with the taxid, which I think will be sufficient. If you want to see the size of this problem go to NCBI taxonomy and enter the term identified as a token set! I think that maintaining the taxid is enough, otherwise the artifical split of terms such as **unidentified diatom endosymbiont of Peridinium foliaceum* * may be a problem, though some of them are intuitive. One last question, I've never tried to fix a bug before, so I've commited a patch as an attachment to Bugzilla for the bug. Do others check this and if okay place it in the code... apologies for the newbie bit... -james genbank.pm line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; a number of species are described as Unknown blah blah blah. The NCBI taxid assigned to unknown taxa is 32644 and has a number of synonyms, none of which are 'unknown'. The list includes: other, unknown organism, not specified, not shown, unspecified, Unknown, None, unclassified , unidentified organism I've changed the _read_GenBank_Species subroutine to allow organism names such as 'unknown marine gamma proteobacterium NOR5'. This will create a Bio::Species object, but the genus=unknown species=marine subspecies=gamma. There is a whole host of species names that ignore the nice rules in _read_GenBank_Species! However this fix will allow the correct taxid to be provided which I think is more than the name! sub _read_GenBank_Species { my( $self,$buffer) = @_; my @organell_names = ("chloroplast", "mitochondr"); # only those carrying DNA, apart from the nucleus #CHANGE my @unkn_names=("other", 'unknown organism', 'not specified', 'not shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified organism'); $_ = $$buffer; my( $sub_species, $species, $genus, $common, $organelle, @class, $ns_name ); # upon first entering the loop, we must not read a new line -- the SOURCE # line is already in the buffer (HL 05/10/2000) while (defined($_) || defined($_ = $self->_readline())) { # de-HTMLify (links that may be encountered here don't contain # escaped '>', so a simple-minded approach suffices) s/<[^>]+>//g; if (/^SOURCE\s+(.*)/o) { # FIXME this is probably mostly wrong (e.g., it yields things like # Homo sapiens adult placenta cDNA to mRNA # which is certainly not what you want) $common = $1; $common =~ s/\.$//; # remove trailing dot } elsif (/^\s{2}ORGANISM/o) { my @spflds = split(' ', $_); ($ns_name) = $_ =~ /\w+\s+(.*)/o; shift(@spflds); # ORGANISM if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { $organelle = shift(@spflds); } $genus = shift(@spflds); if(@spflds) { $species = shift(@spflds); } elsif ( grep { $genus } @unkn_names){ $species = ''; } else {$species='sp.';} #there's no species name but it isn't unclassified $sub_species = shift(@spflds) if(@spflds); } elsif (/^\s+(.+)/o) { # only split on ';' or '.' so that # classification that is 2 words will # still get matched # use map to remove trailing/leading spaces push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, $1); } else { last; } $_ = undef; # Empty $_ to trigger read of next line } $$buffer = $_; # Don't make a species object if it's empty or "Unknown" or "None" my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; return unless $genus and $unkn==0; # Bio::Species array needs array in Species -> Kingdom direction if ($class[0] eq 'Viruses') { push( @class, $ns_name ); } elsif ($class[$#class] eq $genus) { push( @class, $species ); } else { push( @class, $genus, $species ); } @class = reverse @class; my $make = Bio::Species->new(); $make->classification( \@class, "FORCE" ); # no name validation please $make->common_name( $common ) if $common; unless ($class[-1] eq 'Viruses') { $make->sub_species( $sub_species ) if $sub_species; } $make->organelle($organelle) if $organelle; return $make; } Brian Osborne wrote: >James, > >Your guess is right, no Species is made because of the name. That's because >genbank.pm normally looks at: > >ORGANISM Bos taurus > >And makes "Bos" the genus, and so on. > >If it sees: > >ORGANISM Unknown > >It refuses to make a Species object, and it's interpreting your ORGANISM >line in the same way because it can't make a valid genus, that's the current >rule. Personally I'd say that I agree with its principle - how can we make a >Species object without genus and species? > >You can get the taxid from a SeqFeature object, you already knew that. > >Brian O. > > >-----Original Message----- >From: bioperl-guts-l-bounces@portal.open-bio.org >[mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of >bugzilla-daemon@portal.open-bio.org >Sent: Thursday, March 11, 2004 4:21 AM >To: bioperl-guts-l@bioperl.org >Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >http://bugzilla.bioperl.org/show_bug.cgi?id=1600 > > Summary: $gb->species->ncbi_taxid > Product: Bioperl > Version: unspecified > Platform: PC > OS/Version: Linux > Status: NEW > Severity: normal > Priority: P2 > Component: Bio::SeqIO > AssignedTo: bioperl-guts-l@bioperl.org > ReportedBy: james.wasmuth@ed.ac.uk > > >I've included a genbank file for which I have been unable to extract the >ncbi_taxid for using > >$gb->species->ncbi_taxid > >the error is: >Can't call method "ncbi_taxid" on an undefined value > >infact I don't get a Bio::Species object. I'm sure its because of the name, >which is correct. > >I've tried looking into it, but could not find which Seq object creates the >Bio::Species object. > > > >LOCUS AY007676 1389 bp DNA linear BCT >29-OCT-2001 >DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA, > partial sequence. >ACCESSION AY007676 >VERSION AY007676.1 GI:12000362 >KEYWORDS . >SOURCE unknown marine gamma proteobacterium NOR5 > ORGANISM unknown marine gamma proteobacterium NOR5 > Bacteria; Proteobacteria; Gammaproteobacteria. >REFERENCE 1 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. >and > Amann,R. > TITLE Isolation of novel pelagic bacteria from the German bight and >their > seasonal contributions to surface picoplankton > JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) > MEDLINE 21536174 > PUBMED 11679337 >REFERENCE 2 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G., > Schuett,C. and Amann,R. > TITLE Identification and seasonal dominance of culturable marine >bacteria > JOURNAL Unpublished >REFERENCE 3 (bases 1 to 1389) > AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., Gerdts,G., > Schuett,C. and Amann,R. > TITLE Direct Submission > JOURNAL Submitted (29-AUG-2000) Molecular Ecology, Max-Planck-Institute, > Celsiusstrasse 1, Bremen 28359, Germany >FEATURES Location/Qualifiers > source 1..1389 > /organism="unknown marine gamma proteobacterium NOR5" > /mol_type="genomic DNA" > /db_xref="taxon:145658" > rRNA <1..>1389 > /product="16S ribosomal RNA" >BASE COUNT 343 a 319 c 453 g 274 t >ORIGIN > 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt aggaatctat > 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc ctaagggaga > 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt agctagttgg > 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg atcagccaca > 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat attgcgcaat > 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg ttgtaaagca > 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat tacctttaga > 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg agcgttaatc > 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg aaagccccgg > 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag ggaggtagaa > 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc gaaggcggcc > 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg attagatacc > 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat ttcttggtgg > 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta aaactcaaat > 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg caacgcgaag > 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg ccttcgggaa > 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt gggttaagtc > 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga actctaagga > 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat ggcccttacg > 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc gcgaggggga > 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac tccgtgaagt > 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg ggccttgtac > 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct aaccttcggg > 1381 agggcgatc >// > > > >------- You are receiving this mail because: ------- >You are the assignee for the bug, or are watching the assignee. >_______________________________________________ >Bioperl-guts-l mailing list >Bioperl-guts-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > > > > -- "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison Nematode Bioinformatics || Blaxter Nematode Genomics Group || School of Biological Sciences || Ashworth Laboratories || King's Buildings || tel: +44 131 650 7403 University of Edinburgh || web: www.nematodes.org Edinburgh || EH9 3JT || UK || From barry.moore at genetics.utah.edu Fri Mar 12 14:54:22 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Mar 12 14:59:57 2004 Subject: [Bioperl-l] load_seqdatabase.pl Message-ID: <4052156E.2040402@genetics.utah.edu> I'm having some trouble with load_seqdatabase.pl. I using BioPerl 1.4 (with some CVS updates including bioperl-db and bioperl-live Bio::DB yesterday), ActiveState Perl 5.8, MySQL version 12.22 distribution 4.0.16, Windows XP. I've successfully created a database mysql with the biosqldb-mysql.sql schema downloaded yesterday. I have a file RefSeq_Human_mRNA_short.gb that has RefSeq mRNA in GenBank format (I pasted the first record from that file below). I run load_seqdatabase.pl like this: >perl -d load_seqdatabase.pl --dbpass ******* RefSeq_Human_mRNA_short.gb All of the script defaults should be O.K., but I've tried setting them all on the command line as well. The script opens the file, and gets sequence out of it O.K., but then somewhere in the eval statement that begins at line 500 it heads off to Bio::Root::Root, and loses the plot with this error: Undefined subroutine &Bio::Root::Root::debug called at C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1526, line 413. Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class('Bio::DB::Bio SQL::SeqAdaptor=HASH(0x1d22200)','Bio::DB::BioSQL::mysql::','Driver','Bio::DB::B ioSQL::SeqAdaptor') called at C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap tor.pm line 1507 Bio::DB::BioSQL::BasePersistenceAdaptor::dbd('Bio::DB::BioSQL::SeqAdapto r=HASH(0x1d22200)') called at C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap tor.pm line 1386 Bio::DB::BioSQL::BasePersistenceAdaptor::rollback('Bio::DB::BioSQL::SeqA daptor=HASH(0x1d22200)') called at load_seqdatabase.pl line 524 I'm happy to try to figure this out myself, but right now I haven't a clue what's going on since the subroutine &Bio::Root::Root::debug seems to me to be where it's supposed to be. Is this possible a OS issue since I'm on Windows? Can anyone nudge me in the right direction? Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT LOCUS NM_000014 4577 bp mRNA linear PRI 20-DEC-2003 DEFINITION Homo sapiens alpha-2-macroglobulin (A2M), mRNA. ACCESSION NM_000014 VERSION NM_000014.3 GI:6226959 KEYWORDS . SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 4577) AUTHORS Mathew,S., Arandjelovic,S., Beyer,W.F., Gonias,S.L. and Pizzo,S.V. TITLE Characterization of the interaction between alpha2-macroglobulin and fibroblast growth factor-2: the role of hydrophobic interactions JOURNAL Biochem. J. 374 (Pt 1), 123-129 (2003) PUBMED 12755687 REMARK GeneRIF: FGF-2 and this protein interact at specific binding sites, involving different FGF-2 sequences. REFERENCE 2 (bases 1 to 4577) AUTHORS Athauda,S.B., Nishigai,M., Arakawa,H., Ikai,A., Ukai,M. and Takahashi,K. TITLE Inhibition of human pepsin and gastricsin by alpha2-macroglobulin JOURNAL J Enzyme Inhib Med Chem 18 (3), 219-224 (2003) PUBMED 14506912 REMARK GeneRIF: alpha2-macroglobulin inhibits human pepsin adn gastricsin REFERENCE 3 (bases 1 to 4577) AUTHORS Arandjelovic,S., Freed,T.A. and Gonias,S.L. TITLE Growth factor-binding sequence in human alpha2-macroglobulin targets the receptor-binding site in transforming growth factor-beta JOURNAL Biochemistry 42 (20), 6121-6127 (2003) PUBMED 12755614 REMARK GeneRIF: alpha(2)M-derived peptides target the receptor-binding sequence in TGF-beta REFERENCE 4 (bases 1 to 4577) AUTHORS Shibata,M., Sakai,H., Sakai,E., Okamoto,K., Nishishita,K., Yasuda,Y., Kato,Y. and Yamamoto,K. TITLE Disruption of structural and functional integrity of alpha 2-macroglobulin by cathepsin E JOURNAL Eur. J. Biochem. 270 (6), 1189-1198 (2003) PUBMED 12631277 REMARK GeneRIF: These results suggest the possible involvement of cathepsin E in disruption of the structural and functional integrity of alpha 2-macroglobulin in the endolysosome system. REFERENCE 5 (bases 1 to 4577) AUTHORS Zappia,M., Cittadella,R., Manna,I., Nicoletti,G., Andreoli,V., Bonavita,S., Gambardella,A. and Quattrone,A. TITLE Genetic association of alpha2-macroglobulin polymorphisms with AD in southern Italy JOURNAL Neurology 59 (5), 756-758 (2002) PUBMED 12221172 REMARK GeneRIF: Genetic association of alpha2-macroglobulin polymorphisms with Alzheimer's disease REFERENCE 6 (bases 1 to 4577) AUTHORS Ghebremedhin,E., Schultz,C., Thal,D.R., Del Tredici,K., Rueb,U. and Braak,H. TITLE Genetic association of argyrophilic grain disease with polymorphisms in alpha-2 macroglobulin and low-density lipoprotein receptor-related protein genes JOURNAL Neuropathol Appl Neurobiol 28 (4), 308-313 (2002) PUBMED 12175343 REMARK GeneRIF: Genetic association of argyrophilic grain disease with polymorphisms in alpha-2 macroglobulin. REFERENCE 7 (bases 1 to 4577) AUTHORS Kolodziej,S.J., Wagenknecht,T., Strickland,D.K. and Stoops,J.K. TITLE The three-dimensional structure of the human alpha 2-macroglobulin dimer reveals its structural organization in the tetrameric native and chymotrypsin alpha 2-macroglobulin complexes JOURNAL J. Biol. Chem. 277 (31), 28031-28037 (2002) PUBMED 12015318 REMARK GeneRIF: The three-dimensional structure of the dimer reveals its structural organization in the tetrameric native and chymotrypsin alpha 2-macroglobulin complexes. REFERENCE 8 (bases 1 to 4577) AUTHORS McElhinney,B., Ardill,J., Caldwell,C., Lloyd,F. and McClure,N. TITLE Ovarian hyperstimulation syndrome and assisted reproductive technologies: why some and not others? JOURNAL Hum. Reprod. 17 (6), 1548-1553 (2002) PUBMED 12042276 REMARK GeneRIF: relationship between serum VEGF levels, alpha(2)M levels and the development of OHSS in hyperstimulated subjects undergoing IVF REFERENCE 9 (bases 1 to 4577) AUTHORS Mettenburg,J.M., Webb,D.J. and Gonias,S.L. TITLE Distinct binding sites in the structure of alpha 2-macroglobulin mediate the interaction with beta-amyloid peptide and growth factors JOURNAL J. Biol. Chem. 277 (15), 13338-13345 (2002) PUBMED 11823454 REMARK GeneRIF: distinct binding sites mediate interaction with beta-amyloid peptide and growth factors REFERENCE 10 (bases 1 to 4577) AUTHORS Cvirn,G., Gallistl,S., Koestenberger,M., Kutschera,J., Leschnik,B. and Muntean,W. TITLE Alpha 2-macroglobulin enhances prothrombin activation and thrombin potential by inhibiting the anticoagulant protein C/protein S system in cord and adult plasma JOURNAL Thromb. Res. 105 (5), 433-439 (2002) PUBMED 12062545 REMARK GeneRIF: Alpha 2-macroglobulin enhances prothrombin activation and thrombin potential by inhibiting the anticoagulant protein C/protein S system in cord and adult plasma. REFERENCE 11 (bases 1 to 4577) AUTHORS Janka,Z., Juhasz,A., Rimanoczy,A., Boda,K., Marki-Zay,J., Palotas,M., Kuk,I., Zollei,M., Jakab,K. and Kalman,J. TITLE Alpha2-macroglobulin exon 24 (Val-1000-Ile) polymorphism is not associated with late-onset sporadic Alzheimer's dementia in the Hungarian population JOURNAL Psychiatr. Genet. 12 (1), 49-54 (2002) PUBMED 11901360 REMARK GeneRIF: has an important role in the AD-specific neurodegenerative process but its exon 24 Val-1000-Ile polymorphism is not likely to be associated with late-onset sporadic AD in the Hungarian population REFERENCE 12 (bases 1 to 4577) AUTHORS Chiabrando,G.A., Vides,M.A. and Sanchez,M.C. TITLE Differential binding properties of human pregnancy zone protein- and alpha2-macroglobulin-proteinase complexes to low-density lipoprotein receptor-related protein JOURNAL Arch. Biochem. Biophys. 398 (1), 73-78 (2002) PUBMED 11811950 REMARK GeneRIF: Differential binding to ldl receptor related protein REFERENCE 13 (bases 1 to 4577) AUTHORS Toombs,C.F. TITLE Alfimeprase: pharmacology of a novel fibrinolytic metalloproteinase for thrombolysis JOURNAL Haemostasis 31 (3-6), 141-147 (2001) PUBMED 11910179 REMARK GeneRIF: REVIEW: binds and neutralizes alfimeprase, which has direct proteolytic activity against the fibrinogen Aalpha chain REFERENCE 14 (bases 1 to 4577) AUTHORS Borth,W. TITLE Alpha 2-macroglobulin, a multifunctional binding protein with targeting characteristics JOURNAL FASEB J. 6 (15), 3345-3353 (1992) PUBMED 1281457 REFERENCE 15 (bases 1 to 4577) AUTHORS Poller,W., Faber,J.P., Klobeck,G. and Olek,K. TITLE Cloning of the human alpha 2-macroglobulin gene and detection of mutations in two functional domains: the bait region and the thiolester site JOURNAL Hum. Genet. 88 (3), 313-319 (1992) PUBMED 1370808 REFERENCE 16 (bases 1 to 4577) AUTHORS Poller,W., Faber,J.P. and Olek,K. TITLE Sequence polymorphism in the human alpha-2-macroglobulin (A2M) gene JOURNAL Nucleic Acids Res. 19 (1), 198 (1991) PUBMED 1707161 REFERENCE 17 (bases 1 to 4577) AUTHORS Bell,G.I., Rall,L.B., Sanchez-Pescador,R., Merryweather,J.P., Scott,J., Eddy,R.L. and Shows,T.B. TITLE Human alpha 2-macroglobulin gene is located on chromosome 12 JOURNAL Somat. Cell Mol. Genet. 11 (3), 285-289 (1985) PUBMED 2408344 REFERENCE 18 (bases 1 to 4577) AUTHORS Kan,C.C., Solomon,E., Belt,K.T., Chain,A.C., Hiorns,L.R. and Fey,G. TITLE Nucleotide sequence of cDNA encoding human alpha 2-macroglobulin and assignment of the chromosomal locus JOURNAL Proc. Natl. Acad. Sci. U.S.A. 82 (8), 2282-2286 (1985) PUBMED 2581245 COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from M11313.1. On Nov 4, 1999 this sequence version replaced gi:6226762. Summary: Alpha-2-macroglobulin is a protease inhibitor and cytokine transporter. It inhibits many proteases, including trypsin, thrombin and collagenase. A2M is implicated in Alzheimer disease (AD) due to its ability to mediate the clearance and degradation of A-beta, the major component of beta-amyloid deposits. FEATURES Location/Qualifiers source 1..4577 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="12" /map="12p13.3-p12.3" gene 1..4577 /gene="A2M" /db_xref="GeneID:2" /db_xref="LocusID:2" /db_xref="MIM:103950" CDS 44..4468 /gene="A2M" /note="go_function: protein carrier activity [goid 0008320] [evidence NR]; go_function: endopeptidase inhibitor activity [goid 0004866] [evidence NR]; go_function: wide-spectrum protease inhibitor activity [goid 0017114] [evidence IEA]; go_function: serine protease inhibitor activity [goid 0004867] [evidence IEA]; go_function: alpha-2 macroglobulin [goid 0016975] [evidence NAS]; go_process: intracellular protein transport [goid 0006886] [evidence NR]" /codon_start=1 /product="alpha 2 macroglobulin precursor" /protein_id="NP_000005.1" /db_xref="GI:4557225" /db_xref="GeneID:2" /db_xref="LocusID:2" /db_xref="MIM:103950" /translation="MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETT EKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMF LTVQVKGPTQEFKKRTTVMVKNEDSLVFVQTDKSIYKPGQTVKFRVVSMDENFHPLNE LIPLVYIQDPKGNRIAQWQSFQLEGGLKQFSFPLSSEPFQGSYKVVVQKKSGGRTEHP FTVEEFVLPKFEVQVTVPKIITILEEEMNVSVCGLYTYGKPVPGHVTVSICRKYSDAS DCHGEDSQAFCEKFSGQLNSHGCFYQQVKTKVFQLKRKEYEMKLHTEAQIQEEGTVVE LTGRQSSEITRTITKLSFVKVDSHFRQGIPFFGQVRLVDGKGVPIPNKVIFIRGNEAN YYSNATTDEHGLVQFSINTTNVMGTSLTVRVNYKDRSPCYGYQWVSEEHEEAHHTAYL VFSPSKSFVHLEPMSHELPCGHTQTVQAHYILNGGTLLGLKKLSFYYLIMAKGGIVRT GTHGLLVKQEDMKGHFSISIPVKSDIAPVARLLIYAVLPTGDVIGDSAKYDVENCLAN KVDLSFSPSQSLPASHAHLRVTAAPQSVCALRAVDQSVLLMKPDAELSASSVYNLLPE KDLTGFPGPLNDQDDEDCINRHNVYINGITYTPVSSTNEKDMYSFLEDMGLKAFTNSK IRKPKMCPQLQQYEMHGPEGLRVGFYESDVMGRGHARLVHVEEPHTETVRKYFPETWI WDLVVVNSAGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFVELTM PYSVIRGEAFTLKATVLNYLPKCIRVSVQLEASPAFLAVPVEKEQAPHCICANGRQTV SWAVTPKSLGNVNFTVSAEALESQELCGTEVPSVPEHGRKDTVIKPLLVEPEGLEKET TFNSLLCPSGGEVSEELSLKLPPNVVEESARASVSVLGDILGSAMQNTQNLLQMPYGC GEQNMVLFAPNIYVLDYLNETQQLTPEVKSKAIGYLNTGYQRQLNYKHYDGSYSTFGE RYGRNQGNTWLTAFVLKTFAQARAYIFIDEAHITQALIWLSQRQKDNGCFRSSGSLLN NAIKGGVEDEVTLSAYITIALLEIPLTVTHPVVRNALFCLESAWKTAQEGDHGSHVYT KALLAYAFALAGNQDKRKEVLKSLNEEAVKKDNSVHWERPQKPKAPVGHFYEPQAPSA EVEMTSYVLLAYLTAQPAPTSEDLTSATNIVKWITKQQNAQGGFSSTQDTVVALHALS KYGAATFTRTGKAAQVTIQSSGTFSSKFQVDNNNRLLLQQVSLPELPGEYSMKVTGEG CVYLQTSLKYNILPEKEEFPFALGVQTLPQTCDEPKAHTSFQISLSVSYTGSRSASNM AIVDVKMVSGFIPLKPTVKMLERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVLQD VPVRDLKPAIVKVYDYYETDEFAIAEYNAPCSKDLGNA" sig_peptide 44..112 /gene="A2M" /note="alpha-2-macroglobulin signal peptide" misc_feature 104..4465 /gene="A2M" /note="KOG1366; Region: Alpha-macroglobulin [Posttranslational modification, protein turnover, chaperones]" /db_xref="CDD:19155" misc_feature 110..1927 /gene="A2M" /note="A2M_N; Region: Alpha-2-macroglobulin family N-terminal region" /db_xref="CDD:17056" mat_peptide 113..4465 /gene="A2M" /product="alpha-2-macroglobulin" misc_feature 2216..4432 /gene="A2M" /note="Region: Alpha-2-macroglobulin family" /db_xref="CDD:5952" variation 1122 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:2229298" variation 1282 /gene="A2M" /replace="T" /replace="C" /db_xref="dbSNP:1049134" variation 1339 /gene="A2M" /replace="T" /replace="C" /db_xref="dbSNP:2228222" variation 1354 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:226396" variation 1958 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:226405" variation 2154 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:1800434" variation 2431 /gene="A2M" /replace="T" /replace="C" /db_xref="dbSNP:1049143" variation 2487 /gene="A2M" /replace="T" /replace="A" /db_xref="dbSNP:3180392" variation 2487 /gene="A2M" /replace="T" /replace="A" /db_xref="dbSNP:3210107" variation 2958 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:1800433" variation 3041 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:669" variation 3988 /gene="A2M" /replace="G" /replace="A" /db_xref="dbSNP:1802964" variation 4334 /gene="A2M" /replace="T" /replace="C" /db_xref="dbSNP:1802965" variation 4474 /gene="A2M" /replace="C" /replace="A" /db_xref="dbSNP:1130840" variation 4508 /gene="A2M" /replace="T" /replace="C" /db_xref="dbSNP:1049985" variation 4511 /gene="A2M" /replace="T" /replace="A" /db_xref="dbSNP:1802966" variation 4519 /gene="A2M" /replace="C" /replace="A" /db_xref="dbSNP:3190224" ORIGIN 1 gctacaatcc atctggtctc ctccagctcc ttctttctgc aacatgggga agaacaaact 61 ccttcatcca agtctggttc ttctcctctt ggtcctcctg cccacagacg cctcagtctc 121 tggaaaaccg cagtatatgg ttctggtccc ctccctgctc cacactgaga ccactgagaa 181 gggctgtgtc cttctgagct acctgaatga gacagtgact gtaagtgctt ccttggagtc 241 tgtcagggga aacaggagcc tcttcactga cctggaggcg gagaatgacg tactccactg 301 tgtcgccttc gctgtcccaa agtcttcatc caatgaggag gtaatgttcc tcactgtcca 361 agtgaaagga ccaacccaag aatttaagaa gcggaccaca gtgatggtta agaacgagga 421 cagtctggtc tttgtccaga cagacaaatc aatctacaaa ccagggcaga cagtgaaatt 481 tcgtgttgtc tccatggatg aaaactttca ccccctgaat gagttgattc cactagtata 541 cattcaggat cccaaaggaa atcgcatcgc acaatggcag agtttccagt tagagggtgg 601 cctcaagcaa ttttcttttc ccctctcatc agagcccttc cagggctcct acaaggtggt 661 ggtacagaag aaatcaggtg gaaggacaga gcaccctttc accgtggagg aatttgttct 721 tcccaagttt gaagtacaag taacagtgcc aaagataatc accatcttgg aagaagagat 781 gaatgtatca gtgtgtggcc tatacacata tgggaagcct gtccctggac atgtgactgt 841 gagcatttgc agaaagtata gtgacgcttc cgactgccac ggtgaagatt cacaggcttt 901 ctgtgagaaa ttcagtggac agctaaacag ccatggctgc ttctatcagc aagtaaaaac 961 caaggtcttc cagctgaaga ggaaggagta tgaaatgaaa cttcacactg aggcccagat 1021 ccaagaagaa ggaacagtgg tggaattgac tggaaggcag tccagtgaaa tcacaagaac 1081 cataaccaaa ctctcatttg tgaaagtgga ctcacacttt cgacagggaa ttcccttctt 1141 tgggcaggtg cgcctagtag atgggaaagg cgtccctata ccaaataaag tcatattcat 1201 cagaggaaat gaagcaaact attactccaa tgctaccacg gatgagcatg gccttgtaca 1261 gttctctatc aacaccacca acgttatggg tacctctctt actgttaggg tcaattacaa 1321 ggatcgtagt ccctgttacg gctaccagtg ggtgtcagaa gaacacgaag aggcacatca 1381 cactgcttat cttgtgttct ccccaagcaa gagctttgtc caccttgagc ccatgtctca 1441 tgaactaccc tgtggccata ctcagacagt ccaggcacat tatattctga atggaggcac 1501 cctgctgggg ctgaagaagc tctcctttta ttatctgata atggcaaagg gaggcattgt 1561 ccgaactggg actcatggac tgcttgtgaa gcaggaagac atgaagggcc atttttccat 1621 ctcaatccct gtgaagtcag acattgctcc tgtcgctcgg ttgctcatct atgctgtttt 1681 acctaccggg gacgtgattg gggattctgc aaaatatgat gttgaaaatt gtctggccaa 1741 caaggtggat ttgagcttca gcccatcaca aagtctccca gcctcacacg cccacctgcg 1801 agtcacagcg gctcctcagt ccgtctgcgc cctccgtgct gtggaccaaa gcgtgctgct 1861 catgaagcct gatgctgagc tctcggcgtc ctcggtttac aacctgctac cagaaaagga 1921 cctcactggc ttccctgggc ctttgaatga ccaggacgat gaagactgca tcaatcgtca 1981 taatgtctat attaatggaa tcacatatac tccagtatca agtacaaatg aaaaggatat 2041 gtacagcttc ctagaggaca tgggcttaaa ggcattcacc aactcaaaga ttcgtaaacc 2101 caaaatgtgt ccacagcttc aacagtatga aatgcatgga cctgaaggtc tacgtgtagg 2161 tttttatgag tcagatgtaa tgggaagagg ccatgcacgc ctggtgcatg ttgaagagcc 2221 tcacacggag accgtacgaa agtacttccc tgagacatgg atctgggatt tggtggtggt 2281 aaactcagca ggggtggctg aggtaggagt aacagtccct gacaccatca ccgagtggaa 2341 ggcaggggcc ttctgcctgt ctgaagatgc tggacttggt atctcttcca ctgcctctct 2401 ccgagccttc cagcccttct ttgtggagct tacaatgcct tactctgtga ttcgtggaga 2461 ggccttcaca ctcaaggcca cggtcctaaa ctaccttccc aaatgcatcc gggtcagtgt 2521 gcagctggaa gcctctcccg ccttccttgc tgtcccagtg gagaaggaac aagcgcctca 2581 ctgcatctgt gcaaacgggc ggcaaactgt gtcctgggca gtaaccccaa agtcattagg 2641 aaatgtgaat ttcactgtga gcgcagaggc actagagtct caagagctgt gtgggactga 2701 ggtgccttca gttcctgaac acggaaggaa agacacagtc atcaagcctc tgttggttga 2761 acctgaagga ctagagaagg aaacaacatt caactcccta ctttgtccat caggtggtga 2821 ggtttctgaa gaattatccc tgaaactgcc accaaatgtg gtagaagaat ctgcccgagc 2881 ttctgtctca gttttgggag acatattagg ctctgccatg caaaacacac aaaatcttct 2941 ccagatgccc tatggctgtg gagagcagaa tatggtcctc tttgctccta acatctatgt 3001 actggattat ctaaatgaaa cacagcagct tactccagag gtcaagtcca aggccattgg 3061 ctatctcaac actggttacc agagacagtt gaactacaaa cactatgatg gctcctacag 3121 cacctttggg gagcgatatg gcaggaacca gggcaacacc tggctcacag cctttgttct 3181 gaagactttt gcccaagctc gagcctacat cttcatcgat gaagcacaca ttacccaagc 3241 cctcatatgg ctctcccaga ggcagaagga caatggctgt ttcaggagct ctgggtcact 3301 gctcaacaat gccataaagg gaggagtaga agatgaagtg accctctccg cctatatcac 3361 catcgccctt ctggagattc ctctcacagt cactcaccct gttgtccgca atgccctgtt 3421 ttgcctggag tcagcctgga agacagcaca agaaggggac catggcagcc atgtatatac 3481 caaagcactg ctggcctatg cttttgccct ggcaggtaac caggacaaga ggaaggaagt 3541 actcaagtca cttaatgagg aagctgtgaa gaaagacaac tctgtccatt gggagcgccc 3601 tcagaaaccc aaggcaccag tggggcattt ttacgaaccc caggctccct ctgctgaggt 3661 ggagatgaca tcctatgtgc tcctcgctta tctcacggcc cagccagccc caacctcgga 3721 ggacctgacc tctgcaacca acatcgtgaa gtggatcacg aagcagcaga atgcccaggg 3781 cggtttctcc tccacccagg acacagtggt ggctctccat gctctgtcca aatatggagc 3841 cgccacattt accaggactg ggaaggctgc acaggtgact atccagtctt cagggacatt 3901 ttccagcaaa ttccaagtgg acaacaacaa tcgcctgtta ctgcagcagg tctcattgcc 3961 agagctgcct ggggaataca gcatgaaagt gacaggagaa ggatgtgtct acctccagac 4021 ctccttgaaa tacaatattc tcccagaaaa ggaagagttc ccctttgctt taggagtgca 4081 gactctgcct caaacttgtg atgaacccaa agcccacacc agcttccaaa tctccctaag 4141 tgtcagttac acagggagcc gctctgcctc caacatggcg atcgttgatg tgaagatggt 4201 ctctggcttc attcccctga agccaacagt gaaaatgctt gaaagatcta accatgtgag 4261 ccggacagaa gtcagcagca accatgtctt gatttacctt gataaggtgt caaatcagac 4321 actgagcttg ttcttcacgg ttctgcaaga tgtcccagta agagatctca aaccagccat 4381 agtgaaagtc tatgattact acgagacgga tgagtttgca atcgctgagt acaatgctcc 4441 ttgcagcaaa gatcttggaa atgcttgaag accacaaggc tgaaaagtgc tttgctggag 4501 tcctgttctc tgagctccac agaagacacg tgtttttgta tctttaaaga cttgatgaat 4561 aaacactttt tctggtc // From radams at staffmail.ed.ac.uk Fri Mar 12 16:22:44 2004 From: radams at staffmail.ed.ac.uk (Richard Adams) Date: Fri Mar 12 16:28:19 2004 Subject: [Bioperl-l] protein networks Message-ID: <1079126564.40522a2475877@staffmail.ed.ac.uk> Hi Boris, Thanks for the tips. I've put some modules in CVS in Bio::Graph namespace. The module representing a protein interaction network is called ProteinGraph.pm, but you're right, including the word "interaction" would clarify it. The base class, Nat Goodman's SimpleGraph is totally generic for any graph, not just biological graphs. ProteinGraph.pm uses Bio::Seq objects to represent the nodes and only subclasses a few methods from SimpleGraph. I would imagine that a protein::DNA and DNA/DNA interactions could also be represented using this class, using the alphabet() method to distinguish proteins from DNA. If you think that additional data fields /methods would be needed I'd love to know - methods in common between the classes could then be abstracted into a common Bio::Graph::Base class. I've include a basic XML parser for parsing PSI XML records. e.g., my $io = Bio::Graph::IO->new(-file => 'myfile', -format =>'psixml'); my $gr = $io->next_network(); At present it reads the minimun infor to construct a graph but does not make an effort to get all the data. If you know of the existence of an industrial strength PSI-XML parser, I'd be really pleased, there must be one out there somewhere. Richard From allenday at ucla.edu Fri Mar 12 17:31:17 2004 From: allenday at ucla.edu (Allen Day) Date: Fri Mar 12 17:36:51 2004 Subject: [Bioperl-l] How to display newick tree in graphics? In-Reply-To: <20040312174150.GA5204@batch107a> References: <20040312024941.17553.qmail@web13303.mail.yahoo.com> <20040312174150.GA5204@batch107a> Message-ID: this can be done using Bio::TreIO::svggraph. this module will write SVG images of a Bio::Tree. there is a dependency of this module on SVG::Graph and SVG. -allen On Fri, 12 Mar 2004, Josh Lauricha wrote: > On Fri 03/12/04 10:49, Yuhui wrote: > > hi, > > a newbie to perl here, can someone teach me how to > > output a newick file in the form of a image on a > > webpage. > > The sort version is, right now you can't, but I've got some code that > will let you, its not to well documented now and is probably buggy, but > seems to be working for me. > > The problem is, Bio::Graphics is geared towards sequence objects, so > drawing a tree won't work to well. Since there was some interest in > generalizing Bio::Graphics, I've added Bio::Graphics::Image (basically > just a wraper around GD::Image (contains one, not inherits)) and > Bio::Graphics::Widget{.pm,::Tree.pm} which aims to be a generic "here's > a chunk of space, draw something" object. But neither of these have been > added to bioperl, but I've been planning on making them availible for > critique for a while, just been a little to busy to get around to it. > > From barry.moore at genetics.utah.edu Fri Mar 12 12:24:26 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri Mar 12 18:15:21 2004 Subject: [Bioperl-l] Parsing features In-Reply-To: References: Message-ID: <4051F24A.10107@genetics.utah.edu> Jonathon, I looks like what you are trying to do is print your @features array as if it were a tidy list of features. In fact it is a complex data structure that holds the values of the Generic SeqFeature object. You will need to step through it and collect the goodies yourself. (At least I don't think there is a prepackaged way to just "get it all" - although the list can correct me if I'm wrong on that.) If you are after certain values of the GenBank features table, the following document may be of some help in getting at it. (If the pasted document doesn't come to you well formatted let me know, and I can mail it directly to you as an attachement.) Barry --------------------------------------------------------------------------- How to get values in a GenBank file with BioPerl This is a guide to accessing the value of each item in a GenBank file with BioPerl. Underneath each value in the sample GenBank file there is a number and a 3-letter code. The 3-letter code represents the object where the associated value is stored. Table 1 at the end of this file gives the object for each code. By looking up the numbers in Table 2 at the end of this file you will find the object where this information can be called from, and the method to get (and sometimes set) the value. Some values may be stored, and accessible by methods in more than one object. There is perl code at the end that you can use as a starting point to get at all of the objects and their methods. ----------------------------------------------------------------------------------- LOCUS NM_079543 1821 bp mRNA linear INV 10-DEC-2003 1-BSR 2-BPS 3-BSR 4-BSR 5-BSR 6-BSR DEFINITION Drosophila melanogaster alpha-Esterase-3 CG1257-PA (alpha-Est3) mRNA, complete cds. 7-BPS ACCESSION NM_079543 XX_123456 8-BPS 9-BSR VERSION NM_079543.2 GI:24644853 | | 10-BPS 11-BSR KEYWORDS Esterases 12-BSR SOURCE Drosophila melanogaster (fruit fly) 13-BSC ORGANISM Drosophila melanogaster 14-BSC 15-BSC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila. 16-BSC REFERENCE 1 (bases 1 to 1821) 17-BAR 18-BAR AUTHORS Adams,M.D. et al.(additional authors deleted for brevity) 19-BAR TITLE The genome sequence of Drosophila melanogaster 20-BAR JOURNAL Science 287 (5461), 2185-2195 (2000) 21-BAR MEDLINE 20196006 22-BAR PUBMED 10731132 23-BAR COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. This record is derived from an annotated genomic sequence (NT_033777). The reference sequence was derived from CG1257-RA. On Nov 6, 2002 this sequence version replaced gi:17737826. 24-BAC FEATURES Location/Qualifiers source 1..1821 25-BLS 26-BLS /organism="Drosophila melanogaster" 27-BSG /mol_type="mRNA" /db_xref="taxon:7227" /chromosome="3R" /note="genotype: y[1]; cn[1] bw[1] sp[1]; Rh6[1]" gene 1..1821 /gene="alpha-Est3" /locus_tag="CG1257" /note="alpha-Esterase-3; synonyms: B, aE3, CG1257, alphaE3, alpha-Ests, fragment B; go_function: carboxylesterase activity [goid 0004091] [evidence NAS]" /map="84D9-84D9" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" CDS 119..1750 /gene="alpha-Est3" /locus_tag="CG1257" /EC_number="3.1.1.1" /note="alpha-Est3 gene product" /codon_start=1 /product="alpha-Esterase-3 CG1257-PA" /protein_id="NP_524267.2" /db_xref="GI:24644854" /db_xref="FLYBASE:FBgn0015571" /db_xref="GeneID:40907" /db_xref="LocusID:40907" /translation="MESLQVNTTSGPVLGKQCTGVYGDEYVSFERIPYAQPPVGHLRF MAPLPVEPWSQPLDCTKPGQKPLQFNHYSKQLEGVEDCLYLNVYAKELDSPRPLPLIV FFFGGGFEKGDPTKELHSPDYFMMRDVVVVTVSYRVGPLGFLSLNDPAVGVPGNAGLK DQLLAMEWIKENAERFNGDPKNVTAFGESAGAASVHYLMLNPKAEGLFHKAILQSGNV LCSWALCTIKNLPHRLAVNLGMESAEHVTDAMVLDFLQKLPGEKLVRPYLLSAEEHLD DCVFQFGPMVEPYKTEHCALPNHPQELLDKAWGNRIPVLMSGTSFEGLLMYARVQMAP YLLTSLKKEPEHMLPLDVKRNLPQALARHLGQRLQETHFGGNDPSAMSPESLKAYCEY ASYKVFWHPILKTLRSRVKSSSASTYLYRFDFDSPTFNHQRLKYCGDKLRGVAHVDDH SYLWYGDFSWKLDKHTPEFLTIERMIDMLTSFARTSNPNCKLIQDQLPRAKEWKPLNS KSALECLNISENIKMMELPELQKLRVWESVCQSTG" ORIGIN 1 gtactatggc aaatggtact atgggcagtc gcgataataa taataaatga ggctttaaat 61 gtttttccac tacaagataa aaagttacga gtgcgcaccg agcatttagt agacgaacat 28-BPS ... (additional sequence deleted for brevity) // ----------------------------------------------------------------------------------- Table 1. Object Key BPS - Bio::PrimarySeq BSR - Bio::Seq::RichSeq BSC - Bio::Species BAC - Bio::Annotation::Comment BAR - Bio::Annotation::Reference BLS ? Bio::Location::Simple BSG - Bio::SeqFeature::Generic ----------------------------------------------------------------------------------- Table 2. Usage key 1. Bio::Seq::RichSeq $scalar = $self->display_name() or ->display_id() 2. Bio::PrimarySeq $scalar = $self->length() 3. Bio::Seq::RichSeq $scalar = $self->molecule() 4. Bio::PrimarySeq $scalar = $self->is_circular 5. Bio::Seq::RichSeq $scalar = $self->division() 6. Bio::seq::Richseq @array = $self->get_dates 7. Bio::PrimarySeq $scalar = $self->description() 8. Bio::PrimarySeq $scalar = $self->accession_number() Bio::Seq::RichSeq $scalar = $self->accession() 9. Bio::Seq::RichSeq @array = $self->get_secondary_accessions 10. Bio::PrimarySeq $scalar = $self->version() Bio::Seq::RichSeq $scalar = $self->seq_version() 11. Bio::PrimarySeq $scalar = $self->primary_id() 12. Bio::Seq::RichSeq @array = $self->get_keywords 13. Bio::Species $scalar = $self->common_name() 14. Bio::Species $scalar = $self->genus() 15. Bio::Species $scalar = $self->species() 16. Bio::Species @array = $self->classification() 17. Bio::Annotation::Reference $scalar = $self->start() 18. Bio::Annotation::Reference $scalar = $self->end() 19. Bio::Annotation::Reference $scalar = $self->authors() 20. Bio::Annotation::Reference $scalar = $self->title() 21. Bio::Annotation::Reference $scalar = $self->location() 22. Bio::Annotation::Reference $scalar = $self->medline() 23. Bio::Annotation::Reference $scalar = $self->pubmed() 24. Bio::Annotation::Comment $scalar = $self->text() or ->as_text 25. Bio::SeqFeature::Generic $scalar = $self->start() 26. Bio::SeqFeature::Generic $scalar = $self->end() 27. Bio::SeqFeature::Generic Get all features from the features table using a variation on the code below. You will need to vary the primary_tag (e.g. source, gene, CDS) and the get_tag_values (e.g. organism, db_xref, chromosome, note, gene, locus_tag, go_function, map, EC_number, codon_start, protein_id, etc.). If there is more than one primary tag associated with a give value (e.g. more than one gene) then you will have to step through the @source_feats array to find what you want rather than simply shifting the first scalar off the top. my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); 28. Bio::PrimarySeq $scalar = $self->seq() ----------------------------------------------------------------------------------- #!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::DB::GenBank; #use Bio::DB::GenPept or Bio::DB::RefSeq if needed #Get some sequence IDs either like below, or read in from a file. Note that #this sample script works with the accession numbers below (at least at the time #it was written). If you add different accession numbers, and you get errors, #you may be calling for something that the sequence doesn't have. You'll have #to add your own error trapping code to handle that. my @ids = ('U59228', 'AB039327', 'BC035972'); #Create the GenBank database object to read from the database. my $gb = new Bio::DB::GenBank(); #Create a sequence stream to pass the sequences from the database to the program. my $seqio = $gb->get_Stream_by_id(\@ids); #Loop over all of the sequences that you requested. while (my $seq = $seqio->next_seq) { #Here is how you get methods directly from the RichSeq object. Replace #'display_name' with any other method in Table 2. that can be called on #either the RichSeq object directly, or the PrimarySeq object which it has #inherited. print $seq->display_name,"\n"; #Here is how to access the classification data from the species object. my $species = $seq->species; print $species->common_name,"\n"; my @class = $species->classification; print "@class\n"; #Here is a general way to call things that are stored as a Bio::SeqFeature:: #Generic object. Replace 'source' with any other of the "major" headings in #the feature table (e.g gene, CDS, etc.) and replace 'organism' with any of #the tag values found under that heading (mol_type, locus_tag, gene, etc.) my @source_feats = grep { $_->primary_tag eq 'source' } $seq->get_SeqFeatures(); my $source_feat = shift @source_feats; my @mol_type = $source_feat->get_tag_values('mol_type'); print "@mol_type\n"; #Here is a general way to call things that are stored as some type of a #Bio::Annotation oject. This includes reference information, and comments. #Replace reference with 'comment' to get the comment, and replace #$ref->authors with $ref->title (or location, medline, etc.) to get other #reference categories my $ann = $seq->annotation(); my @references = ($ann->get_Annotations('reference')); my $ref = shift @references; my ($title, $authors, $location, $pubmed, $reference); if (defined $ref) { $authors = $ref->authors; print "$authors\n"; } print "\n"; } --------------------------------------------------------------------- This file is without copyright. It may be reproduced, edited, and redistributed at will without notice to the author, however I would appreciate it if any corrections or improvements were sent to barry.moore@genetics.utah.edu From cjm at fruitfly.org Fri Mar 12 20:22:18 2004 From: cjm at fruitfly.org (Chris Mungall) Date: Fri Mar 12 20:27:51 2004 Subject: [Bioperl-l] new GFF3 support methods added In-Reply-To: Message-ID: On Mon, 8 Mar 2004, Hilmar Lapp wrote: > > On Monday, March 8, 2004, at 01:07 PM, Chris Mungall wrote: > > > Perhaps it would be better to have a Bio::SeqFeature::Tools::IDHandler > > class? This would contain methods > > > > generate_unique_persistent_id($feat) # uses $feat->seq_id > > generate_unique_persistent_id($feat, $seq_id) > > > > create_hierarchy_from_ParentIDs($featholder); > > set_ParentIDs_from_hierarchy($featholder); > > > > Any preference? I'm leaving them as is for now if that's ok, but I > > have no > > objections to moving everything to a seperate class if that's prefered. > > > > I like your suggestion. Keeps FeatureHolderI lighter, and is easier to > change behaviour. But maybe it's just me who likes this better. Well, no one else seems to care much. I've created Bio::SeqFeature::Tools::IDHandler which takes care of these methods keeping the core interfaces light Cheers Chris > -hilmar From hlapp at gnf.org Fri Mar 12 21:01:01 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Fri Mar 12 21:06:41 2004 Subject: [Bioperl-l] load_seqdatabase.pl In-Reply-To: <4052156E.2040402@genetics.utah.edu> Message-ID: <471DCDBA-7492-11D8-86B3-000A959EB4C4@gnf.org> I have seen this before I believe from someone on a Windows machine. The problem could be some trouble with the dynamic loading of modules. The -d option to perl invokes the debugger. Do you see the same problem without invoking the debugger? Did the bioperl-db tests pass? Root::debug() is invoked all over the place many many times. By default, you won't see any of that since $obj->verbose() governs whether the messages are printed or suppressed. You can try to pass --debug to load_seqdatabase.pl and see when it crashes then. (All messages that you see in addition after enabling --debug will have been routed through Root::debug.) -hilmar On Friday, March 12, 2004, at 11:54 AM, Barry Moore wrote: > I'm having some trouble with load_seqdatabase.pl. I using BioPerl 1.4 > (with some CVS updates including bioperl-db and bioperl-live Bio::DB > yesterday), ActiveState Perl 5.8, MySQL version 12.22 distribution > 4.0.16, Windows XP. I've successfully created a database mysql with > the biosqldb-mysql.sql schema downloaded yesterday. I have a file > RefSeq_Human_mRNA_short.gb that has RefSeq mRNA in GenBank format (I > pasted the first record from that file below). I run > load_seqdatabase.pl like this: > > >perl -d load_seqdatabase.pl --dbpass ******* > RefSeq_Human_mRNA_short.gb > > All of the script defaults should be O.K., but I've tried setting them > all on the command line as well. > > The script opens the file, and gets sequence out of it O.K., but then > somewhere in the eval statement that begins at line 500 it heads off > to Bio::Root::Root, and loses the plot with this error: > > Undefined subroutine &Bio::Root::Root::debug called at > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1526, > line 413. > Bio::DB::BioSQL::BasePersistenceAdaptor::_get_driver_class('Bio::DB::Bi > o > SQL::SeqAdaptor=HASH(0x1d22200)','Bio::DB::BioSQL::mysql::','Driver','B > io::DB::B > ioSQL::SeqAdaptor') called at > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > tor.pm line 1507 > Bio::DB::BioSQL::BasePersistenceAdaptor::dbd('Bio::DB::BioSQL::SeqAdapt > o > r=HASH(0x1d22200)') called at > C:/Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdap > tor.pm line 1386 > Bio::DB::BioSQL::BasePersistenceAdaptor::rollback('Bio::DB::BioSQL::Seq > A > daptor=HASH(0x1d22200)') called at load_seqdatabase.pl line 524 > > I'm happy to try to figure this out myself, but right now I haven't a > clue what's going on since the subroutine &Bio::Root::Root::debug > seems to me to be where it's supposed to be. Is this possible a OS > issue since I'm on Windows? Can anyone nudge me in the right > direction? > > Barry > -- > Barry Moore > Dept. of Human Genetics > University of Utah > Salt Lake City, UT > > > LOCUS NM_000014 4577 bp mRNA linear PRI 20-DEC-2003 > DEFINITION Homo sapiens alpha-2-macroglobulin (A2M), mRNA. > ACCESSION NM_000014 > VERSION NM_000014.3 GI:6226959 > KEYWORDS . > SOURCE Homo sapiens (human) > ORGANISM Homo sapiens > Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; > Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. > REFERENCE 1 (bases 1 to 4577) > AUTHORS Mathew,S., Arandjelovic,S., Beyer,W.F., Gonias,S.L. and > Pizzo,S.V. > TITLE Characterization of the interaction between alpha2-macroglobulin > and fibroblast growth factor-2: the role of hydrophobic > interactions > JOURNAL Biochem. J. 374 (Pt 1), 123-129 (2003) > PUBMED 12755687 > REMARK GeneRIF: FGF-2 and this protein interact at specific binding > sites, > involving different FGF-2 sequences. > REFERENCE 2 (bases 1 to 4577) > AUTHORS Athauda,S.B., Nishigai,M., Arakawa,H., Ikai,A., Ukai,M. and > Takahashi,K. > TITLE Inhibition of human pepsin and gastricsin by alpha2-macroglobulin > JOURNAL J Enzyme Inhib Med Chem 18 (3), 219-224 (2003) > PUBMED 14506912 > REMARK GeneRIF: alpha2-macroglobulin inhibits human pepsin adn > gastricsin > REFERENCE 3 (bases 1 to 4577) > AUTHORS Arandjelovic,S., Freed,T.A. and Gonias,S.L. > TITLE Growth factor-binding sequence in human alpha2-macroglobulin > targets the receptor-binding site in transforming growth > factor-beta > JOURNAL Biochemistry 42 (20), 6121-6127 (2003) > PUBMED 12755614 > REMARK GeneRIF: alpha(2)M-derived peptides target the receptor-binding > sequence in TGF-beta > REFERENCE 4 (bases 1 to 4577) > AUTHORS Shibata,M., Sakai,H., Sakai,E., Okamoto,K., Nishishita,K., > Yasuda,Y., Kato,Y. and Yamamoto,K. > TITLE Disruption of structural and functional integrity of alpha > 2-macroglobulin by cathepsin E > JOURNAL Eur. J. Biochem. 270 (6), 1189-1198 (2003) > PUBMED 12631277 > REMARK GeneRIF: These results suggest the possible involvement of > cathepsin E in disruption of the structural and functional > integrity of alpha 2-macroglobulin in the endolysosome system. > REFERENCE 5 (bases 1 to 4577) > AUTHORS Zappia,M., Cittadella,R., Manna,I., Nicoletti,G., Andreoli,V., > Bonavita,S., Gambardella,A. and Quattrone,A. > TITLE Genetic association of alpha2-macroglobulin polymorphisms with AD > in southern Italy > JOURNAL Neurology 59 (5), 756-758 (2002) > PUBMED 12221172 > REMARK GeneRIF: Genetic association of alpha2-macroglobulin > polymorphisms > with Alzheimer's disease > REFERENCE 6 (bases 1 to 4577) > AUTHORS Ghebremedhin,E., Schultz,C., Thal,D.R., Del Tredici,K., > Rueb,U. and > Braak,H. > TITLE Genetic association of argyrophilic grain disease with > polymorphisms in alpha-2 macroglobulin and low-density lipoprotein > receptor-related protein genes > JOURNAL Neuropathol Appl Neurobiol 28 (4), 308-313 (2002) > PUBMED 12175343 > REMARK GeneRIF: Genetic association of argyrophilic grain disease with > polymorphisms in alpha-2 macroglobulin. > REFERENCE 7 (bases 1 to 4577) > AUTHORS Kolodziej,S.J., Wagenknecht,T., Strickland,D.K. and Stoops,J.K. > TITLE The three-dimensional structure of the human alpha > 2-macroglobulin > dimer reveals its structural organization in the tetrameric native > and chymotrypsin alpha 2-macroglobulin complexes > JOURNAL J. Biol. Chem. 277 (31), 28031-28037 (2002) > PUBMED 12015318 > REMARK GeneRIF: The three-dimensional structure of the dimer reveals > its > structural organization in the tetrameric native and chymotrypsin > alpha 2-macroglobulin complexes. > REFERENCE 8 (bases 1 to 4577) > AUTHORS McElhinney,B., Ardill,J., Caldwell,C., Lloyd,F. and McClure,N. > TITLE Ovarian hyperstimulation syndrome and assisted reproductive > technologies: why some and not others? > JOURNAL Hum. Reprod. 17 (6), 1548-1553 (2002) > PUBMED 12042276 > REMARK GeneRIF: relationship between serum VEGF levels, alpha(2)M > levels > and the development of OHSS in hyperstimulated subjects undergoing > IVF > REFERENCE 9 (bases 1 to 4577) > AUTHORS Mettenburg,J.M., Webb,D.J. and Gonias,S.L. > TITLE Distinct binding sites in the structure of alpha 2-macroglobulin > mediate the interaction with beta-amyloid peptide and growth > factors > JOURNAL J. Biol. Chem. 277 (15), 13338-13345 (2002) > PUBMED 11823454 > REMARK GeneRIF: distinct binding sites mediate interaction with > beta-amyloid peptide and growth factors > REFERENCE 10 (bases 1 to 4577) > AUTHORS Cvirn,G., Gallistl,S., Koestenberger,M., Kutschera,J., > Leschnik,B. > and Muntean,W. > TITLE Alpha 2-macroglobulin enhances prothrombin activation and > thrombin > potential by inhibiting the anticoagulant protein C/protein S > system in cord and adult plasma > JOURNAL Thromb. Res. 105 (5), 433-439 (2002) > PUBMED 12062545 > REMARK GeneRIF: Alpha 2-macroglobulin enhances prothrombin activation > and > thrombin potential by inhibiting the anticoagulant protein > C/protein S system in cord and adult plasma. > REFERENCE 11 (bases 1 to 4577) > AUTHORS Janka,Z., Juhasz,A., Rimanoczy,A., Boda,K., Marki-Zay,J., > Palotas,M., Kuk,I., Zollei,M., Jakab,K. and Kalman,J. > TITLE Alpha2-macroglobulin exon 24 (Val-1000-Ile) polymorphism is not > associated with late-onset sporadic Alzheimer's dementia in the > Hungarian population > JOURNAL Psychiatr. Genet. 12 (1), 49-54 (2002) > PUBMED 11901360 > REMARK GeneRIF: has an important role in the AD-specific > neurodegenerative > process but its exon 24 Val-1000-Ile polymorphism is not likely to > be associated with late-onset sporadic AD in the Hungarian > population > REFERENCE 12 (bases 1 to 4577) > AUTHORS Chiabrando,G.A., Vides,M.A. and Sanchez,M.C. > TITLE Differential binding properties of human pregnancy zone protein- > and alpha2-macroglobulin-proteinase complexes to low-density > lipoprotein receptor-related protein > JOURNAL Arch. Biochem. Biophys. 398 (1), 73-78 (2002) > PUBMED 11811950 > REMARK GeneRIF: Differential binding to ldl receptor related protein > REFERENCE 13 (bases 1 to 4577) > AUTHORS Toombs,C.F. > TITLE Alfimeprase: pharmacology of a novel fibrinolytic > metalloproteinase > for thrombolysis > JOURNAL Haemostasis 31 (3-6), 141-147 (2001) > PUBMED 11910179 > REMARK GeneRIF: REVIEW: binds and neutralizes alfimeprase, which has > direct proteolytic activity against the fibrinogen Aalpha chain > REFERENCE 14 (bases 1 to 4577) > AUTHORS Borth,W. > TITLE Alpha 2-macroglobulin, a multifunctional binding protein with > targeting characteristics > JOURNAL FASEB J. 6 (15), 3345-3353 (1992) > PUBMED 1281457 > REFERENCE 15 (bases 1 to 4577) > AUTHORS Poller,W., Faber,J.P., Klobeck,G. and Olek,K. > TITLE Cloning of the human alpha 2-macroglobulin gene and detection of > mutations in two functional domains: the bait region and the > thiolester site > JOURNAL Hum. Genet. 88 (3), 313-319 (1992) > PUBMED 1370808 > REFERENCE 16 (bases 1 to 4577) > AUTHORS Poller,W., Faber,J.P. and Olek,K. > TITLE Sequence polymorphism in the human alpha-2-macroglobulin (A2M) > gene > JOURNAL Nucleic Acids Res. 19 (1), 198 (1991) > PUBMED 1707161 > REFERENCE 17 (bases 1 to 4577) > AUTHORS Bell,G.I., Rall,L.B., Sanchez-Pescador,R., Merryweather,J.P., > Scott,J., Eddy,R.L. and Shows,T.B. > TITLE Human alpha 2-macroglobulin gene is located on chromosome 12 > JOURNAL Somat. Cell Mol. Genet. 11 (3), 285-289 (1985) > PUBMED 2408344 > REFERENCE 18 (bases 1 to 4577) > AUTHORS Kan,C.C., Solomon,E., Belt,K.T., Chain,A.C., Hiorns,L.R. and > Fey,G. > TITLE Nucleotide sequence of cDNA encoding human alpha 2-macroglobulin > and assignment of the chromosomal locus > JOURNAL Proc. Natl. Acad. Sci. U.S.A. 82 (8), 2282-2286 (1985) > PUBMED 2581245 > COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. > The > reference sequence was derived from M11313.1. > On Nov 4, 1999 this sequence version replaced gi:6226762. > > Summary: Alpha-2-macroglobulin is a protease inhibitor and cytokine > transporter. It inhibits many proteases, including trypsin, > thrombin and collagenase. A2M is implicated in Alzheimer disease > (AD) due to its ability to mediate the clearance and degradation of > A-beta, the major component of beta-amyloid deposits. > FEATURES Location/Qualifiers > source 1..4577 > /organism="Homo sapiens" > /mol_type="mRNA" > /db_xref="taxon:9606" > /chromosome="12" > /map="12p13.3-p12.3" > gene 1..4577 > /gene="A2M" > /db_xref="GeneID:2" > /db_xref="LocusID:2" > /db_xref="MIM:103950" > CDS 44..4468 > /gene="A2M" > /note="go_function: protein carrier activity [goid > 0008320] [evidence NR]; > go_function: endopeptidase inhibitor activity [goid > 0004866] [evidence NR]; > go_function: wide-spectrum protease inhibitor activity > [goid 0017114] [evidence IEA]; > go_function: serine protease inhibitor activity [goid > 0004867] [evidence IEA]; > go_function: alpha-2 macroglobulin [goid 0016975] > [evidence NAS]; > go_process: intracellular protein transport [goid 0006886] > [evidence NR]" > /codon_start=1 > /product="alpha 2 macroglobulin precursor" > /protein_id="NP_000005.1" > /db_xref="GI:4557225" > /db_xref="GeneID:2" > /db_xref="LocusID:2" > /db_xref="MIM:103950" > /translation="MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETT > EKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMF > LTVQVKGPTQEFKKRTTVMVKNEDSLVFVQTDKSIYKPGQTVKFRVVSMDENFHPLNE > LIPLVYIQDPKGNRIAQWQSFQLEGGLKQFSFPLSSEPFQGSYKVVVQKKSGGRTEHP > FTVEEFVLPKFEVQVTVPKIITILEEEMNVSVCGLYTYGKPVPGHVTVSICRKYSDAS > DCHGEDSQAFCEKFSGQLNSHGCFYQQVKTKVFQLKRKEYEMKLHTEAQIQEEGTVVE > LTGRQSSEITRTITKLSFVKVDSHFRQGIPFFGQVRLVDGKGVPIPNKVIFIRGNEAN > YYSNATTDEHGLVQFSINTTNVMGTSLTVRVNYKDRSPCYGYQWVSEEHEEAHHTAYL > VFSPSKSFVHLEPMSHELPCGHTQTVQAHYILNGGTLLGLKKLSFYYLIMAKGGIVRT > GTHGLLVKQEDMKGHFSISIPVKSDIAPVARLLIYAVLPTGDVIGDSAKYDVENCLAN > KVDLSFSPSQSLPASHAHLRVTAAPQSVCALRAVDQSVLLMKPDAELSASSVYNLLPE > KDLTGFPGPLNDQDDEDCINRHNVYINGITYTPVSSTNEKDMYSFLEDMGLKAFTNSK > IRKPKMCPQLQQYEMHGPEGLRVGFYESDVMGRGHARLVHVEEPHTETVRKYFPETWI > WDLVVVNSAGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFVELTM > PYSVIRGEAFTLKATVLNYLPKCIRVSVQLEASPAFLAVPVEKEQAPHCICANGRQTV > SWAVTPKSLGNVNFTVSAEALESQELCGTEVPSVPEHGRKDTVIKPLLVEPEGLEKET > TFNSLLCPSGGEVSEELSLKLPPNVVEESARASVSVLGDILGSAMQNTQNLLQMPYGC > GEQNMVLFAPNIYVLDYLNETQQLTPEVKSKAIGYLNTGYQRQLNYKHYDGSYSTFGE > RYGRNQGNTWLTAFVLKTFAQARAYIFIDEAHITQALIWLSQRQKDNGCFRSSGSLLN > NAIKGGVEDEVTLSAYITIALLEIPLTVTHPVVRNALFCLESAWKTAQEGDHGSHVYT > KALLAYAFALAGNQDKRKEVLKSLNEEAVKKDNSVHWERPQKPKAPVGHFYEPQAPSA > EVEMTSYVLLAYLTAQPAPTSEDLTSATNIVKWITKQQNAQGGFSSTQDTVVALHALS > KYGAATFTRTGKAAQVTIQSSGTFSSKFQVDNNNRLLLQQVSLPELPGEYSMKVTGEG > CVYLQTSLKYNILPEKEEFPFALGVQTLPQTCDEPKAHTSFQISLSVSYTGSRSASNM > AIVDVKMVSGFIPLKPTVKMLERSNHVSRTEVSSNHVLIYLDKVSNQTLSLFFTVLQD > VPVRDLKPAIVKVYDYYETDEFAIAEYNAPCSKDLGNA" > sig_peptide 44..112 > /gene="A2M" > /note="alpha-2-macroglobulin signal peptide" > misc_feature 104..4465 > /gene="A2M" > /note="KOG1366; Region: Alpha-macroglobulin > [Posttranslational modification, protein turnover, > chaperones]" > /db_xref="CDD:19155" > misc_feature 110..1927 > /gene="A2M" > /note="A2M_N; Region: Alpha-2-macroglobulin family > N-terminal region" > /db_xref="CDD:17056" > mat_peptide 113..4465 > /gene="A2M" > /product="alpha-2-macroglobulin" > misc_feature 2216..4432 > /gene="A2M" > /note="Region: Alpha-2-macroglobulin family" > /db_xref="CDD:5952" > variation 1122 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:2229298" > variation 1282 > /gene="A2M" > /replace="T" > /replace="C" > /db_xref="dbSNP:1049134" > variation 1339 > /gene="A2M" > /replace="T" > /replace="C" > /db_xref="dbSNP:2228222" > variation 1354 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:226396" > variation 1958 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:226405" > variation 2154 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:1800434" > variation 2431 > /gene="A2M" > /replace="T" > /replace="C" > /db_xref="dbSNP:1049143" > variation 2487 > /gene="A2M" > /replace="T" > /replace="A" > /db_xref="dbSNP:3180392" > variation 2487 > /gene="A2M" > /replace="T" > /replace="A" > /db_xref="dbSNP:3210107" > variation 2958 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:1800433" > variation 3041 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:669" > variation 3988 > /gene="A2M" > /replace="G" > /replace="A" > /db_xref="dbSNP:1802964" > variation 4334 > /gene="A2M" > /replace="T" > /replace="C" > /db_xref="dbSNP:1802965" > variation 4474 > /gene="A2M" > /replace="C" > /replace="A" > /db_xref="dbSNP:1130840" > variation 4508 > /gene="A2M" > /replace="T" > /replace="C" > /db_xref="dbSNP:1049985" > variation 4511 > /gene="A2M" > /replace="T" > /replace="A" > /db_xref="dbSNP:1802966" > variation 4519 > /gene="A2M" > /replace="C" > /replace="A" > /db_xref="dbSNP:3190224" > ORIGIN > 1 gctacaatcc atctggtctc ctccagctcc ttctttctgc aacatgggga agaacaaact > 61 ccttcatcca agtctggttc ttctcctctt ggtcctcctg cccacagacg cctcagtctc > 121 tggaaaaccg cagtatatgg ttctggtccc ctccctgctc cacactgaga ccactgagaa > 181 gggctgtgtc cttctgagct acctgaatga gacagtgact gtaagtgctt ccttggagtc > 241 tgtcagggga aacaggagcc tcttcactga cctggaggcg gagaatgacg tactccactg > 301 tgtcgccttc gctgtcccaa agtcttcatc caatgaggag gtaatgttcc tcactgtcca > 361 agtgaaagga ccaacccaag aatttaagaa gcggaccaca gtgatggtta agaacgagga > 421 cagtctggtc tttgtccaga cagacaaatc aatctacaaa ccagggcaga cagtgaaatt > 481 tcgtgttgtc tccatggatg aaaactttca ccccctgaat gagttgattc cactagtata > 541 cattcaggat cccaaaggaa atcgcatcgc acaatggcag agtttccagt tagagggtgg > 601 cctcaagcaa ttttcttttc ccctctcatc agagcccttc cagggctcct acaaggtggt > 661 ggtacagaag aaatcaggtg gaaggacaga gcaccctttc accgtggagg aatttgttct > 721 tcccaagttt gaagtacaag taacagtgcc aaagataatc accatcttgg aagaagagat > 781 gaatgtatca gtgtgtggcc tatacacata tgggaagcct gtccctggac atgtgactgt > 841 gagcatttgc agaaagtata gtgacgcttc cgactgccac ggtgaagatt cacaggcttt > 901 ctgtgagaaa ttcagtggac agctaaacag ccatggctgc ttctatcagc aagtaaaaac > 961 caaggtcttc cagctgaaga ggaaggagta tgaaatgaaa cttcacactg aggcccagat > 1021 ccaagaagaa ggaacagtgg tggaattgac tggaaggcag tccagtgaaa tcacaagaac > 1081 cataaccaaa ctctcatttg tgaaagtgga ctcacacttt cgacagggaa ttcccttctt > 1141 tgggcaggtg cgcctagtag atgggaaagg cgtccctata ccaaataaag tcatattcat > 1201 cagaggaaat gaagcaaact attactccaa tgctaccacg gatgagcatg gccttgtaca > 1261 gttctctatc aacaccacca acgttatggg tacctctctt actgttaggg tcaattacaa > 1321 ggatcgtagt ccctgttacg gctaccagtg ggtgtcagaa gaacacgaag aggcacatca > 1381 cactgcttat cttgtgttct ccccaagcaa gagctttgtc caccttgagc ccatgtctca > 1441 tgaactaccc tgtggccata ctcagacagt ccaggcacat tatattctga atggaggcac > 1501 cctgctgggg ctgaagaagc tctcctttta ttatctgata atggcaaagg gaggcattgt > 1561 ccgaactggg actcatggac tgcttgtgaa gcaggaagac atgaagggcc atttttccat > 1621 ctcaatccct gtgaagtcag acattgctcc tgtcgctcgg ttgctcatct atgctgtttt > 1681 acctaccggg gacgtgattg gggattctgc aaaatatgat gttgaaaatt gtctggccaa > 1741 caaggtggat ttgagcttca gcccatcaca aagtctccca gcctcacacg cccacctgcg > 1801 agtcacagcg gctcctcagt ccgtctgcgc cctccgtgct gtggaccaaa gcgtgctgct > 1861 catgaagcct gatgctgagc tctcggcgtc ctcggtttac aacctgctac cagaaaagga > 1921 cctcactggc ttccctgggc ctttgaatga ccaggacgat gaagactgca tcaatcgtca > 1981 taatgtctat attaatggaa tcacatatac tccagtatca agtacaaatg aaaaggatat > 2041 gtacagcttc ctagaggaca tgggcttaaa ggcattcacc aactcaaaga ttcgtaaacc > 2101 caaaatgtgt ccacagcttc aacagtatga aatgcatgga cctgaaggtc tacgtgtagg > 2161 tttttatgag tcagatgtaa tgggaagagg ccatgcacgc ctggtgcatg ttgaagagcc > 2221 tcacacggag accgtacgaa agtacttccc tgagacatgg atctgggatt tggtggtggt > 2281 aaactcagca ggggtggctg aggtaggagt aacagtccct gacaccatca ccgagtggaa > 2341 ggcaggggcc ttctgcctgt ctgaagatgc tggacttggt atctcttcca ctgcctctct > 2401 ccgagccttc cagcccttct ttgtggagct tacaatgcct tactctgtga ttcgtggaga > 2461 ggccttcaca ctcaaggcca cggtcctaaa ctaccttccc aaatgcatcc gggtcagtgt > 2521 gcagctggaa gcctctcccg ccttccttgc tgtcccagtg gagaaggaac aagcgcctca > 2581 ctgcatctgt gcaaacgggc ggcaaactgt gtcctgggca gtaaccccaa agtcattagg > 2641 aaatgtgaat ttcactgtga gcgcagaggc actagagtct caagagctgt gtgggactga > 2701 ggtgccttca gttcctgaac acggaaggaa agacacagtc atcaagcctc tgttggttga > 2761 acctgaagga ctagagaagg aaacaacatt caactcccta ctttgtccat caggtggtga > 2821 ggtttctgaa gaattatccc tgaaactgcc accaaatgtg gtagaagaat ctgcccgagc > 2881 ttctgtctca gttttgggag acatattagg ctctgccatg caaaacacac aaaatcttct > 2941 ccagatgccc tatggctgtg gagagcagaa tatggtcctc tttgctccta acatctatgt > 3001 actggattat ctaaatgaaa cacagcagct tactccagag gtcaagtcca aggccattgg > 3061 ctatctcaac actggttacc agagacagtt gaactacaaa cactatgatg gctcctacag > 3121 cacctttggg gagcgatatg gcaggaacca gggcaacacc tggctcacag cctttgttct > 3181 gaagactttt gcccaagctc gagcctacat cttcatcgat gaagcacaca ttacccaagc > 3241 cctcatatgg ctctcccaga ggcagaagga caatggctgt ttcaggagct ctgggtcact > 3301 gctcaacaat gccataaagg gaggagtaga agatgaagtg accctctccg cctatatcac > 3361 catcgccctt ctggagattc ctctcacagt cactcaccct gttgtccgca atgccctgtt > 3421 ttgcctggag tcagcctgga agacagcaca agaaggggac catggcagcc atgtatatac > 3481 caaagcactg ctggcctatg cttttgccct ggcaggtaac caggacaaga ggaaggaagt > 3541 actcaagtca cttaatgagg aagctgtgaa gaaagacaac tctgtccatt gggagcgccc > 3601 tcagaaaccc aaggcaccag tggggcattt ttacgaaccc caggctccct ctgctgaggt > 3661 ggagatgaca tcctatgtgc tcctcgctta tctcacggcc cagccagccc caacctcgga > 3721 ggacctgacc tctgcaacca acatcgtgaa gtggatcacg aagcagcaga atgcccaggg > 3781 cggtttctcc tccacccagg acacagtggt ggctctccat gctctgtcca aatatggagc > 3841 cgccacattt accaggactg ggaaggctgc acaggtgact atccagtctt cagggacatt > 3901 ttccagcaaa ttccaagtgg acaacaacaa tcgcctgtta ctgcagcagg tctcattgcc > 3961 agagctgcct ggggaataca gcatgaaagt gacaggagaa ggatgtgtct acctccagac > 4021 ctccttgaaa tacaatattc tcccagaaaa ggaagagttc ccctttgctt taggagtgca > 4081 gactctgcct caaacttgtg atgaacccaa agcccacacc agcttccaaa tctccctaag > 4141 tgtcagttac acagggagcc gctctgcctc caacatggcg atcgttgatg tgaagatggt > 4201 ctctggcttc attcccctga agccaacagt gaaaatgctt gaaagatcta accatgtgag > 4261 ccggacagaa gtcagcagca accatgtctt gatttacctt gataaggtgt caaatcagac > 4321 actgagcttg ttcttcacgg ttctgcaaga tgtcccagta agagatctca aaccagccat > 4381 agtgaaagtc tatgattact acgagacgga tgagtttgca atcgctgagt acaatgctcc > 4441 ttgcagcaaa gatcttggaa atgcttgaag accacaaggc tgaaaagtgc tttgctggag > 4501 tcctgttctc tgagctccac agaagacacg tgtttttgta tctttaaaga cttgatgaat > 4561 aaacactttt tctggtc > // > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From vesko_baev at abv.bg Sat Mar 13 07:05:03 2004 From: vesko_baev at abv.bg (Vesko Baev) Date: Sat Mar 13 09:57:36 2004 Subject: [Bioperl-l] RNA analysis Message-ID: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> Is there a bioperl module(s) for RNA analysis: folding, free energy, RNA/RNA align or modules that connect the script with ext. RNA progs? Thenks! Vesko ----------------------------------------------------------------- http://zavedenia.gbg.bg - ???? ?? ?????? ???? ?????? From jason at cgt.duhs.duke.edu Sat Mar 13 10:18:36 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sat Mar 13 10:24:17 2004 Subject: [Bioperl-l] RNA analysis In-Reply-To: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> References: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> Message-ID: See ViennaRNA package from Ivo Hofacker's group and their RNAFold.pl script - there is a nice XS perl interface to the C library. http://www.tbi.univie.ac.at/~ivo/RNA/ -jason On Sat, 13 Mar 2004, Vesko Baev wrote: > Is there a bioperl module(s) for RNA analysis: folding, free energy, > RNA/RNA align or modules that connect the script with ext. RNA progs? > > Thenks! > Vesko > > ----------------------------------------------------------------- > http://zavedenia.gbg.bg - Êúäå ùå õîäèòå òàçè âå÷åð? -- Jason Stajich Duke University jason at cgt.mc.duke.edu From james.wasmuth at ed.ac.uk Sat Mar 13 10:34:01 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Sat Mar 13 10:39:45 2004 Subject: [Bioperl-l] Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid In-Reply-To: References: Message-ID: <405329E9.4000805@ed.ac.uk> Brian, >Yes, I could read your patch but I'm lazy. You said: > > >>>create a Bio::Species object, but the genus=unknown species=marine >>> >>> >subspecies=gamma. > I was highlighting the problem my patch would create. I hadn't thought too hard about its consequences, but realise that it may have some knock-on effects. > >Shouldn't the values be the same for all these "species" for which the genus >is not known? Like: > >Genus=unknown, species=unknown, subspecies=unknown > >That way you can check, since one can no longer use "unless defined >$species_object" to see if real species information is lacking or not. Have >I missed something here? > NCBI taxonomy considers the term 'unknown marine gamma proteobacterium NOR5' to represent a species, though for this example there remaining taxonomy classification is awarded no rank until 'class'. So one possible fix, would be: if (ORGANISM ne "synonym for taxid 32644") { then add rest of name into $species. } therefore $genus = unknown and $species = marine gamma proteobacterium NOR5 other problems are organisms such as "leaf litter basidiomycete sp. Collb2-39". Currently $genus = leaf, $species = litter and $subsp = basidiomycete. Perhaps $subsp should contain everything left over? Thoughts? Also does anyone know off hand if it copes with 'varietas' and 'var.' for plants? I expect not. I will have a look at the genbank.pm on Monday and suggest a patch. I expect these issues will also be pertinent in embl.pm and other database format modules... hmmmm, anyone with thoughts? -james > >Brian O. > > >-----Original Message----- >From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] >Sent: Thursday, March 11, 2004 9:40 AM >To: Brian Osborne >Cc: bioperl-guts-l@bioperl.org >Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >Brian and all at bioperl-guts, > > >below is the comment I've added to the bug[1600]. I think it may need >some discussion, but the patch I've added works to the extent that it >allows creation of a Bio::Species object but the subsequent genus, >species, subspecies calls will be 'wrong'. Personally I'm more >concerned with the taxid, which I think will be sufficient. > >If you want to see the size of this problem go to NCBI taxonomy and >enter the term identified as a token set! I think that maintaining the >taxid is enough, otherwise the artifical split of terms such as >**unidentified diatom endosymbiont of Peridinium foliaceum* >&lvl=3&lin=f&keep=1&srchmode=3&unlock>* >may be a problem, though some of them are intuitive. > >One last question, I've never tried to fix a bug before, so I've >commited a patch as an attachment to Bugzilla for the bug. Do others >check this and if okay place it in the code... >apologies for the newbie bit... > >-james > > > >genbank.pm > >line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; > >a number of species are described as Unknown blah blah blah. > >The NCBI taxid assigned to unknown taxa is 32644 and has a number of >synonyms, none of which are 'unknown'. > >The list includes: other, unknown organism, not specified, not shown, >unspecified, Unknown, None, unclassified , unidentified organism > >I've changed the _read_GenBank_Species subroutine to allow organism >names such as 'unknown marine gamma proteobacterium NOR5'. This will >create a Bio::Species object, but the genus=unknown species=marine >subspecies=gamma. > >There is a whole host of species names that ignore the nice rules in >_read_GenBank_Species! However this fix will allow the correct taxid to >be provided which I think is more than the name! > > > >sub _read_GenBank_Species { > my( $self,$buffer) = @_; > my @organell_names = ("chloroplast", "mitochondr"); > # only those carrying DNA, apart from the nucleus > > #CHANGE > my @unkn_names=("other", 'unknown organism', 'not specified', 'not >shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified >organism'); > > $_ = $$buffer; > > my( $sub_species, $species, $genus, $common, $organelle, @class, >$ns_name ); > # upon first entering the loop, we must not read a new line -- the >SOURCE > # line is already in the buffer (HL 05/10/2000) > while (defined($_) || defined($_ = $self->_readline())) { > # de-HTMLify (links that may be encountered here don't contain > # escaped '>', so a simple-minded approach suffices) > s/<[^>]+>//g; > if (/^SOURCE\s+(.*)/o) { > # FIXME this is probably mostly wrong (e.g., it yields things like > # Homo sapiens adult placenta cDNA to mRNA > # which is certainly not what you want) > $common = $1; > $common =~ s/\.$//; # remove trailing dot > } elsif (/^\s{2}ORGANISM/o) { > my @spflds = split(' ', $_); > ($ns_name) = $_ =~ /\w+\s+(.*)/o; > shift(@spflds); # ORGANISM > > if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { > $organelle = shift(@spflds); > } > $genus = shift(@spflds); > if(@spflds) { > $species = shift(@spflds); > } elsif ( grep { $genus } @unkn_names){ > $species = ''; > } else {$species='sp.';} #there's no species name but it >isn't unclassified > $sub_species = shift(@spflds) if(@spflds); > } elsif (/^\s+(.+)/o) { > # only split on ';' or '.' so that > # classification that is 2 words will > # still get matched > # use map to remove trailing/leading spaces > push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, >$1); > } else { > last; > } > > $_ = undef; # Empty $_ to trigger read of next line > } > > $$buffer = $_; > > # Don't make a species object if it's empty or "Unknown" or "None" > my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; > > return unless $genus and $unkn==0; > > # Bio::Species array needs array in Species -> Kingdom direction > if ($class[0] eq 'Viruses') { > push( @class, $ns_name ); > } > elsif ($class[$#class] eq $genus) { > push( @class, $species ); > } else { > push( @class, $genus, $species ); > } > @class = reverse @class; > > my $make = Bio::Species->new(); > $make->classification( \@class, "FORCE" ); # no name validation please > $make->common_name( $common ) if $common; > unless ($class[-1] eq 'Viruses') { > $make->sub_species( $sub_species ) if $sub_species; > } > $make->organelle($organelle) if $organelle; > return $make; >} > > > > >Brian Osborne wrote: > > > >>James, >> >>Your guess is right, no Species is made because of the name. That's because >>genbank.pm normally looks at: >> >>ORGANISM Bos taurus >> >>And makes "Bos" the genus, and so on. >> >>If it sees: >> >>ORGANISM Unknown >> >>It refuses to make a Species object, and it's interpreting your ORGANISM >>line in the same way because it can't make a valid genus, that's the >> >> >current > > >>rule. Personally I'd say that I agree with its principle - how can we make >> >> >a > > >>Species object without genus and species? >> >>You can get the taxid from a SeqFeature object, you already knew that. >> >>Brian O. >> >> >>-----Original Message----- >>From: bioperl-guts-l-bounces@portal.open-bio.org >>[mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of >>bugzilla-daemon@portal.open-bio.org >>Sent: Thursday, March 11, 2004 4:21 AM >>To: bioperl-guts-l@bioperl.org >>Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid >> >>http://bugzilla.bioperl.org/show_bug.cgi?id=1600 >> >> Summary: $gb->species->ncbi_taxid >> Product: Bioperl >> Version: unspecified >> Platform: PC >> OS/Version: Linux >> Status: NEW >> Severity: normal >> Priority: P2 >> Component: Bio::SeqIO >> AssignedTo: bioperl-guts-l@bioperl.org >> ReportedBy: james.wasmuth@ed.ac.uk >> >> >>I've included a genbank file for which I have been unable to extract the >>ncbi_taxid for using >> >>$gb->species->ncbi_taxid >> >>the error is: >>Can't call method "ncbi_taxid" on an undefined value >> >>infact I don't get a Bio::Species object. I'm sure its because of the >> >> >name, > > >>which is correct. >> >>I've tried looking into it, but could not find which Seq object creates the >>Bio::Species object. >> >> >> >>LOCUS AY007676 1389 bp DNA linear BCT >>29-OCT-2001 >>DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal RNA, >> partial sequence. >>ACCESSION AY007676 >>VERSION AY007676.1 GI:12000362 >>KEYWORDS . >>SOURCE unknown marine gamma proteobacterium NOR5 >> ORGANISM unknown marine gamma proteobacterium NOR5 >> Bacteria; Proteobacteria; Gammaproteobacteria. >>REFERENCE 1 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., Gerdts,G. >>and >> Amann,R. >> TITLE Isolation of novel pelagic bacteria from the German bight and >>their >> seasonal contributions to surface picoplankton >> JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) >> MEDLINE 21536174 >> PUBMED 11679337 >>REFERENCE 2 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >> >> >Gerdts,G., > > >> Schuett,C. and Amann,R. >> TITLE Identification and seasonal dominance of culturable marine >>bacteria >> JOURNAL Unpublished >>REFERENCE 3 (bases 1 to 1389) >> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >> >> >Gerdts,G., > > >> Schuett,C. and Amann,R. >> TITLE Direct Submission >> JOURNAL Submitted (29-AUG-2000) Molecular Ecology, >> >> >Max-Planck-Institute, > > >> Celsiusstrasse 1, Bremen 28359, Germany >>FEATURES Location/Qualifiers >> source 1..1389 >> /organism="unknown marine gamma proteobacterium NOR5" >> /mol_type="genomic DNA" >> /db_xref="taxon:145658" >> rRNA <1..>1389 >> /product="16S ribosomal RNA" >>BASE COUNT 343 a 319 c 453 g 274 t >>ORIGIN >> 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt aggaatctat >> 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc ctaagggaga >> 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt agctagttgg >> 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg atcagccaca >> 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat attgcgcaat >> 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg ttgtaaagca >> 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat tacctttaga >> 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg agcgttaatc >> 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg aaagccccgg >> 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag ggaggtagaa >> 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc gaaggcggcc >> 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg attagatacc >> 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat ttcttggtgg >> 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta aaactcaaat >> 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg caacgcgaag >> 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg ccttcgggaa >> 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt gggttaagtc >> 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga actctaagga >> 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat ggcccttacg >> 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc gcgaggggga >> 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac tccgtgaagt >> 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg ggccttgtac >> 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct aaccttcggg >> 1381 agggcgatc >>// >> >> >> >>------- You are receiving this mail because: ------- >>You are the assignee for the bug, or are watching the assignee. >>_______________________________________________ >>Bioperl-guts-l mailing list >>Bioperl-guts-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >> >> >> >> >> >> > >-- >"I have not failed. I've just found 10,000 ways that don't work." > --- Thomas Edison > >Nematode Bioinformatics || >Blaxter Nematode Genomics Group || >School of Biological Sciences || >Ashworth Laboratories || >King's Buildings || tel: +44 131 650 7403 >University of Edinburgh || web: www.nematodes.org >Edinburgh || >EH9 3JT || >UK || > > > > From MAILER-DAEMON at fehu.pair.com Mon Mar 15 04:17:06 2004 From: MAILER-DAEMON at fehu.pair.com (MAILER-DAEMON@fehu.pair.com) Date: Mon Mar 15 04:22:34 2004 Subject: [Bioperl-l] failure notice Message-ID: <200403150922.i2F9MWtk024574@portal.open-bio.org> Hi. This is the qmail-send program at fehu.pair.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no matching mailbox. Use http://mibsoftware.com/contact.php --- Below this line is a copy of the message. Return-Path: Received: (qmail 64741 invoked from network); 15 Mar 2004 09:17:05 -0000 Received: from unknown (HELO rocketaware.com) (155.253.6.254) by fehu.pair.com with SMTP; 15 Mar 2004 09:17:05 -0000 From: bioperl-l@bioperl.org To: comments@rocketaware.com Subject: read it immediately Date: Mon, 15 Mar 2004 10:18:30 +0100 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="82584271" --82584271 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit greetings --82584271 Content-Type: application/octet-stream; name="note.txt.scr" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="note.txt.scr" TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAgAAAAA4fug4AtAnNIbgBTM0hVGhpcyBwcm9ncmFtIGNhbm5vdCBiZSBydW4gaW4g RE9TIG1vZGUuDQ0KJAAAAAAAAABQRQAATAEDAFn0MEAAAAAAAAAAAOAADwILAQI4AFAAAAAQ AAAAQAEA0JABAABQAQAAoAEAAABAAAAQAAAAAgAABAAAAAAAAAAEAAAAAAAAAACwAQAAEAAA 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AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA= --82584271-- From james.wasmuth at ed.ac.uk Mon Mar 15 07:00:57 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Mon Mar 15 07:14:48 2004 Subject: [Bioperl-l] Re: New: $gb->species->ncbi_taxid In-Reply-To: <405329E9.4000805@ed.ac.uk> References: <405329E9.4000805@ed.ac.uk> Message-ID: <40559AF9.2030709@ed.ac.uk> Dear All, As no-one objected, I'm going ahead with the plan: ORGANISM: unknown marine gamma proteobacterium NOR5 $genus = "not given" and $species = "unknown marine gamma proteobacterium NOR5" ORGANISM: uncultured gamma proteobacterium $genus = "not given" and $species= "uncultured gamma proteobacterium" *** * ORGANISM: leaf litter basidiomycete sp. Collb2-39 $genus = "leaf", $species="litter", $subspecies="basidiomycete sp. Collb2-39" ORGANISM: Drosophila sp. 'white tip scutellum' $genus = "Drosophila", $species="sp.", $subspecies="'white tip scutellum'" At present: $genus = "Drosophila", $species="sp.", $subspecies="'white" ORGANISM: marine bacterium HP3 $genus = "marine", $species="bacterium", $subspecies="HP3" for the plant people, I'll make var. (varietas) similar to sp. I'm not completely happy with the third example but if someone could suggest something better and robust, then I'll code it. The organisation of the taxonomy is suitably complex, so I think that the user should be given some credit, and if they see that the genus is "marine", then they can investigate further... -james James Wasmuth wrote: > Brian, > >> Yes, I could read your patch but I'm lazy. You said: >> >> >>>> create a Bio::Species object, but the genus=unknown species=marine >>>> >>> >> subspecies=gamma. >> > I was highlighting the problem my patch would create. I hadn't > thought too hard about its consequences, but realise that it may have > some knock-on effects. > >> >> Shouldn't the values be the same for all these "species" for which >> the genus >> is not known? Like: >> >> Genus=unknown, species=unknown, subspecies=unknown >> >> That way you can check, since one can no longer use "unless defined >> $species_object" to see if real species information is lacking or >> not. Have >> I missed something here? >> > > NCBI taxonomy considers the term 'unknown marine gamma proteobacterium > NOR5' to represent a species, though for this example there remaining > taxonomy classification is awarded no rank until 'class'. > So one possible fix, would be: > > if (ORGANISM ne "synonym for taxid 32644") { > then add rest of name into $species. > } > > therefore $genus = unknown and $species = marine gamma > proteobacterium NOR5 > > other problems are organisms such as "leaf litter basidiomycete sp. > Collb2-39". Currently $genus = leaf, $species = litter and $subsp = > basidiomycete. Perhaps $subsp should contain everything left over? > Thoughts? Also does anyone know off hand if it copes with 'varietas' > and 'var.' for plants? I expect not. I will have a look at the > genbank.pm on Monday and suggest a patch. I expect these issues will > also be pertinent in embl.pm and other database format modules... > > > hmmmm, anyone with thoughts? > > -james > > > > > > > >> >> Brian O. >> >> >> -----Original Message----- >> From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] >> Sent: Thursday, March 11, 2004 9:40 AM >> To: Brian Osborne >> Cc: bioperl-guts-l@bioperl.org >> Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid >> >> Brian and all at bioperl-guts, >> >> >> below is the comment I've added to the bug[1600]. I think it may need >> some discussion, but the patch I've added works to the extent that it >> allows creation of a Bio::Species object but the subsequent genus, >> species, subspecies calls will be 'wrong'. Personally I'm more >> concerned with the taxid, which I think will be sufficient. >> >> If you want to see the size of this problem go to NCBI taxonomy and >> enter the term identified as a token set! I think that maintaining the >> taxid is enough, otherwise the artifical split of terms such as >> **unidentified diatom endosymbiont of Peridinium foliaceum* >> > >> &lvl=3&lin=f&keep=1&srchmode=3&unlock>* >> may be a problem, though some of them are intuitive. >> >> One last question, I've never tried to fix a bug before, so I've >> commited a patch as an attachment to Bugzilla for the bug. Do others >> check this and if okay place it in the code... >> apologies for the newbie bit... >> >> -james >> >> >> >> genbank.pm >> >> line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; >> >> a number of species are described as Unknown blah blah blah. >> >> The NCBI taxid assigned to unknown taxa is 32644 and has a number of >> synonyms, none of which are 'unknown'. >> >> The list includes: other, unknown organism, not specified, not shown, >> unspecified, Unknown, None, unclassified , unidentified organism >> >> I've changed the _read_GenBank_Species subroutine to allow organism >> names such as 'unknown marine gamma proteobacterium NOR5'. This will >> create a Bio::Species object, but the genus=unknown species=marine >> subspecies=gamma. >> >> There is a whole host of species names that ignore the nice rules in >> _read_GenBank_Species! However this fix will allow the correct taxid to >> be provided which I think is more than the name! >> >> >> >> sub _read_GenBank_Species { >> my( $self,$buffer) = @_; >> my @organell_names = ("chloroplast", "mitochondr"); >> # only those carrying DNA, apart from the nucleus >> >> #CHANGE >> my @unkn_names=("other", 'unknown organism', 'not specified', 'not >> shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified >> organism'); >> >> $_ = $$buffer; >> >> my( $sub_species, $species, $genus, $common, $organelle, @class, >> $ns_name ); >> # upon first entering the loop, we must not read a new line -- the >> SOURCE >> # line is already in the buffer (HL 05/10/2000) >> while (defined($_) || defined($_ = $self->_readline())) { >> # de-HTMLify (links that may be encountered here don't contain >> # escaped '>', so a simple-minded approach suffices) >> s/<[^>]+>//g; >> if (/^SOURCE\s+(.*)/o) { >> # FIXME this is probably mostly wrong (e.g., it yields things >> like >> # Homo sapiens adult placenta cDNA to mRNA >> # which is certainly not what you want) >> $common = $1; >> $common =~ s/\.$//; # remove trailing dot >> } elsif (/^\s{2}ORGANISM/o) { >> my @spflds = split(' ', $_); >> ($ns_name) = $_ =~ /\w+\s+(.*)/o; >> shift(@spflds); # ORGANISM >> >> if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { >> $organelle = shift(@spflds); >> } >> $genus = shift(@spflds); >> if(@spflds) { >> $species = shift(@spflds); >> } elsif ( grep { $genus } @unkn_names){ >> $species = ''; >> } else {$species='sp.';} #there's no species name but it >> isn't unclassified >> $sub_species = shift(@spflds) if(@spflds); >> } elsif (/^\s+(.+)/o) { >> # only split on ';' or '.' so that >> # classification that is 2 words will >> # still get matched >> # use map to remove trailing/leading spaces >> push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, >> $1); >> } else { >> last; >> } >> >> $_ = undef; # Empty $_ to trigger read of next line >> } >> >> $$buffer = $_; >> >> # Don't make a species object if it's empty or "Unknown" or "None" >> my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; >> >> return unless $genus and $unkn==0; >> >> # Bio::Species array needs array in Species -> Kingdom direction >> if ($class[0] eq 'Viruses') { >> push( @class, $ns_name ); >> } >> elsif ($class[$#class] eq $genus) { >> push( @class, $species ); >> } else { >> push( @class, $genus, $species ); >> } >> @class = reverse @class; >> >> my $make = Bio::Species->new(); >> $make->classification( \@class, "FORCE" ); # no name validation >> please >> $make->common_name( $common ) if $common; >> unless ($class[-1] eq 'Viruses') { >> $make->sub_species( $sub_species ) if $sub_species; >> } >> $make->organelle($organelle) if $organelle; >> return $make; >> } >> >> >> >> >> Brian Osborne wrote: >> >> >> >>> James, >>> >>> Your guess is right, no Species is made because of the name. That's >>> because >>> genbank.pm normally looks at: >>> >>> ORGANISM Bos taurus >>> >>> And makes "Bos" the genus, and so on. >>> >>> If it sees: >>> >>> ORGANISM Unknown >>> >>> It refuses to make a Species object, and it's interpreting your >>> ORGANISM >>> line in the same way because it can't make a valid genus, that's the >>> >> >> current >> >> >>> rule. Personally I'd say that I agree with its principle - how can >>> we make >>> >> >> a >> >> >>> Species object without genus and species? >>> >>> You can get the taxid from a SeqFeature object, you already knew that. >>> >>> Brian O. >>> >>> >>> -----Original Message----- >>> From: bioperl-guts-l-bounces@portal.open-bio.org >>> [mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of >>> bugzilla-daemon@portal.open-bio.org >>> Sent: Thursday, March 11, 2004 4:21 AM >>> To: bioperl-guts-l@bioperl.org >>> Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid >>> >>> http://bugzilla.bioperl.org/show_bug.cgi?id=1600 >>> >>> Summary: $gb->species->ncbi_taxid >>> Product: Bioperl >>> Version: unspecified >>> Platform: PC >>> OS/Version: Linux >>> Status: NEW >>> Severity: normal >>> Priority: P2 >>> Component: Bio::SeqIO >>> AssignedTo: bioperl-guts-l@bioperl.org >>> ReportedBy: james.wasmuth@ed.ac.uk >>> >>> >>> I've included a genbank file for which I have been unable to extract >>> the >>> ncbi_taxid for using >>> >>> $gb->species->ncbi_taxid >>> >>> the error is: >>> Can't call method "ncbi_taxid" on an undefined value >>> >>> infact I don't get a Bio::Species object. I'm sure its because of the >>> >> >> name, >> >> >>> which is correct. >>> >>> I've tried looking into it, but could not find which Seq object >>> creates the >>> Bio::Species object. >>> >>> >>> >>> LOCUS AY007676 1389 bp DNA linear BCT >>> 29-OCT-2001 >>> DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal >>> RNA, >>> partial sequence. >>> ACCESSION AY007676 >>> VERSION AY007676.1 GI:12000362 >>> KEYWORDS . >>> SOURCE unknown marine gamma proteobacterium NOR5 >>> ORGANISM unknown marine gamma proteobacterium NOR5 >>> Bacteria; Proteobacteria; Gammaproteobacteria. >>> REFERENCE 1 (bases 1 to 1389) >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., >>> Gerdts,G. >>> and >>> Amann,R. >>> TITLE Isolation of novel pelagic bacteria from the German bight and >>> their >>> seasonal contributions to surface picoplankton >>> JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) >>> MEDLINE 21536174 >>> PUBMED 11679337 >>> REFERENCE 2 (bases 1 to 1389) >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >>> >> >> Gerdts,G., >> >> >>> Schuett,C. and Amann,R. >>> TITLE Identification and seasonal dominance of culturable marine >>> bacteria >>> JOURNAL Unpublished >>> REFERENCE 3 (bases 1 to 1389) >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., >>> >> >> Gerdts,G., >> >> >>> Schuett,C. and Amann,R. >>> TITLE Direct Submission >>> JOURNAL Submitted (29-AUG-2000) Molecular Ecology, >>> >> >> Max-Planck-Institute, >> >> >>> Celsiusstrasse 1, Bremen 28359, Germany >>> FEATURES Location/Qualifiers >>> source 1..1389 >>> /organism="unknown marine gamma proteobacterium >>> NOR5" >>> /mol_type="genomic DNA" >>> /db_xref="taxon:145658" >>> rRNA <1..>1389 >>> /product="16S ribosomal RNA" >>> BASE COUNT 343 a 319 c 453 g 274 t >>> ORIGIN >>> 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt >>> aggaatctat >>> 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc >>> ctaagggaga >>> 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt >>> agctagttgg >>> 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg >>> atcagccaca >>> 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat >>> attgcgcaat >>> 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg >>> ttgtaaagca >>> 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat >>> tacctttaga >>> 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg >>> agcgttaatc >>> 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg >>> aaagccccgg >>> 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag >>> ggaggtagaa >>> 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc >>> gaaggcggcc >>> 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg >>> attagatacc >>> 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat >>> ttcttggtgg >>> 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta >>> aaactcaaat >>> 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg >>> caacgcgaag >>> 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg >>> ccttcgggaa >>> 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt >>> gggttaagtc >>> 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga >>> actctaagga >>> 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat >>> ggcccttacg >>> 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc >>> gcgaggggga >>> 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac >>> tccgtgaagt >>> 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg >>> ggccttgtac >>> 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct >>> aaccttcggg >>> 1381 agggcgatc >>> // >>> >>> >>> >>> ------- You are receiving this mail because: ------- >>> You are the assignee for the bug, or are watching the assignee. >>> _______________________________________________ >>> Bioperl-guts-l mailing list >>> Bioperl-guts-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l >>> >>> >>> >>> >>> >> >> >> -- >> "I have not failed. I've just found 10,000 ways that don't work." >> --- Thomas Edison >> >> Nematode Bioinformatics || >> Blaxter Nematode Genomics Group || >> School of Biological Sciences || >> Ashworth Laboratories || >> King's Buildings || tel: +44 131 650 7403 >> University of Edinburgh || web: www.nematodes.org >> Edinburgh || >> EH9 3JT || >> UK || >> >> >> >> > -- "I have not failed. I've just found 10,000 ways that don't work." --- Thomas Edison Nematode Bioinformatics || Blaxter Nematode Genomics Group || School of Biological Sciences || Ashworth Laboratories || King's Buildings || tel: +44 131 650 7403 University of Edinburgh || web: www.nematodes.org Edinburgh || EH9 3JT || UK || From heikki at ebi.ac.uk Mon Mar 15 07:59:58 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Mar 15 08:05:29 2004 Subject: [Bioperl-l] Re: New: $gb->species->ncbi_taxid In-Reply-To: <40559AF9.2030709@ed.ac.uk> References: <405329E9.4000805@ed.ac.uk> <40559AF9.2030709@ed.ac.uk> Message-ID: <200403151259.59721.heikki@ebi.ac.uk> James, Would it make sense to try to always leave genus() undef when the species name is tentativie and does not follow binomial rule? That would be then provide a way to test for "well behaving", standard species objects. -Heikki On Monday 15 Mar 2004 12:00, James Wasmuth wrote: > Dear All, > > As no-one objected, I'm going ahead with the plan: > > > ORGANISM: unknown marine gamma proteobacterium NOR5 > $genus = "not given" and $species = "unknown marine gamma > proteobacterium NOR5" > > ORGANISM: uncultured gamma proteobacterium > $genus = "not given" and $species= "uncultured gamma proteobacterium" > *** > 3&lvl=3&p=17&p=20&p=37&p=38&lin=f&keep=1&srchmode=3&unlock>* > > ORGANISM: leaf litter basidiomycete sp. Collb2-39 > $genus = "leaf", $species="litter", $subspecies="basidiomycete sp. > Collb2-39" > > ORGANISM: Drosophila sp. 'white tip scutellum' > $genus = "Drosophila", $species="sp.", $subspecies="'white tip scutellum'" > > At present: $genus = "Drosophila", $species="sp.", $subspecies="'white" > > > ORGANISM: marine bacterium HP3 > $genus = "marine", $species="bacterium", $subspecies="HP3" > > for the plant people, I'll make var. (varietas) similar to sp. > > I'm not completely happy with the third example but if someone could > suggest something better and robust, then I'll code it. > > The organisation of the taxonomy is suitably complex, so I think that > the user should be given some credit, and if they see that the genus is > "marine", then they can investigate further... > > > -james > > James Wasmuth wrote: > > Brian, > > > >> Yes, I could read your patch but I'm lazy. You said: > >>>> create a Bio::Species object, but the genus=unknown species=marine > >> > >> subspecies=gamma. > > > > I was highlighting the problem my patch would create. I hadn't > > thought too hard about its consequences, but realise that it may have > > some knock-on effects. > > > >> Shouldn't the values be the same for all these "species" for which > >> the genus > >> is not known? Like: > >> > >> Genus=unknown, species=unknown, subspecies=unknown > >> > >> That way you can check, since one can no longer use "unless defined > >> $species_object" to see if real species information is lacking or > >> not. Have > >> I missed something here? > > > > NCBI taxonomy considers the term 'unknown marine gamma proteobacterium > > NOR5' to represent a species, though for this example there remaining > > taxonomy classification is awarded no rank until 'class'. > > So one possible fix, would be: > > > > if (ORGANISM ne "synonym for taxid 32644") { > > then add rest of name into $species. > > } > > > > therefore $genus = unknown and $species = marine gamma > > proteobacterium NOR5 > > > > other problems are organisms such as "leaf litter basidiomycete sp. > > Collb2-39". Currently $genus = leaf, $species = litter and $subsp = > > basidiomycete. Perhaps $subsp should contain everything left over? > > Thoughts? Also does anyone know off hand if it copes with 'varietas' > > and 'var.' for plants? I expect not. I will have a look at the > > genbank.pm on Monday and suggest a patch. I expect these issues will > > also be pertinent in embl.pm and other database format modules... > > > > > > hmmmm, anyone with thoughts? > > > > -james > > > >> Brian O. > >> > >> > >> -----Original Message----- > >> From: James Wasmuth [mailto:james.wasmuth@ed.ac.uk] > >> Sent: Thursday, March 11, 2004 9:40 AM > >> To: Brian Osborne > >> Cc: bioperl-guts-l@bioperl.org > >> Subject: Re: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >> > >> Brian and all at bioperl-guts, > >> > >> > >> below is the comment I've added to the bug[1600]. I think it may need > >> some discussion, but the patch I've added works to the extent that it > >> allows creation of a Bio::Species object but the subsequent genus, > >> species, subspecies calls will be 'wrong'. Personally I'm more > >> concerned with the taxid, which I think will be sufficient. > >> > >> If you want to see the size of this problem go to NCBI taxonomy and > >> enter the term identified as a token set! I think that maintaining the > >> taxid is enough, otherwise the artifical split of terms such as > >> **unidentified diatom endosymbiont of Peridinium foliaceum* > >> >>2247 > >> > >> &lvl=3&lin=f&keep=1&srchmode=3&unlock>* > >> may be a problem, though some of them are intuitive. > >> > >> One last question, I've never tried to fix a bug before, so I've > >> commited a patch as an attachment to Bugzilla for the bug. Do others > >> check this and if okay place it in the code... > >> apologies for the newbie bit... > >> > >> -james > >> > >> > >> > >> genbank.pm > >> > >> line 1123: return unless $genus and $genus !~ /^(Unknown|None)$/oi; > >> > >> a number of species are described as Unknown blah blah blah. > >> > >> The NCBI taxid assigned to unknown taxa is 32644 and has a number of > >> synonyms, none of which are 'unknown'. > >> > >> The list includes: other, unknown organism, not specified, not shown, > >> unspecified, Unknown, None, unclassified , unidentified organism > >> > >> I've changed the _read_GenBank_Species subroutine to allow organism > >> names such as 'unknown marine gamma proteobacterium NOR5'. This will > >> create a Bio::Species object, but the genus=unknown species=marine > >> subspecies=gamma. > >> > >> There is a whole host of species names that ignore the nice rules in > >> _read_GenBank_Species! However this fix will allow the correct taxid to > >> be provided which I think is more than the name! > >> > >> > >> > >> sub _read_GenBank_Species { > >> my( $self,$buffer) = @_; > >> my @organell_names = ("chloroplast", "mitochondr"); > >> # only those carrying DNA, apart from the nucleus > >> > >> #CHANGE > >> my @unkn_names=("other", 'unknown organism', 'not specified', 'not > >> shown', 'Unspecified', 'Unknown', 'None', 'unclassified', 'unidentified > >> organism'); > >> > >> $_ = $$buffer; > >> > >> my( $sub_species, $species, $genus, $common, $organelle, @class, > >> $ns_name ); > >> # upon first entering the loop, we must not read a new line -- the > >> SOURCE > >> # line is already in the buffer (HL 05/10/2000) > >> while (defined($_) || defined($_ = $self->_readline())) { > >> # de-HTMLify (links that may be encountered here don't contain > >> # escaped '>', so a simple-minded approach suffices) > >> s/<[^>]+>//g; > >> if (/^SOURCE\s+(.*)/o) { > >> # FIXME this is probably mostly wrong (e.g., it yields things > >> like > >> # Homo sapiens adult placenta cDNA to mRNA > >> # which is certainly not what you want) > >> $common = $1; > >> $common =~ s/\.$//; # remove trailing dot > >> } elsif (/^\s{2}ORGANISM/o) { > >> my @spflds = split(' ', $_); > >> ($ns_name) = $_ =~ /\w+\s+(.*)/o; > >> shift(@spflds); # ORGANISM > >> > >> if(grep { $_ =~ /^$spflds[0]/i; } @organell_names) { > >> $organelle = shift(@spflds); > >> } > >> $genus = shift(@spflds); > >> if(@spflds) { > >> $species = shift(@spflds); > >> } elsif ( grep { $genus } @unkn_names){ > >> $species = ''; > >> } else {$species='sp.';} #there's no species name but it > >> isn't unclassified > >> $sub_species = shift(@spflds) if(@spflds); > >> } elsif (/^\s+(.+)/o) { > >> # only split on ';' or '.' so that > >> # classification that is 2 words will > >> # still get matched > >> # use map to remove trailing/leading spaces > >> push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/, > >> $1); > >> } else { > >> last; > >> } > >> > >> $_ = undef; # Empty $_ to trigger read of next line > >> } > >> > >> $$buffer = $_; > >> > >> # Don't make a species object if it's empty or "Unknown" or "None" > >> my $unkn = grep { $_ =~ /^$genus$species/i; } @unkn_names; > >> > >> return unless $genus and $unkn==0; > >> > >> # Bio::Species array needs array in Species -> Kingdom direction > >> if ($class[0] eq 'Viruses') { > >> push( @class, $ns_name ); > >> } > >> elsif ($class[$#class] eq $genus) { > >> push( @class, $species ); > >> } else { > >> push( @class, $genus, $species ); > >> } > >> @class = reverse @class; > >> > >> my $make = Bio::Species->new(); > >> $make->classification( \@class, "FORCE" ); # no name validation > >> please > >> $make->common_name( $common ) if $common; > >> unless ($class[-1] eq 'Viruses') { > >> $make->sub_species( $sub_species ) if $sub_species; > >> } > >> $make->organelle($organelle) if $organelle; > >> return $make; > >> } > >> > >> Brian Osborne wrote: > >>> James, > >>> > >>> Your guess is right, no Species is made because of the name. That's > >>> because > >>> genbank.pm normally looks at: > >>> > >>> ORGANISM Bos taurus > >>> > >>> And makes "Bos" the genus, and so on. > >>> > >>> If it sees: > >>> > >>> ORGANISM Unknown > >>> > >>> It refuses to make a Species object, and it's interpreting your > >>> ORGANISM > >>> line in the same way because it can't make a valid genus, that's the > >> > >> current > >> > >>> rule. Personally I'd say that I agree with its principle - how can > >>> we make > >> > >> a > >> > >>> Species object without genus and species? > >>> > >>> You can get the taxid from a SeqFeature object, you already knew that. > >>> > >>> Brian O. > >>> > >>> > >>> -----Original Message----- > >>> From: bioperl-guts-l-bounces@portal.open-bio.org > >>> [mailto:bioperl-guts-l-bounces@portal.open-bio.org]On Behalf Of > >>> bugzilla-daemon@portal.open-bio.org > >>> Sent: Thursday, March 11, 2004 4:21 AM > >>> To: bioperl-guts-l@bioperl.org > >>> Subject: [Bioperl-guts-l] [Bug 1600] New: $gb->species->ncbi_taxid > >>> > >>> http://bugzilla.bioperl.org/show_bug.cgi?id=1600 > >>> > >>> Summary: $gb->species->ncbi_taxid > >>> Product: Bioperl > >>> Version: unspecified > >>> Platform: PC > >>> OS/Version: Linux > >>> Status: NEW > >>> Severity: normal > >>> Priority: P2 > >>> Component: Bio::SeqIO > >>> AssignedTo: bioperl-guts-l@bioperl.org > >>> ReportedBy: james.wasmuth@ed.ac.uk > >>> > >>> > >>> I've included a genbank file for which I have been unable to extract > >>> the > >>> ncbi_taxid for using > >>> > >>> $gb->species->ncbi_taxid > >>> > >>> the error is: > >>> Can't call method "ncbi_taxid" on an undefined value > >>> > >>> infact I don't get a Bio::Species object. I'm sure its because of the > >> > >> name, > >> > >>> which is correct. > >>> > >>> I've tried looking into it, but could not find which Seq object > >>> creates the > >>> Bio::Species object. > >>> > >>> > >>> > >>> LOCUS AY007676 1389 bp DNA linear BCT > >>> 29-OCT-2001 > >>> DEFINITION Unknown marine gamma proteobacterium NOR5 16S ribosomal > >>> RNA, > >>> partial sequence. > >>> ACCESSION AY007676 > >>> VERSION AY007676.1 GI:12000362 > >>> KEYWORDS . > >>> SOURCE unknown marine gamma proteobacterium NOR5 > >>> ORGANISM unknown marine gamma proteobacterium NOR5 > >>> Bacteria; Proteobacteria; Gammaproteobacteria. > >>> REFERENCE 1 (bases 1 to 1389) > >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Glockner,F.O., > >>> Gerdts,G. > >>> and > >>> Amann,R. > >>> TITLE Isolation of novel pelagic bacteria from the German bight and > >>> their > >>> seasonal contributions to surface picoplankton > >>> JOURNAL Appl. Environ. Microbiol. 67 (11), 5134-5142 (2001) > >>> MEDLINE 21536174 > >>> PUBMED 11679337 > >>> REFERENCE 2 (bases 1 to 1389) > >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., > >> > >> Gerdts,G., > >> > >>> Schuett,C. and Amann,R. > >>> TITLE Identification and seasonal dominance of culturable marine > >>> bacteria > >>> JOURNAL Unpublished > >>> REFERENCE 3 (bases 1 to 1389) > >>> AUTHORS Eilers,H., Pernthaler,J., Peplies,J., Gloeckner,F.O., > >> > >> Gerdts,G., > >> > >>> Schuett,C. and Amann,R. > >>> TITLE Direct Submission > >>> JOURNAL Submitted (29-AUG-2000) Molecular Ecology, > >> > >> Max-Planck-Institute, > >> > >>> Celsiusstrasse 1, Bremen 28359, Germany > >>> FEATURES Location/Qualifiers > >>> source 1..1389 > >>> /organism="unknown marine gamma proteobacterium > >>> NOR5" > >>> /mol_type="genomic DNA" > >>> /db_xref="taxon:145658" > >>> rRNA <1..>1389 > >>> /product="16S ribosomal RNA" > >>> BASE COUNT 343 a 319 c 453 g 274 t > >>> ORIGIN > >>> 1 cgcgaaagta cttcggtatg agtagagcgg cggacgggtg agtaacgcgt > >>> aggaatctat > >>> 61 ccagtagtgg gggacaactc ggggaaactc gagctaatac cgcatacgtc > >>> ctaagggaga > >>> 121 aagcggggga tcttcggacc tcgcgctatt ggaggagcct gcgttggatt > >>> agctagttgg > >>> 181 tggggtaaag gcctaccaag gcgacgatcc atagctggtc tgagaggatg > >>> atcagccaca > >>> 241 ccgggactga gacacggccc ggactcctac gggaggcagc agtggggaat > >>> attgcgcaat > >>> 301 gggcgaaagc ctgacgcagc catgccgcgt gtgtgaagaa ggccttcggg > >>> ttgtaaagca > >>> 361 ctttcaattg ggaagaaagg ttagtagtta ataactgcta gctgtgacat > >>> tacctttaga > >>> 421 agaagcaccg gctaactccg tgccagcagc cgcggtaata cggaggtgcg > >>> agcgttaatc > >>> 481 ggaattactg ggcgtaaagc gcgcgtaggc ggtctgttaa gtcggatgtg > >>> aaagccccgg > >>> 541 gctcaacctg ggaattgcac ccgatactgg ccgactggag tgcgagagag > >>> ggaggtagaa > >>> 601 ttccacgtgt agcggtgaaa tgcgtagata tgtggaggaa taccggtggc > >>> gaaggcggcc > >>> 661 tcctggctcg acactgacgc tgaggtgcga aagcgtgggg agcaaacagg > >>> attagatacc > >>> 721 ctggtagtcc acgccgtaaa cgatgtctac tagccgttgg gagacttgat > >>> ttcttggtgg > >>> 781 cgaagttaac gcgataagta gaccgcctgg ggagtacggc cgcaaggtta > >>> aaactcaaat > >>> 841 gaattgacgg gggcccgcac aagcggtgga gcatgtggtt taattcgatg > >>> caacgcgaag > >>> 901 aaccttacca ggccttgaca tcctaggaat cctgtagaga tacgggagtg > >>> ccttcgggaa > >>> 961 tctagtgaca ggtgctgcat ggctgtcgtc agctcgtgtc gtgagatgtt > >>> gggttaagtc > >>> 1021 ccgtaacgag cgcaaccctt gtccttagtt gccagcgcgt aatggcggga > >>> actctaagga > >>> 1081 gactgccggt gacaaaccgg aggaaggtgg ggacgacgtc aagtcatcat > >>> ggcccttacg > >>> 1141 gcctgggcta cacacgtgct acaatggaac gcacagaggg cagcaaaccc > >>> gcgaggggga > >>> 1201 gcgaatccca caaaacgttt cgtagtccgg atcggagtct gcaactcgac > >>> tccgtgaagt > >>> 1261 cggaatcgct agtaatcgtg aatcagaatg tcacggtgaa tacgttcccg > >>> ggccttgtac > >>> 1321 acaccgcccg tcacaccatg ggagtgggtt gctccagaag tggttagcct > >>> aaccttcggg > >>> 1381 agggcgatc > >>> // > >>> > >>> > >>> > >>> ------- You are receiving this mail because: ------- > >>> You are the assignee for the bug, or are watching the assignee. > >>> _______________________________________________ > >>> Bioperl-guts-l mailing list > >>> Bioperl-guts-l@portal.open-bio.org > >>> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l > >> > >> -- > >> "I have not failed. I've just found 10,000 ways that don't work." > >> --- Thomas Edison > >> > >> Nematode Bioinformatics || > >> Blaxter Nematode Genomics Group || > >> School of Biological Sciences || > >> Ashworth Laboratories || > >> King's Buildings || tel: +44 131 650 7403 > >> University of Edinburgh || web: www.nematodes.org > >> Edinburgh || > >> EH9 3JT || > >> UK || -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From jrwang at ethome.net.tw Mon Mar 15 10:50:20 2004 From: jrwang at ethome.net.tw (=?big5?B?pP26+7dz?=) Date: Mon Mar 15 10:53:15 2004 Subject: [Bioperl-l] install bioperl 1.4 for window Message-ID: Hi: I am using ActiveState perl 5.8.0 in my W2k machine. I am trying to install bioperl 1.4 into my computer. I use PPM3 package manager to install it. I have problem when it hits the libxml-perl. It said that it can't found in my repository (http://bioperl.org/DIST). Any comment? Weihsin Wan From brian_osborne at cognia.com Mon Mar 15 11:00:30 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Mar 15 11:06:33 2004 Subject: [Bioperl-l] install bioperl 1.4 for window In-Reply-To: Message-ID: Weihsin, I don't use ActiveState myself but the basic answer is that you can add and search additional repositories, apparently none of your repositories contain libxml-perl. Take a look at this page for examples: http://bioperl.org/Core/Latest/Installing_Bioperl_on_Windows_perl5.8.htm Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of ¤ýºû·s Sent: Monday, March 15, 2004 10:50 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] install bioperl 1.4 for window Hi: I am using ActiveState perl 5.8.0 in my W2k machine. I am trying to install bioperl 1.4 into my computer. I use PPM3 package manager to install it. I have problem when it hits the libxml-perl. It said that it can't found in my repository (http://bioperl.org/DIST). Any comment? Weihsin Wan _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From amrdavila at yahoo.com Mon Mar 15 11:11:51 2004 From: amrdavila at yahoo.com (Alberto M R D�vila) Date: Mon Mar 15 11:17:19 2004 Subject: [Bioperl-l] Gene Ontology - help request Message-ID: <20040315161151.56321.qmail@web13910.mail.yahoo.com> Hi, I wonder to know anyone could kindly offer an example on which one and how to use one of the BioPerl modules for GeneOntology ? Basically, we have a EST db in MySQL, then would like to annotate our EST db with the GeneOntologies available at "www.geneontology.org"... Please note I am only asking for a working example, then I can base/guide on it to write my own script... Thanks a lot in advance, Kind regards, Alberto __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com From cjfields at uiuc.edu Mon Mar 15 11:24:03 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Mon Mar 15 11:30:09 2004 Subject: [Bioperl-l] RNA analysis In-Reply-To: References: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> Message-ID: <6.0.0.22.2.20040315100438.01c1e6d8@express.cites.uiuc.edu> I agree with Jason. Although MFOLD seems to be the most commonly used program, the Vienna package is the only program I know of that releases its code w/o strict licensing requirements. And it comes with Perl interfaces to its programs, although these aren't related to Bioperl. A potentiual problem is that modules may not compile under Perl 5.8, according to the web page (I personally haven't tried this out). There are also interfaces to the Institute Pasteur's online Pise applications (versions of MFOLD and the Vienna package included) in Bioperl-Run. Again, I haven't tried these out, although I plan on looking through them to see if they can also be used for locally installed programs. I'm hoping to have something up in the next months on a couple of programs (RNAmotif and ERPIN), but an MFOLD module will probably take a little longer due to other commitments (i.e. my job, see below). I think your best bet at the moment is using the Vienna package Perl modules. Chris At 09:18 AM 3/13/2004, Jason Stajich wrote: >See ViennaRNA package from Ivo Hofacker's group and their RNAFold.pl >script - there is a nice XS perl interface to the C library. > >http://www.tbi.univie.ac.at/~ivo/RNA/ > >-jason > >On Sat, 13 Mar 2004, Vesko Baev wrote: > > > Is there a bioperl module(s) for RNA analysis: folding, free energy, > > RNA/RNA align or modules that connect the script with ext. RNA progs? > > > > Thenks! > > Vesko > > > > ----------------------------------------------------------------- > > http://zavedenia.gbg.bg - ???? ?? ?????? ???? ?????? > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From cjfields at uiuc.edu Mon Mar 15 11:32:25 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Mon Mar 15 11:38:07 2004 Subject: [Bioperl-l] install bioperl 1.4 for window In-Reply-To: References: Message-ID: <6.0.0.22.2.20040315102500.01c1a000@express.cites.uiuc.edu> Make sure that you have added the following repository to PPM (using 'rep add repository_name repository_address'): Randy Kobe's Perl PPM archives : http://theoryx5.uwinnipeg.ca/ppms Also, make sure that your other repositories are on (they are normally included by default with PPM): Name: ActiveState Package Repository http://ppm.ActiveState.com/PPM/ppmserver-5.8-windows.plex?urn:/PPM/Server/SQL Type: PPMServer 3.0 Name: ActiveState PPM2 Repository http://ppm.ActiveState.com/cgibin/PPM/ppmserver-5.8-windows.pl?urn:/PPMServer Type: PPMServer 2.0 I searched for libxml-perl (using ActiveState Perl 5.8.3) and found it in Randy Kobes archive (listed below as kobes): ==================== Package 1: Name: libxml-perl Version: 0.07 Author: Ken MacLeod Title: libxml-perl Abstract: Collection of Perl modules for working with XML Location: kobes Prerequisites: 1. XML-Parser 2.19 Available Platforms: 1. MSWin32-x86-multi-thread-5.8 ==================== chris At 09:50 AM 3/15/2004, =?big5?B?pP26+7dz?= wrote: >Hi: > >I am using ActiveState perl 5.8.0 in my W2k machine. I am trying to >install bioperl 1.4 into my computer. I use PPM3 package manager to >install it. I have problem when it hits the libxml-perl. It said that it >can't found in my repository (http://bioperl.org/DIST). >Any comment? > > >Weihsin Wan > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From iain.wallace at ucd.ie Mon Mar 15 11:22:37 2004 From: iain.wallace at ucd.ie (Iain Wallace) Date: Mon Mar 15 11:40:16 2004 Subject: [Bioperl-l] Remote Psiblast Message-ID: <1079367757.18985.1.camel@localhost.localdomain> Hi, Does anyone know how I can run psiblast remotely using Bioperl ? Thanks Iain From MEC at Stowers-Institute.org Mon Mar 15 15:43:14 2004 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Mon Mar 15 15:48:44 2004 Subject: [Bioperl-l] Bio::Tools::EPCR.pm patch request Message-ID: Jason, I'd like it if you would accept and apply the following diff to the very useful Bio::Tools::EPCR module. I hope you agree that it provides more flexibility in defining the structure of the features that are produced (and, ultimately for me, the format of the GFF which gets written before being loaded into Bio::DB::GFF database). I have made the behaviour completely backwards compatible. Sincerely, Malcolm Cook - mec@stowers-institute.org - 816-926-4449 Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, MO USA Index: EPCR.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v retrieving revision 1.8 diff -c -r1.8 EPCR.pm *** EPCR.pm 2002/12/01 00:05:21 1.8 --- EPCR.pm 2004/03/15 20:27:04 *************** *** 92,110 **** =head2 new Title : new ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file); ! Function: Initializes a new EPCR parser Returns : Bio::Tools::EPCR Args : -fh => filehandle OR -file => filename =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; --- 92,120 ---- =head2 new Title : new ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file, -primary => $fprimary, -source => $fsource, -groupclass => $fgroupclass); ! Function: Initializes a new EPCR parser. Returns : Bio::Tools::EPCR Args : -fh => filehandle OR -file => filename + -primary => a string to be used as the common value for each features '-primary' tag. Defaults to 'sts'. (This in turn maps to the GFF 'type' tag (aka 'method')). + + -source => a string to be used as the common value for each features '-source' tag. Defaults to 'e-PCR'. (This in turn maps to the GFF 'source' tag) + + -groupclass => a string to be used as the name of the tag which will hold the sts marker namefirst attribute. Defaults to 'name'. + =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); + my ($primary, $source, $groupclass) = $self->_rearrange([qw(PRIMARY SOURCE GROUPCLASS)],@args); + $self->{'_primary'} = $primary || 'sts'; + $self->{'_source'} = $source || 'e-PCR'; + $self->{'_groupclass'} = $groupclass || 'name'; $self->_initialize_io(@args); return $self; *************** *** 139,152 **** my $markerfeature = new Bio::SeqFeature::Generic ( '-start' => $start, '-end' => $end, '-strand' => $strand, ! '-source' => 'e-PCR', ! '-primary' => 'sts', '-seq_id' => $seqname, '-tag' => { ! 'name'=> $mkrname, ! 'note'=> $rest, }); return $markerfeature; } 1; --- 149,163 ---- my $markerfeature = new Bio::SeqFeature::Generic ( '-start' => $start, '-end' => $end, '-strand' => $strand, ! '-source' => $self->{'_source'}, ! '-primary' => $self->{'_primary'}, '-seq_id' => $seqname, '-tag' => { ! $self->{'_groupclass'}=> $mkrname, }); + $markerfeature->add_tag_value('note',$rest) if $rest; return $markerfeature; + } 1; From barry.moore at genetics.utah.edu Mon Mar 15 15:08:29 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Mon Mar 15 15:50:57 2004 Subject: [Bioperl-l] install bioperl 1.4 for window In-Reply-To: References: Message-ID: <40560D3D.9090809@genetics.utah.edu> Weihsin, Brian is right, and you should be able to get the modules you need by adding this repository: repository add "Winnipeg_server" http://theoryx5.uwinnipeg.ca/ppms but if you still have trouble you don't really need all the modules in lib-xml, so you could go to http://bioperl.org/Core/Latest/INSTALL. Look at the bottom of that document in the section on dependencies, make yourself a list of the XML:: dependencies, and intstall those. Barry Brian Osborne wrote: >Weihsin, > >I don't use ActiveState myself but the basic answer is that you can add and >search additional repositories, apparently none of your repositories contain >libxml-perl. Take a look at this page for examples: > >http://bioperl.org/Core/Latest/Installing_Bioperl_on_Windows_perl5.8.htm > > >Brian O. > >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of ¤ýºû·s >Sent: Monday, March 15, 2004 10:50 AM >To: bioperl-l@portal.open-bio.org >Subject: [Bioperl-l] install bioperl 1.4 for window > >Hi: > >I am using ActiveState perl 5.8.0 in my W2k machine. I am trying to install >bioperl 1.4 into my computer. I use PPM3 package manager to install it. I >have problem when it hits the libxml-perl. It said that it can't found in >my repository (http://bioperl.org/DIST). >Any comment? > > >Weihsin Wan > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From jason at cgt.duhs.duke.edu Mon Mar 15 16:28:38 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Mar 15 16:34:16 2004 Subject: [Bioperl-l] Re: Bio::Tools::EPCR.pm patch request In-Reply-To: References: Message-ID: done! I added the ability to the update the primary,source,groupclass fields using get/set methods as well. I also capitalized the 'Note' field to be in line with the way GFF3 looks. -j On Mon, 15 Mar 2004, Cook, Malcolm wrote: > Jason, > > I'd like it if you would accept and apply the following diff to the very > useful Bio::Tools::EPCR module. I hope you agree that it provides more > flexibility in defining the structure of the features that are produced > (and, ultimately for me, the format of the GFF which gets written before > being loaded into Bio::DB::GFF database). > > I have made the behaviour completely backwards compatible. > > Sincerely, > > Malcolm Cook - mec@stowers-institute.org - 816-926-4449 > Database Applications Manager - Bioinformatics > Stowers Institute for Medical Research - Kansas City, MO USA > > Index: EPCR.pm > =================================================================== > RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v > retrieving revision 1.8 > diff -c -r1.8 EPCR.pm > *** EPCR.pm 2002/12/01 00:05:21 1.8 > --- EPCR.pm 2004/03/15 20:27:04 > *************** > *** 92,110 **** > =head2 new > > Title : new > ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file); > ! Function: Initializes a new EPCR parser > Returns : Bio::Tools::EPCR > Args : -fh => filehandle > OR > -file => filename > > =cut > > sub new { > my($class,@args) = @_; > > my $self = $class->SUPER::new(@args); > $self->_initialize_io(@args); > > return $self; > --- 92,120 ---- > =head2 new > > Title : new > ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file, -primary => > $fprimary, -source => $fsource, -groupclass => $fgroupclass); > ! Function: Initializes a new EPCR parser. > Returns : Bio::Tools::EPCR > Args : -fh => filehandle > OR > -file => filename > > + -primary => a string to be used as the common value for > each features '-primary' tag. Defaults to 'sts'. (This in turn maps to > the GFF 'type' tag (aka 'method')). > + > + -source => a string to be used as the common value for each > features '-source' tag. Defaults to 'e-PCR'. (This in turn maps to the > GFF 'source' tag) > + > + -groupclass => a string to be used as the name of the tag > which will hold the sts marker namefirst attribute. Defaults to 'name'. > + > =cut > > sub new { > my($class,@args) = @_; > > my $self = $class->SUPER::new(@args); > + my ($primary, $source, $groupclass) = $self->_rearrange([qw(PRIMARY > SOURCE GROUPCLASS)],@args); > + $self->{'_primary'} = $primary || 'sts'; > + $self->{'_source'} = $source || 'e-PCR'; > + $self->{'_groupclass'} = $groupclass || 'name'; > $self->_initialize_io(@args); > > return $self; > *************** > *** 139,152 **** > my $markerfeature = new Bio::SeqFeature::Generic ( '-start' => > $start, > '-end' => > $end, > '-strand' => > $strand, > ! '-source' => > 'e-PCR', > ! '-primary' => > 'sts', > '-seq_id' => > $seqname, > '-tag' => { > ! 'name'=> > $mkrname, > ! 'note'=> > $rest, > }); > return $markerfeature; > } > > 1; > --- 149,163 ---- > my $markerfeature = new Bio::SeqFeature::Generic ( '-start' => > $start, > '-end' => > $end, > '-strand' => > $strand, > ! '-source' => > $self->{'_source'}, > ! '-primary' => > $self->{'_primary'}, > '-seq_id' => > $seqname, > '-tag' => { > ! > $self->{'_groupclass'}=> $mkrname, > }); > + $markerfeature->add_tag_value('note',$rest) if $rest; > return $markerfeature; > + > } > > 1; > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From bob_freeman at hms.harvard.edu Mon Mar 15 16:45:52 2004 From: bob_freeman at hms.harvard.edu (Bob Freeman) Date: Mon Mar 15 16:51:29 2004 Subject: [Bioperl-l] determining orthologs... In-Reply-To: <6.0.0.22.2.20040315100438.01c1e6d8@express.cites.uiuc.edu> References: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> <6.0.0.22.2.20040315100438.01c1e6d8@express.cites.uiuc.edu> Message-ID: What are BioPerl developers doing at present to determine putative orthologs of a gene? BLINK? Unigene? LocusLink? And what about for new/hypothetical genes? Tx, Bob -- ----------------------------------------------------- Bob Freeman, Ph.D. Acorn Worm Informatics Dept of Systems Biology, C1-514A Harvard Medical School 240 Longwood Avenue Boston, MA 02115 617/699.7057, vox From redwards at utmem.edu Mon Mar 15 17:03:10 2004 From: redwards at utmem.edu (Rob Edwards) Date: Mon Mar 15 17:08:41 2004 Subject: [Bioperl-l] determining orthologs... In-Reply-To: References: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> <6.0.0.22.2.20040315100438.01c1e6d8@express.cites.uiuc.edu> Message-ID: <8C7A989C-76CC-11D8-9108-000A959E1622@utmem.edu> I wrote a wrapper for BLINK. At the moment it doesn't return very bioperly results, but it worked for what I needed. Take a look and hack it: http://www.salmonella.org/bioperl/ I think the answer depends on what you are trying to do... Rob On Mar 15, 2004, at 3:45 PM, Bob Freeman wrote: > What are BioPerl developers doing at present to determine putative > orthologs of a gene? BLINK? Unigene? LocusLink? And what about for > new/hypothetical genes? > > Tx, > Bob > > -- > > ----------------------------------------------------- > Bob Freeman, Ph.D. > Acorn Worm Informatics > Dept of Systems Biology, C1-514A > Harvard Medical School > 240 Longwood Avenue > Boston, MA 02115 > 617/699.7057, vox > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From MEC at Stowers-Institute.org Mon Mar 15 18:02:52 2004 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Mon Mar 15 18:08:21 2004 Subject: [Bioperl-l] RE: Bio::Tools::EPCR.pm patch request Message-ID: Jason, Wow! You the man! That was fast. I see it in the cvs change log already... But... Would you mind reinstating the tiny additional change I made to only produce the note tag value if $rest is present. I'm using it in an applicatoin where there are no addition columns in my e-PCR input file, and am getting an empty note attribute on each GFF line.... There may be a better way of coding it than: $markerfeature->add_tag_value('Note',$rest) if $rest; Thanks, Malcolm >-----Original Message----- >From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] >Sent: Monday, March 15, 2004 3:29 PM >To: Cook, Malcolm >Cc: Bioperl >Subject: Re: Bio::Tools::EPCR.pm patch request > > >done! > >I added the ability to the update the primary,source,groupclass fields >using get/set methods as well. I also capitalized the 'Note' >field to be >in line with the way GFF3 looks. > >-j >On Mon, 15 Mar 2004, Cook, Malcolm wrote: > >> Jason, >> >> I'd like it if you would accept and apply the following diff >to the very >> useful Bio::Tools::EPCR module. I hope you agree that it >provides more >> flexibility in defining the structure of the features that >are produced >> (and, ultimately for me, the format of the GFF which gets >written before >> being loaded into Bio::DB::GFF database). >> >> I have made the behaviour completely backwards compatible. >> >> Sincerely, >> >> Malcolm Cook - mec@stowers-institute.org - 816-926-4449 >> Database Applications Manager - Bioinformatics >> Stowers Institute for Medical Research - Kansas City, MO USA >> >> Index: EPCR.pm >> =================================================================== >> RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v >> retrieving revision 1.8 >> diff -c -r1.8 EPCR.pm >> *** EPCR.pm 2002/12/01 00:05:21 1.8 >> --- EPCR.pm 2004/03/15 20:27:04 >> *************** >> *** 92,110 **** >> =head2 new >> >> Title : new >> ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file); >> ! Function: Initializes a new EPCR parser >> Returns : Bio::Tools::EPCR >> Args : -fh => filehandle >> OR >> -file => filename >> >> =cut >> >> sub new { >> my($class,@args) = @_; >> >> my $self = $class->SUPER::new(@args); >> $self->_initialize_io(@args); >> >> return $self; >> --- 92,120 ---- >> =head2 new >> >> Title : new >> ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file, >-primary => >> $fprimary, -source => $fsource, -groupclass => $fgroupclass); >> ! Function: Initializes a new EPCR parser. >> Returns : Bio::Tools::EPCR >> Args : -fh => filehandle >> OR >> -file => filename >> >> + -primary => a string to be used as the common value for >> each features '-primary' tag. Defaults to 'sts'. (This in >turn maps to >> the GFF 'type' tag (aka 'method')). >> + >> + -source => a string to be used as the common >value for each >> features '-source' tag. Defaults to 'e-PCR'. (This in turn >maps to the >> GFF 'source' tag) >> + >> + -groupclass => a string to be used as the name >of the tag >> which will hold the sts marker namefirst attribute. >Defaults to 'name'. >> + >> =cut >> >> sub new { >> my($class,@args) = @_; >> >> my $self = $class->SUPER::new(@args); >> + my ($primary, $source, $groupclass) = >$self->_rearrange([qw(PRIMARY >> SOURCE GROUPCLASS)],@args); >> + $self->{'_primary'} = $primary || 'sts'; >> + $self->{'_source'} = $source || 'e-PCR'; >> + $self->{'_groupclass'} = $groupclass || 'name'; >> $self->_initialize_io(@args); >> >> return $self; >> *************** >> *** 139,152 **** >> my $markerfeature = new Bio::SeqFeature::Generic ( >'-start' => >> $start, >> '-end' => >> $end, >> '-strand' => >> $strand, >> ! '-source' => >> 'e-PCR', >> ! '-primary' => >> 'sts', >> '-seq_id' => >> $seqname, >> '-tag' => { >> ! 'name'=> >> $mkrname, >> ! 'note'=> >> $rest, >> }); >> return $markerfeature; >> } >> >> 1; >> --- 149,163 ---- >> my $markerfeature = new Bio::SeqFeature::Generic ( >'-start' => >> $start, >> '-end' => >> $end, >> '-strand' => >> $strand, >> ! '-source' => >> $self->{'_source'}, >> ! '-primary' => >> $self->{'_primary'}, >> '-seq_id' => >> $seqname, >> '-tag' => { >> ! >> $self->{'_groupclass'}=> $mkrname, >> }); >> + $markerfeature->add_tag_value('note',$rest) if $rest; >> return $markerfeature; >> + >> } >> >> 1; >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu > From paulo.david at netvisao.pt Mon Mar 15 18:05:13 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Mon Mar 15 18:10:43 2004 Subject: [Bioperl-l] determining orthologs... In-Reply-To: References: <1226365086.1079179503958.JavaMail.nobody@app2.ni.bg> <6.0.0.22.2.20040315100438.01c1e6d8@express.cites.uiuc.edu> Message-ID: <405636A9.8050502@netvisao.pt> For new genes, maybe running a remote blast and setting 'expect', or 'percent identity', and 'minimum length' cut-offs (only consider a possible ortholog if it spans, say, 70% of the query sequence). -Paulo Almeida Bob Freeman wrote: > What are BioPerl developers doing at present to determine putative > orthologs of a gene? BLINK? Unigene? LocusLink? And what about for > new/hypothetical genes? > > Tx, > Bob From rangwala at cs.umn.edu Mon Mar 15 18:29:44 2004 From: rangwala at cs.umn.edu (Huzefa Rangwala) Date: Mon Mar 15 18:35:11 2004 Subject: [Bioperl-l] How to get the PSSm from blastpgp or PSI-Blast run Message-ID: Hello Is there any command by which I can get the PSSM(Position Specific Scoring Matrices) in ASCII format. Note blastpgp with -C option creates the matrix in binary. Regards Huzefa -------------------------------------------------------------------------- Huzefa Rangwala Email:rangwala@cs.umn.edu Research Assistant, Tel: 612-625-3796 Dept. of Computer Sci & Engg. URL: http://www.cs.umn.edu/~rangwala University of Minnesota -------------------------------------------------------------------------- From amackey at pcbi.upenn.edu Mon Mar 15 21:44:49 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Mon Mar 15 21:50:15 2004 Subject: [Bioperl-l] How to get the PSSm from blastpgp or PSI-Blast run In-Reply-To: References: Message-ID: -Q checkpoint.txt -Aaron On Mar 15, 2004, at 6:29 PM, Huzefa Rangwala wrote: > > Hello > > Is there any command by which I can get the PSSM(Position Specific > Scoring > Matrices) in ASCII format. Note blastpgp with -C option creates the > matrix > in binary. > > Regards > Huzefa > > ----------------------------------------------------------------------- > --- > Huzefa Rangwala Email:rangwala@cs.umn.edu > Research Assistant, Tel: 612-625-3796 > Dept. of Computer Sci & Engg. URL: http://www.cs.umn.edu/~rangwala > University of Minnesota > ----------------------------------------------------------------------- > --- > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From postmaster at ebi.ac.uk Tue Mar 16 01:42:35 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Tue Mar 16 01:48:02 2004 Subject: [Bioperl-l] Warning: E-mail containing attachment(s) blocked Message-ID: <200403160642.i2G6gZD28597@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: senger@ebi.ac.uk Subject: Re: Document Date: Tue Mar 16 06:42:35 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: (Text.zip) -- MailScanner Email Virus Scanner www.mailscanner.info From birney at ebi.ac.uk Tue Mar 16 04:07:10 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Tue Mar 16 04:13:01 2004 Subject: [Bioperl-l] determining orthologs... In-Reply-To: Message-ID: On Mon, 15 Mar 2004, Bob Freeman wrote: > What are BioPerl developers doing at present to determine putative > orthologs of a gene? BLINK? Unigene? LocusLink? And what about for > new/hypothetical genes? Just to mention Bob, Ensembl, which is not a Bioperl thing per-se, calculates orthologs across its clades (eg, all vertebrates) which includes a dn/ds estimation for close species (eg, inter-mammal) from PAML, where you can get out dn, ds, k (that's Kappa, not K :)) etc from the database. This is all accessible in the underlying databases and in the Mart data mining tool (go to Ensembl --> Human --> Data mining and have a play...) > > Tx, > Bob > > -- > > ----------------------------------------------------- > Bob Freeman, Ph.D. > Acorn Worm Informatics > Dept of Systems Biology, C1-514A > Harvard Medical School > 240 Longwood Avenue > Boston, MA 02115 > 617/699.7057, vox > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From j.abbott at imperial.ac.uk Tue Mar 16 09:28:30 2004 From: j.abbott at imperial.ac.uk (James Abbott) Date: Tue Mar 16 09:33:57 2004 Subject: [Bioperl-l] Parsing EMBL DR lines with 1 accession Message-ID: <40570F0E.5020905@imperial.ac.uk> Greetings bioperlers... I have been using Bio::SeqIO to parse EMBL files, and noticed that some of the database cross-references (DR lines) were missing from the returned RichSeq object. The missing references were to the GOA database, which only have a primary id - the secondary id/accession usually found in (for example) swissprot/trembl references is missing i.e. (from EMBL:AE000562) DR GOA; O25226. DR GOA; P96551. DR SPTREMBL; O25217; O25217. DR SPTREMBL; O25218; O25218. These SPTREMBL cross references are parsed fine, however the GOA references are skipped. Looking at the code in question in Bio::SeqIO::embl, although there is provision for dbxrefs with a single id, the regex requires a trailing ';' after the primary accession. I have included a diff against embl.pm v 1.72 (see below...) which alters this regex to optionally match the second ';', allowing the id in DR lines with a single accesion to be parsed as the primary accession. Writing these entries back out again using Bio::SeqIO::embl results in these DR lines appearing as: DR GOA; 025226; . however the examples given in the EMBL user manual, and all those I've found in EMBL, lack this second ';' and following whitespace present. The second modification in the diff modifies the behaviour of Bio::SeqIO::embl when there is secondary accession present, ensuring that the DR line is written out as DR GOA; 025226. Cheers, James -- Dr. James Abbott Bioinformatics Software Developer, Bioinformatics Support Service Imperial College, London *** embl.pm Tue Mar 16 13:52:35 2004 --- embl1.72.pm Tue Mar 16 13:00:00 2004 *************** *** 594,600 **** my $prim = $dr->primary_id; my $opt = $dr->optional_id || ''; ! my $line = $opt ? "$db_name; $prim; $opt." : "$db_name; $prim."; $self->_write_line_EMBL_regex("DR ", "DR ", $line, '\s+|$', 80); #' } $self->_print("XX\n"); --- 594,600 ---- my $prim = $dr->primary_id; my $opt = $dr->optional_id || ''; ! my $line = "$db_name; $prim; $opt."; $self->_write_line_EMBL_regex("DR ", "DR ", $line, '\s+|$', 80); #' } $self->_print("XX\n"); *************** *** 919,925 **** while (defined( $_ ||= $self->_readline )) { if (my($databse, $prim_id, $sec_id) ! = /^DR ([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?\.$/) { my $link = Bio::Annotation::DBLink->new(); $link->database ( $databse ); $link->primary_id ( $prim_id ); --- 919,925 ---- while (defined( $_ ||= $self->_readline )) { if (my($databse, $prim_id, $sec_id) ! = /^DR ([^\s;]+);\s*([^\s;]+);\s*([^\s;]+)?\.$/) { my $link = Bio::Annotation::DBLink->new(); $link->database ( $databse ); $link->primary_id ( $prim_id ); From jason at cgt.duhs.duke.edu Tue Mar 16 11:39:39 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 16 11:45:20 2004 Subject: [Bioperl-l] RE: Bio::Tools::EPCR.pm patch request In-Reply-To: References: Message-ID: oops - my fault - I missed that accidently - had trouble applying the patch so was doing it by hand. will do. -jason On Mon, 15 Mar 2004, Cook, Malcolm wrote: > Jason, > > Wow! You the man! That was fast. I see it in the cvs change log > already... > > But... > > Would you mind reinstating the tiny additional change I made to only > produce the note tag value if $rest is present. I'm using it in an > applicatoin where there are no addition columns in my e-PCR input file, > and am getting an empty note attribute on each GFF line.... > > There may be a better way of coding it than: > > $markerfeature->add_tag_value('Note',$rest) if $rest; > > Thanks, > > Malcolm > > >-----Original Message----- > >From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu] > >Sent: Monday, March 15, 2004 3:29 PM > >To: Cook, Malcolm > >Cc: Bioperl > >Subject: Re: Bio::Tools::EPCR.pm patch request > > > > > >done! > > > >I added the ability to the update the primary,source,groupclass fields > >using get/set methods as well. I also capitalized the 'Note' > >field to be > >in line with the way GFF3 looks. > > > >-j > >On Mon, 15 Mar 2004, Cook, Malcolm wrote: > > > >> Jason, > >> > >> I'd like it if you would accept and apply the following diff > >to the very > >> useful Bio::Tools::EPCR module. I hope you agree that it > >provides more > >> flexibility in defining the structure of the features that > >are produced > >> (and, ultimately for me, the format of the GFF which gets > >written before > >> being loaded into Bio::DB::GFF database). > >> > >> I have made the behaviour completely backwards compatible. > >> > >> Sincerely, > >> > >> Malcolm Cook - mec@stowers-institute.org - 816-926-4449 > >> Database Applications Manager - Bioinformatics > >> Stowers Institute for Medical Research - Kansas City, MO USA > >> > >> Index: EPCR.pm > >> =================================================================== > >> RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/EPCR.pm,v > >> retrieving revision 1.8 > >> diff -c -r1.8 EPCR.pm > >> *** EPCR.pm 2002/12/01 00:05:21 1.8 > >> --- EPCR.pm 2004/03/15 20:27:04 > >> *************** > >> *** 92,110 **** > >> =head2 new > >> > >> Title : new > >> ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file); > >> ! Function: Initializes a new EPCR parser > >> Returns : Bio::Tools::EPCR > >> Args : -fh => filehandle > >> OR > >> -file => filename > >> > >> =cut > >> > >> sub new { > >> my($class,@args) = @_; > >> > >> my $self = $class->SUPER::new(@args); > >> $self->_initialize_io(@args); > >> > >> return $self; > >> --- 92,120 ---- > >> =head2 new > >> > >> Title : new > >> ! Usage : my $epcr = new Bio::Tools::EPCR(-file => $file, > >-primary => > >> $fprimary, -source => $fsource, -groupclass => $fgroupclass); > >> ! Function: Initializes a new EPCR parser. > >> Returns : Bio::Tools::EPCR > >> Args : -fh => filehandle > >> OR > >> -file => filename > >> > >> + -primary => a string to be used as the common value for > >> each features '-primary' tag. Defaults to 'sts'. (This in > >turn maps to > >> the GFF 'type' tag (aka 'method')). > >> + > >> + -source => a string to be used as the common > >value for each > >> features '-source' tag. Defaults to 'e-PCR'. (This in turn > >maps to the > >> GFF 'source' tag) > >> + > >> + -groupclass => a string to be used as the name > >of the tag > >> which will hold the sts marker namefirst attribute. > >Defaults to 'name'. > >> + > >> =cut > >> > >> sub new { > >> my($class,@args) = @_; > >> > >> my $self = $class->SUPER::new(@args); > >> + my ($primary, $source, $groupclass) = > >$self->_rearrange([qw(PRIMARY > >> SOURCE GROUPCLASS)],@args); > >> + $self->{'_primary'} = $primary || 'sts'; > >> + $self->{'_source'} = $source || 'e-PCR'; > >> + $self->{'_groupclass'} = $groupclass || 'name'; > >> $self->_initialize_io(@args); > >> > >> return $self; > >> *************** > >> *** 139,152 **** > >> my $markerfeature = new Bio::SeqFeature::Generic ( > >'-start' => > >> $start, > >> '-end' => > >> $end, > >> '-strand' => > >> $strand, > >> ! '-source' => > >> 'e-PCR', > >> ! '-primary' => > >> 'sts', > >> '-seq_id' => > >> $seqname, > >> '-tag' => { > >> ! 'name'=> > >> $mkrname, > >> ! 'note'=> > >> $rest, > >> }); > >> return $markerfeature; > >> } > >> > >> 1; > >> --- 149,163 ---- > >> my $markerfeature = new Bio::SeqFeature::Generic ( > >'-start' => > >> $start, > >> '-end' => > >> $end, > >> '-strand' => > >> $strand, > >> ! '-source' => > >> $self->{'_source'}, > >> ! '-primary' => > >> $self->{'_primary'}, > >> '-seq_id' => > >> $seqname, > >> '-tag' => { > >> ! > >> $self->{'_groupclass'}=> $mkrname, > >> }); > >> + $markerfeature->add_tag_value('note',$rest) if $rest; > >> return $markerfeature; > >> + > >> } > >> > >> 1; > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Mar 16 11:41:22 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 16 11:46:52 2004 Subject: [Bioperl-l] Parsing EMBL DR lines with 1 accession In-Reply-To: <40570F0E.5020905@imperial.ac.uk> References: <40570F0E.5020905@imperial.ac.uk> Message-ID: james - please submit this as bug to http://bugzilla.open-bio.org so we can keep track of when it gets fixed. -jason On Tue, 16 Mar 2004, James Abbott wrote: > Greetings bioperlers... > > I have been using Bio::SeqIO to parse EMBL files, and noticed that some > of the database cross-references (DR lines) were missing from the > returned RichSeq object. The missing references were to the GOA > database, which only have a primary id - the secondary id/accession > usually found in (for example) swissprot/trembl references is missing > i.e. (from EMBL:AE000562) > > DR GOA; O25226. > DR GOA; P96551. > DR SPTREMBL; O25217; O25217. > DR SPTREMBL; O25218; O25218. > > These SPTREMBL cross references are parsed fine, however the GOA > references are skipped. Looking at the code in question in > Bio::SeqIO::embl, although there is provision for dbxrefs with a single > id, the regex requires a trailing ';' after the primary accession. I > have included a diff against embl.pm v 1.72 (see below...) which alters > this regex to optionally match the second ';', allowing the id in DR > lines with a single accesion to be parsed as the primary accession. > > Writing these entries back out again using Bio::SeqIO::embl results in > these DR lines appearing as: > > DR GOA; 025226; . > > however the examples given in the EMBL user manual, and all those I've > found in EMBL, lack this second ';' and following whitespace present. > The second modification in the diff modifies the behaviour of > Bio::SeqIO::embl when there is secondary accession present, ensuring > that the DR line is written out as > > DR GOA; 025226. > > Cheers, > James > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Mar 16 12:30:24 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 16 12:35:54 2004 Subject: [Bioperl-l] Re: a bug in the package Bio::Tools::BPlite::Sbjct. In-Reply-To: References: Message-ID: I applied the fix. On Tue, 16 Mar 2004, Frederic Pecqueur wrote: > Hi everybody, > > I Found a bug in this package. > Sometimes, when I use $hsp->nextHSP, the $hsp->query->end value is null. > I always have this error for the last hit. > > I solved the problem. > You need to change the line 235 by : > > elsif ($_ =~ /^>|^Histogram|^Searching|^Parameters|^\s+Database:|^CPU\stime|^\s*Lambda|^\s*Subset/) > > For example, if you look in the array @hspline for the last hit of one entry, you can see : > > Query: 41 PATLLMLLLKVNKDGPAKKDIWRAPGNQAQVRKLSQVMQHGRLVNIENFTVYTAASVIKK 100 > P+ L L + K G + I R + +V + Q + G+ + + IK > Sbjct: 176 PSFLEKALQFIEKYGTKIEGILRQSADVEEVERRVQEYEQGKTEFTFDEDPHVVGDCIKH 235 > Query: 101 FLSKLPNGIFGRDNEETLFNSASTGMDIEKQRQVFYRIFGSLPVASQHLLVLLFGTFRVV 160 > L +LP+ L + + + I + P ++ LL + + > Sbjct: 236 VLRELPSSPVSASCCTALLEAYRIESKEARISSLRSAIAETFPEPNRRLLQRILKMMHTI 295 > Query: 161 ADSSDGHSNAMNPNAIAISVAPSL 184 > SS H N MNPNA+A +AP L > Sbjct: 296 --SSHSHENRMNPNAVAACMAPLL 317 > Subset of the database(s) listed below > Number of letters searched: 46,987,626 > Number of sequences searched: 126,777 > > If you add "|^\s*Subset" in the test, you should obtain : > > Query: 41 PATLLMLLLKVNKDGPAKKDIWRAPGNQAQVRKLSQVMQHGRLVNIENFTVYTAASVIKK 100 > P+ L L + K G + I R + +V + Q + G+ + + IK > Sbjct: 176 PSFLEKALQFIEKYGTKIEGILRQSADVEEVERRVQEYEQGKTEFTFDEDPHVVGDCIKH 235 > Query: 101 FLSKLPNGIFGRDNEETLFNSASTGMDIEKQRQVFYRIFGSLPVASQHLLVLLFGTFRVV 160 > L +LP+ L + + + I + P ++ LL + + > Sbjct: 236 VLRELPSSPVSASCCTALLEAYRIESKEARISSLRSAIAETFPEPNRRLLQRILKMMHTI 295 > Query: 161 ADSSDGHSNAMNPNAIAISVAPSL 184 > SS H N MNPNA+A +AP L > Sbjct: 296 --SSHSHENRMNPNAVAACMAPLL 317 > > I tested, with a large blast report..ans it works. > > Best regards. > Fr?d?ric. > > Fr?d?ric PECQUEUR > BioInformatic team > Devgen nv > Technologiepark 30 > B - 9052 Zwijnaarde > Belgium > Tel: +32 9 324 24 36 > Fax: +32 9 324 24 25 > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mgear911 at yahoo.com Tue Mar 16 20:01:43 2004 From: mgear911 at yahoo.com (=?iso-8859-1?q?Yuhui?=) Date: Tue Mar 16 20:07:09 2004 Subject: [Bioperl-l] Change SVG image to PNG or other image format. Message-ID: <20040317010143.84880.qmail@web13302.mail.yahoo.com> Hi, How do I change SVG image format to PNG format? btw the svg file, when i click it, it displays a image that is too big, and i cant find a way to show a smaller SVG image except to zoom out manually. Is there any way to make the svg image smaller when i view it, and rotate it b4 i change it to png format? Thanks. __________________________________________________ Do You Yahoo!? Log on to Messenger with your mobile phone! http://sg.messenger.yahoo.com From laurichj at bioinfo.ucr.edu Tue Mar 16 21:39:12 2004 From: laurichj at bioinfo.ucr.edu (Josh Lauricha) Date: Tue Mar 16 21:44:37 2004 Subject: [Bioperl-l] Bio::Index::AbstractSeq.pm Message-ID: <20040317023912.GA12740@bioinfo.ucr.edu> There's a small "feature" fo AbstractSeq.pm which will stomp on any primary_id with the accession_number, if there are no objections (there must have been some reason for this) I'll commit a small change to only do this if there is no other primary id, that way the GI will be easily gotten from the GenBank index. -- ------------------------------------------------------ | Josh Lauricha | Ford, your turning into | | laurichj@bioinfo.ucr.edu | a penguin. Stop it. | | Bioinformatics, UCR | | |----------------------------------------------------| | OpenPG: | | 4E7D 0FC0 DB6C E91D 4D7B C7F3 9BE9 8740 E4DC 6184 | |----------------------------------------------------| From babenko at ncbi.nlm.nih.gov Tue Mar 16 17:55:27 2004 From: babenko at ncbi.nlm.nih.gov (Babenko, Vladimir (NIH/NLM/NCBI)) Date: Tue Mar 16 23:15:28 2004 Subject: [Bioperl-l] phylip wrappers Message-ID: <69BA0F938FAC6A4CBEF49461720696F2029F60AA@nihexchange16.nih.gov> Hi Shawn and bioperl community, I cannot find the phylip run wrappers any more at Bio::Tools::Run::Phylo::Phylip::SeqBoot.pm , Consens, Neighbor etc. at current bioperl version. Do they migrate somewhere else while re-structuring? Thank you and sorry if that?s already discussed. Vladimir ----------------- Vladimir Babenko Bldg 38A 8S816L National Center for Biotechnology Information National Library Of Medicine National Institute of Health Bethesda, 20894 (v) 301-594-8079 (f) 301-480-4637 From shawnh at stanford.edu Tue Mar 16 17:59:07 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Tue Mar 16 23:15:55 2004 Subject: [Bioperl-l] Re: phylip wrappers In-Reply-To: <69BA0F938FAC6A4CBEF49461720696F2029F60AA@nihexchange16.nih.gov> References: <69BA0F938FAC6A4CBEF49461720696F2029F60AA@nihexchange16.nih.gov> Message-ID: <87BCE853-779D-11D8-B0C2-000A95783436@stanford.edu> This is under the bioperl-run package available at: http://bioperl.org/DIST/current_run_stable.tar.gz cheers, shawn On Mar 16, 2004, at 2:55 PM, Babenko, Vladimir (NIH/NLM/NCBI) wrote: > ?? Hi Shawn and bioperl community, > > ? > > I cannot find the phylip run wrappers any more at > Bio::Tools::Run::Phylo::Phylip::SeqBoot.pm , Consens, Neighbor etc. at > current bioperl version. > > ?? Do they migrate somewhere else while re-structuring? > > ????? Thank you and sorry if that?s already discussed. > > ????????? Vladimir > > ----------------- > > Vladimir Babenko > > Bldg 38A 8S816L > > National Center for Biotechnology Information > > National Library Of Medicine > > National Institute of Health > > Bethesda, 20894 > > (v) 301-594-8079 > > (f) 301-480-4637 > > ? -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1964 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040316/7165e02c/attachment.bin From postmaster at mep-instruments.com.au Wed Mar 17 02:57:43 2004 From: postmaster at mep-instruments.com.au (postmaster@mep-instruments.com.au) Date: Wed Mar 17 03:19:42 2004 Subject: [Bioperl-l] MDaemon Warning - Virus Found Message-ID: The following message had attachment(s) which contained viruses: >From : bioperl-l@bioperl.org To : bc@mep-instruments.com.au Subject : Date : Wed, 17 Mar 2004 09:13:14 +0100 Message-ID: Attachment Virus name Action taken ------------------------------------------------------------------------------ part2.pif I-Worm.Moodown.b Removed From sdavis2 at mail.nih.gov Wed Mar 17 07:10:36 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed Mar 17 07:16:14 2004 Subject: [Bioperl-l] phylip wrappers References: <69BA0F938FAC6A4CBEF49461720696F2029F60AA@nihexchange16.nih.gov> Message-ID: <004501c40c18$de4356c0$2f643744@WATSON> Vladimir It looks like phylip is in bioperl-run. http://doc.bioperl.org/bioperl-run/ Sean ----- Original Message ----- From: "Babenko, Vladimir (NIH/NLM/NCBI)" To: Cc: Sent: Tuesday, March 16, 2004 5:55 PM Subject: [Bioperl-l] phylip wrappers Hi Shawn and bioperl community, I cannot find the phylip run wrappers any more at Bio::Tools::Run::Phylo::Phylip::SeqBoot.pm , Consens, Neighbor etc. at current bioperl version. Do they migrate somewhere else while re-structuring? Thank you and sorry if that's already discussed. Vladimir ----------------- Vladimir Babenko Bldg 38A 8S816L National Center for Biotechnology Information National Library Of Medicine National Institute of Health Bethesda, 20894 (v) 301-594-8079 (f) 301-480-4637 ---------------------------------------------------------------------------- ---- > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jreumers at vub.ac.be Wed Mar 17 07:33:25 2004 From: jreumers at vub.ac.be (Joke Reumers) Date: Wed Mar 17 07:38:36 2004 Subject: [Bioperl-l] dbSNP connection Message-ID: <4921D179-780F-11D8-B07C-0030657E217C@vub.ac.be> Hi, I'm a new at using BioPerl and I wondered if there are any bioperl-modules that allow to connect to the SNP database at NCBI (dbSNP)? That would save me a lot of time.. Thanks, Joke Reumers +++++++++++++++++++++++++++++++++++++++ Joke Reumers Switch Laboratory Vrije Universiteit Brussel Flemish Interuniversity Institute for Biotechnology +++++++++++++++++++++++++++++++++++++++ From harris at cshl.edu Wed Mar 17 07:49:14 2004 From: harris at cshl.edu (Todd Harris) Date: Wed Mar 17 07:54:42 2004 Subject: [Bioperl-l] Change SVG image to PNG or other image format. In-Reply-To: <20040317010143.84880.qmail@web13302.mail.yahoo.com> Message-ID: Yuhui - Currently there are no options for setting the size of the SVG image upon generation. This would be a nice enhancement. Still, it's primary purpose is to generate a high quality image, not for navigation on the web. Why do you want to convert the SVG to PNG? The default behavior of the browser is to export PNG images. There are several projects under development to create rasterized images from vector data - see autotrace at sourceforge for one. Todd > On 3/16/04 7:01 PM, Yuhui wrote: > Hi, > How do I change SVG image format to PNG format? btw > the svg file, when i click it, it displays a image > that is too big, and i cant find a way to show a > smaller SVG image except to zoom out manually. Is > there any way to make the svg image smaller when i > view it, and rotate it b4 i change it to png format? > > Thanks. > > __________________________________________________ > Do You Yahoo!? > Log on to Messenger with your mobile phone! > http://sg.messenger.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From Annie.Law at nrc-cnrc.gc.ca Wed Mar 17 11:50:07 2004 From: Annie.Law at nrc-cnrc.gc.ca (Law, Annie) Date: Wed Mar 17 11:55:46 2004 Subject: [Bioperl-l] GO categories and load_ontology.pl Message-ID: <10C94843061E094A98C02EB77CFC328722FE14@nrcmrdex1d.imsb.nrc.ca> Hi, I have used the load_ontology.pl script and bioperl-db to load GO information into a database. The input for this script includes the GO.defs file and each of the files representing each of the ontologies ie. Molecular function, biological process, and cellular component. All of this information is loaded into the table called 'term' in the database. It seems that most of the Entries in the term table are of Ontoloy Id = 1 (Gene ontology) and only around 200 entries molecular function, biological process, and cellular component put together when there are about 16000 entries in the term table. This is only true if I load locuslink into the database. If I don't load locuslink into the database then all of the entries In the database are of Ontology Id 1. When the data is being entered into the database it is already known which GO category the GO identifer fits into. I need to know which category the GO id belongs to. I would appreciate some ideas on how I can get this information. Is there an option in the script that I can use maybe theres another table somewhere that has this information?? Thanks, Annie. From hlapp at gnf.org Wed Mar 17 13:17:30 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Mar 17 13:22:59 2004 Subject: [Bioperl-l] GO categories and load_ontology.pl In-Reply-To: <10C94843061E094A98C02EB77CFC328722FE14@nrcmrdex1d.imsb.nrc.ca> Message-ID: <5AC3B114-783F-11D8-9599-000A959EB4C4@gnf.org> Annie, I still owe you an answer for your earlier email. I haven't managed to get to that yet. See below for my response to this one. On Wednesday, March 17, 2004, at 08:50 AM, Law, Annie wrote: > It seems that most of the Entries in the term table are of Ontoloy Id > = 1 > (Gene ontology) and only around 200 entries molecular function, > biological > process, and cellular component put together when there are about 16000 > entries in the term table. > This is only true if I load locuslink into the database. This is because LocusLink lags behind the latest version of GO in terms of the release that they use for annotating sequences. I.e., LocusLink uses some terms which have meanwhile been retired or obsoleted from GO. Depending on whether they are still in GO's .defs file, they won't be in your database if you chose to ignore obsoleted entries (which is not a bad choice at all per se), or they aren't part of GO anymore at all. LocusLink doesn't give the ontology of GO terms (which would be 'Gene Ontology'); rather it gives the category. Because a term must have an ontology associated, the SeqIO LL parser interprets as the ontology what NCBI really meant to be the category. You'd have the following choices to proceed. - Ignore the 200 entries which aren't in Gene Ontology. You're not going to miss a significant amount of your annotation, and it's annotation with obsoleted terms anyway. - Load GO including obsoleted terms, and see with how many non-Gene Ontology terms that would leave you. If it's a lot less than 200, you may just want to ignore the rest. - Build a SeqProcessor module (see Bio::Factory::SeqProcessorI and Bio::Seq::BaseSeqProcessor) which takes the seq objects as the LL parser returns them, goes in and retrieves all GO term annotations, and replaces the ontology for those with 'Gene Ontology.' Then you pass your SeqProcessor to load_seqdatabase.pl using the --pipeline command-line option (see the script's POD). The last option may sound like but is really not a lot of work if you can program perl. Note, however, that then you still wouldn't have any relationships for those terms - they simply have been retired. Depending on what your project is, just ignoring those 200 may be the most reasonable way to go. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From allenday at ucla.edu Wed Mar 17 14:08:25 2004 From: allenday at ucla.edu (Allen Day) Date: Wed Mar 17 14:13:50 2004 Subject: [Bioperl-l] dbSNP connection In-Reply-To: <4921D179-780F-11D8-B07C-0030657E217C@vub.ac.be> References: <4921D179-780F-11D8-B07C-0030657E217C@vub.ac.be> Message-ID: See Bio::ClusterIO::dbsnp and Bio::Variation::SNP. -Allen On Wed, 17 Mar 2004, Joke Reumers wrote: > Hi, > > I'm a new at using BioPerl and I wondered if there are any > bioperl-modules that allow to connect to the SNP database at NCBI > (dbSNP)? That would save me a lot of time.. > > Thanks, > Joke Reumers > > +++++++++++++++++++++++++++++++++++++++ > Joke Reumers > Switch Laboratory > Vrije Universiteit Brussel > Flemish Interuniversity Institute for Biotechnology > +++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From amrdavila at yahoo.com Wed Mar 17 14:51:38 2004 From: amrdavila at yahoo.com (Alberto M R Davila) Date: Wed Mar 17 14:57:04 2004 Subject: [Bioperl-l] Clustal/T-Coffee to Fasta In-Reply-To: <5AC3B114-783F-11D8-9599-000A959EB4C4@gnf.org> Message-ID: <20040317195138.39516.qmail@web13907.mail.yahoo.com> I was looking in to the SeqIO module trying to know if it could convert multiple alignments done with ClustalW/X (*.aln files) or T-Coffee to Fasta sequences into a single file... no luck... there would be any other Bioperl module to do that format conversion ? Thanks, Alberto __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com From FGTB at mac.com Wed Mar 17 14:53:15 2004 From: FGTB at mac.com (From Genomes To Biomes) Date: Wed Mar 17 14:58:44 2004 Subject: [Bioperl-l] (no subject) Message-ID: Any one succesful in using fink and cpan/bundle bioperl together ? From ralf at bch.ed.ac.uk Wed Mar 17 15:06:58 2004 From: ralf at bch.ed.ac.uk (Ralf Schmid) Date: Wed Mar 17 15:12:23 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing dot_at_the_end_of query_accession Message-ID: Hi, I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my blast parsing scripts. Using the following snippet of code on a blast output (3 input sequences, -b 2 option for retrieving only two alignments, otherwise standard) gives different results: => code #!/usr/bin/perl -w use strict; use Bio::SearchIO; my $in = new Bio::SearchIO( -format => 'blast', -file => "test.out"); my $prot = ''; while( my $result = $in->next_result ) { while (my $hit = $result->next_hit) { $prot=$result->query_accession; print"$prot\n"; } } => output bioperl 1.21: ZPP00163 ZPP00163 ZPP00036_1 ZPP00036_1 ZPP00157 ZPP00157 - query accession is retrieved for each hit where there is an alignment => output bioperl 1.4: ZPP00163. ZPP00163. ZPP00163. ZPP00163. ZPP00163. ZPP00163. ZPP00163. ... - query_accession is retrieved for each hit regardless whether there is an alignment or not - each query_accession ends with a "." So far I have taken advantage of the blast -b option to set the number of hits to be parsed by bioperl, but I can see the ratio in changing bioperl from parsing every hit that has an alignment to parsing every hit. Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the helpful comment in line 769 makes me believe that there is the change in parsing coded, but I couldn't spot any reason for the "." at the end of each query_accession. Not sure whether the two are related anyway. # This is for the case when we specify -b 0 (or B=0 for WU-BLAST) # and still want to construct minimal Hit objects while(my $v = shift @hit_signifs) { next unless defined $v; $self->start_element({ 'Name' => 'Hit'}); ... So far I'm fixing the "dot" issue by an s/\.$// , but ... Cheers, Ralf ------------------------------------------------------------------------------ Dr. Ralf Schmid Nematode Bioinformatics Blaxter Nematode Genomics Group Institute of Cell, Animal and Population Biology Ashworth Labs University of Edinburgh King's Buildings Edinburgh EH9 3JT UK (+44)(0)131 650 7403 From james.wasmuth at ed.ac.uk Wed Mar 17 15:22:47 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Mar 17 15:28:21 2004 Subject: [Bioperl-l] Clustal/T-Coffee to Fasta In-Reply-To: <20040317195138.39516.qmail@web13907.mail.yahoo.com> References: <20040317195138.39516.qmail@web13907.mail.yahoo.com> Message-ID: <4058B397.4000109@ed.ac.uk> Hi Alberto, taken from docs for Bio::AlignIO (http://doc.bioperl.org/releases/bioperl-1.4/Bio/AlignIO.html) $inputfilename = "testaln.fasta"; $in = Bio::AlignIO->new(-file => $inputfilename , '-format' => 'clustal'); $out = Bio::AlignIO->new(-file => ">out.aln.pfam" , '-format' => 'fasta'); while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } if you want the gaps removed then... while ( my $aln = $in->next_aln() ) { $aln->map_chars('\.','') # first arguement is whatever your gap character is... $out->write_aln($aln); } -james Alberto M R Davila wrote: >I was looking in to the SeqIO module trying to know if it could convert >multiple alignments done with ClustalW/X (*.aln files) or T-Coffee to >Fasta sequences into a single file... no luck... there would be any other >Bioperl module to do that format conversion ? > >Thanks, Alberto > > > >__________________________________ >Do you Yahoo!? >Yahoo! Mail - More reliable, more storage, less spam >http://mail.yahoo.com >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From jason at cgt.duhs.duke.edu Wed Mar 17 15:25:56 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 17 15:31:21 2004 Subject: [Bioperl-l] Clustal/T-Coffee to Fasta In-Reply-To: <20040317195138.39516.qmail@web13907.mail.yahoo.com> References: <20040317195138.39516.qmail@web13907.mail.yahoo.com> Message-ID: Alignments are handled by Bio::AlignIO You want Bio::AlignIO::clustalw Bio::AlignIO::fasta -j On Wed, 17 Mar 2004, Alberto M R Davila wrote: > I was looking in to the SeqIO module trying to know if it could convert > multiple alignments done with ClustalW/X (*.aln files) or T-Coffee to > Fasta sequences into a single file... no luck... there would be any other > Bioperl module to do that format conversion ? > > Thanks, Alberto > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - More reliable, more storage, less spam > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Mar 17 15:36:13 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 17 15:41:41 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing dot_at_the_end_of query_accession In-Reply-To: References: Message-ID: ralf - can you send an example report - if I use your code and the t/data/ecolitst.bls report in the bioperl disto I get this jason@jason $ perl ralf_bug.pl AAC73113.1 AAC73113.1 AAC73113.1 AAC73113.1 also see below. -j On Wed, 17 Mar 2004, Ralf Schmid wrote: > > Hi, > > I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my > blast parsing scripts. Using the following snippet of code on a blast output (3 > input sequences, -b 2 option for retrieving only two alignments, otherwise > standard) gives different results: > > => code > > #!/usr/bin/perl -w > use strict; > use Bio::SearchIO; > my $in = new Bio::SearchIO( -format => 'blast', > -file => "test.out"); > my $prot = ''; > while( my $result = $in->next_result ) { > while (my $hit = $result->next_hit) { > $prot=$result->query_accession; > print"$prot\n"; > } > } > > > => output bioperl 1.21: > > ZPP00163 > ZPP00163 > ZPP00036_1 > ZPP00036_1 > ZPP00157 > ZPP00157 > > - query accession is retrieved for each hit where there is an alignment > > => output bioperl 1.4: > > ZPP00163. > ZPP00163. > ZPP00163. > ZPP00163. > ZPP00163. > ZPP00163. > ZPP00163. > ... > > - query_accession is retrieved for each hit regardless whether there is an > alignment or not > - each query_accession ends with a "." > > > So far I have taken advantage of the blast -b option to set the number of hits > to be parsed by bioperl, but I can see the ratio in changing bioperl from > parsing every hit that has an alignment to parsing every hit. > This was a requested feature. You can add a little code which exists the hit loop if the hit doesn't have any hsps last if $hit->num_hsps == 0; > Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the > helpful comment in line 769 makes me believe that there is the change in parsing > coded, but I couldn't spot any reason for the "." at the end of each > query_accession. Not sure whether the two are related anyway. > > > # This is for the case when we specify -b 0 (or B=0 for WU-BLAST) > # and still want to construct minimal Hit objects > while(my $v = shift @hit_signifs) { > next unless defined $v; > $self->start_element({ 'Name' => 'Hit'}); > ... > > > So far I'm fixing the "dot" issue by an s/\.$// , but ... > > > Cheers, > > Ralf > > > > > > > ------------------------------------------------------------------------------ > Dr. Ralf Schmid > Nematode Bioinformatics > Blaxter Nematode Genomics Group > Institute of Cell, Animal and Population Biology > Ashworth Labs > University of Edinburgh > King's Buildings > Edinburgh > EH9 3JT > UK > > (+44)(0)131 650 7403 > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From brian_osborne at cognia.com Wed Mar 17 15:51:04 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Mar 17 15:56:32 2004 Subject: [Bioperl-l] Clustal/T-Coffee to Fasta In-Reply-To: <20040317195138.39516.qmail@web13907.mail.yahoo.com> Message-ID: Alberto, You want to use AlignIO, and 'fasta' is one of its output formats. Unlike SeqIO, AlignIO can't produce output in all of its input formats. Take a look at the bptutorial, section III.2.2 (http://bioperl.org/Core/Latest/bptutorial.html). Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Alberto M R Davila Sent: Wednesday, March 17, 2004 2:52 PM To: bioperl-l@bioperl.org Cc: amrdavila@yahoo.com Subject: [Bioperl-l] Clustal/T-Coffee to Fasta I was looking in to the SeqIO module trying to know if it could convert multiple alignments done with ClustalW/X (*.aln files) or T-Coffee to Fasta sequences into a single file... no luck... there would be any other Bioperl module to do that format conversion ? Thanks, Alberto __________________________________ Do you Yahoo!? Yahoo! Mail - More reliable, more storage, less spam http://mail.yahoo.com _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From james.wasmuth at ed.ac.uk Wed Mar 17 16:10:53 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Mar 17 16:16:47 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing dot_at_the_end_of query_accession In-Reply-To: <4058BE46.9060205@ed.ac.uk> References: <4058BE46.9060205@ed.ac.uk> Message-ID: <4058BEDD.5080708@ed.ac.uk> Hi Jason, I work with Ralf, and sensibly he's gone home, but here's the report file: BLASTP 2.2.6 [Apr-09-2003] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= ZPP00163 (199 letters) Database: swissall.fsa 1,218,016 sequences; 390,760,073 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value NUKM_CAEEL (Q94360) Probable NADH-ubiquinone oxidoreductase 20 k... 177 6e-44 Q9VAK5 (Q9VAK5) CG2014 protein 166 1e-40 NUKM_BOVIN (P42026) NADH-ubiquinone oxidoreductase 20 kDa subuni... 166 2e-40 Q9VXK7 (Q9VXK7) CG9172 protein (LD31474P) 165 4e-40 Q9BV17 (Q9BV17) Similar to CG9172 gene product (NADH:ubiquinone ... 163 1e-39 NUKM_HUMAN (O75251) NADH-ubiquinone oxidoreductase 20 kDa subuni... 163 1e-39 Q7PRW3 (Q7PRW3) ENSANGP00000019428 (Fragment) 162 2e-39 Q9DC70 (Q9DC70) 1010001M04Rik protein (RIKEN cDNA 1010001M04 gene) 159 2e-38 Q86EG3 (Q86EG3) Clone ZZD432 mRNA sequence 155 4e-37 Q7PQT1 (Q7PQT1) ENSANGP00000014787 (Fragment) 150 7e-36 Q7PQU6 (Q7PQU6) ENSANGP00000017108 (Fragment) 150 7e-36 NUKM_RECAM (O21272) NADH-ubiquinone oxidoreductase 20 kDa subuni... 146 2e-34 Q9G8U4 (Q9G8U4) NADH dehydrogenase subunit 10 (EC 1.6.5.3) 144 5e-34 Q8NAS7 (Q8NAS7) Hypothetical protein FLJ34850 144 9e-34 Q7RZB4 (Q7RZB4) Hypothetical protein 143 2e-33 NUKM_NEUCR (O47950) NADH-ubiquinone oxidoreductase 19.3 kDa subu... 143 2e-33 Q8W0E8 (Q8W0E8) Putative NADH dehydrogenase (Ubiquinone) chain PSST 141 6e-33 Q9TCA4 (Q9TCA4) NADH dehydrogenase subunit 10 (EC 1.6.5.3) 140 1e-32 Q9SP38 (Q9SP38) NADH ubiquinone oxidoreductase PSST subunit 139 2e-32 Q9LKG9 (Q9LKG9) NADH-ubiquinone oxidoreductase subunit PSST (Fra... 139 2e-32 NUKM_SOLTU (Q43844) NADH-ubiquinone oxidoreductase 20 kDa subuni... 139 2e-32 NUKM_BRAOL (P42027) NADH-ubiquinone oxidoreductase 20 kDa subuni... 139 2e-32 NUKM_ARATH (Q42577) NADH-ubiquinone oxidoreductase 20 kDa subuni... 138 5e-32 Q9LKH4 (Q9LKH4) NADH-ubiquinone oxidoreductase subunit PSST 137 1e-31 Q9UUT7 (Q9UUT7) Subunit NUKM of protein NADH:ubiquinone oxidored... 134 5e-31 Q7PBK3 (Q7PBK3) NADH dehydrogenase I chain B 134 9e-31 NUOB_RICCN (Q92ID6) NADH-quinone oxidoreductase chain B (EC 1.6.... 134 9e-31 >>NUKM_CAEEL (Q94360) Probable NADH-ubiquinone oxidoreductase 20 kDa > > subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-20KD) (CI-20KD) Length = 199 Score = 177 bits (450), Expect = 6e-44 Identities = 88/161 (54%), Positives = 106/161 (65%) Query: 39 GKGVFGSPFVQSESKGEWALASLDDVINLCGKTSLWPLTFGLXXXXXXXXHFAAPRYDMD 98 G G+PF+ SK E+ALA LDDV+NL + S+WPLTFGL HFAAPRYDMD Sbjct: 31 GIATTGTPFLNPSSKAEYALARLDDVLNLAQRGSIWPLTFGLACCAVEMMHFAAPRYDMD 90 Query: 99 HYGVVFHATPXQVNLILFTGTITNKMAPALHHIYNQMPKPKYVISMESYTNGSGYYHYTY 158 YGVVF A+P Q +LI GT+TNKMAPAL IY+QMP+ K+VISM S NG GYYHY Y Sbjct: 91 RYGVVFRASPRQADLIFVAGTVTNKMAPALRRIYDQMPEAKWVISMGSCANGGGYYHYAY 150 Query: 159 SIVHNYNHMXXXXXXXXXXXXTAKXLLYNILQLQKKIKHSR 199 S++ + + TA+ LLY +LQLQKKIK R Sbjct: 151 SVLRGCDRVIPVDIYVPGCPPTAEALLYGVLQLQKKIKRKR 191 >>Q9VAK5 (Q9VAK5) CG2014 protein > > Length = 212 Score = 166 bits (421), Expect = 1e-40 Identities = 82/162 (50%), Positives = 103/162 (63%), Gaps = 3/162 (1%) Query: 38 WGKGVFGSPFVQSESKGEWALASLDDVINLCGKTSLWPLTFGLXXXXXXXXHFAAPRYDM 97 WG FG ++ GEW A LDD++N K SLWPLTFGL H AAPRYDM Sbjct: 46 WGYSAFGR---NQKTWGEWTCARLDDLLNWGRKGSLWPLTFGLACCAVEMMHIAAPRYDM 102 Query: 98 DHYGVVFHATPXQVNLILFTGTITNKMAPALHHIYNQMPKPKYVISMESYTNGSGYYHYT 157 D YGVVF A+P Q ++++ GT+TNKMAPA IY+QMP+P++VISM S NG GYYHY+ Sbjct: 103 DRYGVVFRASPRQADVLIVAGTLTNKMAPAFRKIYDQMPEPRWVISMGSCANGGGYYHYS 162 Query: 158 YSIVHNYNHMXXXXXXXXXXXXTAKXLLYNILQLQKKIKHSR 199 YS+V + + TA+ L+Y ILQLQKK+K R Sbjct: 163 YSVVRGCDRIVPVDIYVPGCPPTAEALMYGILQLQKKVKRMR 204 Database: swissall.fsa Posted date: Dec 5, 2003 3:22 PM Number of letters in database: 390,760,073 Number of sequences in database: 1,218,016 Lambda K H 0.318 0.134 0.417 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 150,792,462 Number of Sequences: 1218016 Number of extensions: 5616912 Number of successful extensions: 15131 Number of sequences better than 1.0e-30: 27 Number of HSP's better than 0.0 without gapping: 10 Number of HSP's successfully gapped in prelim test: 17 Number of HSP's that attempted gapping in prelim test: 15095 Number of HSP's gapped (non-prelim): 27 length of query: 199 length of database: 390,760,073 effective HSP length: 116 effective length of query: 83 effective length of database: 249,470,217 effective search space: 20706028011 effective search space used: 20706028011 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 336 (134.0 bits) BLASTP 2.2.6 [Apr-09-2003] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= ZPP00036_1 (229 letters) Database: swissall.fsa 1,218,016 sequences; 390,760,073 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value Q95XJ0 (Q95XJ0) Hypothetical protein 256 2e-67 Q95XI9 (Q95XI9) Hypothetical protein 256 2e-67 ATPG_DROME (O01666) ATP synthase gamma chain, mitochondrial prec... 202 2e-51 Q7Q3N8 (Q7Q3N8) AgCP11416 (Fragment) 197 7e-50 ATPG_BOVIN (P05631) ATP synthase gamma chain, mitochondrial prec... 184 1e-45 Q9ERA8 (Q9ERA8) ATP synthase gamma-subunit precursor 178 4e-44 Q8TAS0 (Q8TAS0) Hypothetical protein (Fragment) 178 6e-44 ATPG_MOUSE (Q91VR2) ATP synthase gamma chain, mitochondrial prec... 178 6e-44 ATPG_HUMAN (P36542) ATP synthase gamma chain, mitochondrial prec... 178 6e-44 Q910C3 (Q910C3) Mitochondrial ATP synthase gamma-subunit 177 1e-43 Q9D9D7 (Q9D9D7) 1700094F02Rik protein 175 4e-43 Q86DM7 (Q86DM7) Hypothetical protein Y69A2AR.18 174 1e-42 Q8C2Q8 (Q8C2Q8) ATP synthase 172 2e-42 Q7ZXN3 (Q7ZXN3) Similar to ATP synthase, H+ transporting, mitoch... 172 4e-42 ATPG_RAT (P35435) ATP synthase gamma chain, mitochondrial (EC 3.... 169 2e-41 >>Q95XJ0 (Q95XJ0) Hypothetical protein > > Length = 299 Score = 256 bits (653), Expect = 2e-67 Identities = 131/225 (58%), Positives = 164/225 (72%), Gaps = 4/225 (1%) Query: 5 YGNVEQQRNFATLKDISIRLKSVKNIQKMTXXXXXXXXXXXXXXDRELKGARVYGEGAQA 64 + N EQ R FATLKDISIRLKSVKNIQK+T +RELKGAR YG GA+ Sbjct: 16 FANAEQARGFATLKDISIRLKSVKNIQKITKSMKMVAAAKYAKAERELKGARAYGVGAKT 75 Query: 65 FYNNLAGDDAAVPKADASATTKKLLILMTSDSGLCGAVHTSIIKEAKNLIKNKPDNMEYK 124 F++N+ D V + + K++L+L+TSD GLCG VH+SI+KEAKN++ N D E + Sbjct: 76 FFDNI---DPVVEGVEKQESKKQVLVLITSDRGLCGGVHSSIVKEAKNILNNAGDK-EIR 131 Query: 125 LVCIGDKSKAGMSRIYGNHILYTANEIGRLPPTFEDASIAALEILNSGYEFDEAEILYNR 184 +V IGDKS+AG+ R+Y N IL + NEIGR PP+F DASIAA IL+SGY+F+ IL+NR Sbjct: 132 VVAIGDKSRAGLQRLYANSILLSGNEIGRAPPSFADASIAAKAILDSGYDFETGTILFNR 191 Query: 185 FKTVVSYQTSKLQVPPLATIKSNTKLYTYDSVDDDLLQSYAEYSL 229 FKTVVSY+TSKLQ+ PL IK+ L TYDSVDDD+LQSY+EYSL Sbjct: 192 FKTVVSYETSKLQILPLEAIKAKEALSTYDSVDDDVLQSYSEYSL 236 >>Q95XI9 (Q95XI9) Hypothetical protein > > Length = 313 Score = 256 bits (653), Expect = 2e-67 Identities = 131/225 (58%), Positives = 164/225 (72%), Gaps = 4/225 (1%) Query: 5 YGNVEQQRNFATLKDISIRLKSVKNIQKMTXXXXXXXXXXXXXXDRELKGARVYGEGAQA 64 + N EQ R FATLKDISIRLKSVKNIQK+T +RELKGAR YG GA+ Sbjct: 16 FANAEQARGFATLKDISIRLKSVKNIQKITKSMKMVAAAKYAKAERELKGARAYGVGAKT 75 Query: 65 FYNNLAGDDAAVPKADASATTKKLLILMTSDSGLCGAVHTSIIKEAKNLIKNKPDNMEYK 124 F++N+ D V + + K++L+L+TSD GLCG VH+SI+KEAKN++ N D E + Sbjct: 76 FFDNI---DPVVEGVEKQESKKQVLVLITSDRGLCGGVHSSIVKEAKNILNNAGDK-EIR 131 Query: 125 LVCIGDKSKAGMSRIYGNHILYTANEIGRLPPTFEDASIAALEILNSGYEFDEAEILYNR 184 +V IGDKS+AG+ R+Y N IL + NEIGR PP+F DASIAA IL+SGY+F+ IL+NR Sbjct: 132 VVAIGDKSRAGLQRLYANSILLSGNEIGRAPPSFADASIAAKAILDSGYDFETGTILFNR 191 Query: 185 FKTVVSYQTSKLQVPPLATIKSNTKLYTYDSVDDDLLQSYAEYSL 229 FKTVVSY+TSKLQ+ PL IK+ L TYDSVDDD+LQSY+EYSL Sbjct: 192 FKTVVSYETSKLQILPLEAIKAKEALSTYDSVDDDVLQSYSEYSL 236 Database: swissall.fsa Posted date: Dec 5, 2003 3:22 PM Number of letters in database: 390,760,073 Number of sequences in database: 1,218,016 Lambda K H 0.314 0.132 0.358 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 148,369,851 Number of Sequences: 1218016 Number of extensions: 5173956 Number of successful extensions: 9119 Number of sequences better than 1.0e-30: 15 Number of HSP's better than 0.0 without gapping: 2 Number of HSP's successfully gapped in prelim test: 13 Number of HSP's that attempted gapping in prelim test: 9087 Number of HSP's gapped (non-prelim): 15 length of query: 229 length of database: 390,760,073 effective HSP length: 118 effective length of query: 111 effective length of database: 247,034,185 effective search space: 27420794535 effective search space used: 27420794535 T: 11 A: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 337 (134.4 bits) BLASTP 2.2.6 [Apr-09-2003] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= ZPP00157 (124 letters) Database: swissall.fsa 1,218,016 sequences; 390,760,073 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value RL23_CAEEL (P48158) 60S ribosomal protein L23 207 3e-53 Q7PMD8 (Q7PMD8) ENSANGP00000014430 (Fragment) 199 6e-51 RL23_AEDAE (Q9GNE2) 60S ribosomal protein L23 (L17A) 199 6e-51 Q9W1Y7 (Q9W1Y7) RPL17A protein 199 7e-51 RL23_BRUMA (Q93140) 60S ribosomal protein L23 196 6e-50 Q962Y9 (Q962Y9) Ribosomal protein L17/23 193 4e-49 Q7ZWJ5 (Q7ZWJ5) Hypothetical protein (Fragment) 191 2e-48 Q90YU5 (Q90YU5) Ribosomal protein L23 189 4e-48 Q8IT99 (Q8IT99) Ribosomal protein L17A (Fragment) 189 4e-48 Q9BTQ7 (Q9BTQ7) Similar to ribosomal protein L23 (Fragment) 189 4e-48 RL23_HUMAN (P23131) 60S ribosomal protein L23 (L17) 189 4e-48 Q9DFL3 (Q9DFL3) Ribosomal protein L23 189 6e-48 Q86D71 (Q86D71) Ribosomal protein L23 189 6e-48 RL23_DROME (P48159) 60S ribosomal protein L23 (L17A) 189 8e-48 Q9W6M3 (Q9W6M3) Ribosomal protein L17 188 1e-47 Q9CZE6 (Q9CZE6) 2810009A01Rik protein 188 1e-47 Q9DCQ4 (Q9DCQ4) 2810009A01Rik protein 186 4e-47 Q9XSU3 (Q9XSU3) Ribosomal protein 186 6e-47 Q9YHX0 (Q9YHX0) Ribosomal protein L17 homolog (Fragment) 182 5e-46 O22686 (O22686) F19P19.5 protein 179 6e-45 Q9ATF6 (Q9ATF6) Ribosomal protein L17 179 6e-45 RL23_TOBAC (Q07760) 60S ribosomal protein L23 179 6e-45 RL23_ARATH (P49690) 60S ribosomal protein L23 179 6e-45 Q7X9K1 (Q7X9K1) Ribosomal Pr 117 (Fragment) 178 1e-44 Q8L8P0 (Q8L8P0) Putative 60S ribosomal protein L17 178 1e-44 Q7XDL5 (Q7XDL5) 60S ribosomal protein L17 177 2e-44 Q9AV77 (Q9AV77) 60S ribosomal protein L17 177 2e-44 O65068 (O65068) 60S ribosomal protein L17 (Fragment) 176 5e-44 Q9SMI7 (Q9SMI7) 60S ribosomal protein L17 (Fragment) 174 2e-43 O96636 (O96636) Ribosomal protein L17 172 6e-43 RL23_SCHPO (O42867) 60S ribosomal protein L23 171 2e-42 RL23_YEAST (P04451) 60S ribosomal protein L23 (L17) 171 2e-42 RL23_TORRU (Q9XEK8) 60S ribosomal protein L23 (L17) 171 2e-42 Q7R814 (Q7R814) 60S ribosomal protein L23 164 3e-40 Q7SHJ9 (Q7SHJ9) Hypothetical protein 163 3e-40 Q873R3 (Q873R3) Alkaline serine protease (Fragment) 163 3e-40 Q8IE09 (Q8IE09) 60S ribosomal protein L23, putative 162 6e-40 Q98RY7 (Q98RY7) 60S ribosomal protein L23 154 2e-37 Q7QTA5 (Q7QTA5) GLP_15_22119_21691 149 9e-36 RL23_TRYCR (Q94776) 60S ribosomal protein L23 (L17) (TCEST082) 149 9e-36 Q9HIR9 (Q9HIR9) Probable 50S ribosomal protein L14 134 2e-31 Q97BW6 (Q97BW6) Ribosomal protein large subunit L23 133 4e-31 Q8SRA7 (Q8SRA7) Ribosomal protein L23 132 8e-31 >>RL23_CAEEL (P48158) 60S ribosomal protein L23 > > Length = 140 Score = 207 bits (526), Expect = 3e-53 Identities = 102/113 (90%), Positives = 105/113 (92%) Query: 1 LSLPVGFXINXADNTGANNLFVIAVYGMRGRLNRLPSAGVGDMFVASVKKGKPELRKKVL 60 L LPVG +N ADNTGA NLFVI+VYG+RGRLNRLPSAGVGDMFV SVKKGKPELRKKVL Sbjct: 18 LGLPVGAVMNCADNTGAKNLFVISVYGIRGRLNRLPSAGVGDMFVCSVKKGKPELRKKVL 77 Query: 61 QAVVIRQRKMFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 113 Q VVIRQRK FRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP Sbjct: 78 QGVVIRQRKQFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 130 >>Q7PMD8 (Q7PMD8) ENSANGP00000014430 (Fragment) > > Length = 135 Score = 199 bits (506), Expect = 6e-51 Identities = 97/113 (85%), Positives = 105/113 (92%) Query: 1 LSLPVGFXINXADNTGANNLFVIAVYGMRGRLNRLPSAGVGDMFVASVKKGKPELRKKVL 60 L LPVG IN ADNTGA NL+VIAV+G+RGRLNRLP+AGVGDMFVA+VKKGKPELRKKV+ Sbjct: 13 LGLPVGAVINCADNTGAKNLYVIAVHGIRGRLNRLPAAGVGDMFVATVKKGKPELRKKVM 72 Query: 61 QAVVIRQRKMFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 113 AVVIRQRK FRR+DG F+YFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP Sbjct: 73 PAVVIRQRKPFRRRDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 125 Database: swissall.fsa Posted date: Dec 5, 2003 3:22 PM Number of letters in database: 390,760,073 Number of sequences in database: 1,218,016 Lambda K H 0.321 0.140 0.409 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 83,601,214 Number of Sequences: 1218016 Number of extensions: 3001107 Number of successful extensions: 5578 Number of sequences better than 1.0e-30: 43 Number of HSP's better than 0.0 without gapping: 42 Number of HSP's successfully gapped in prelim test: 1 Number of HSP's that attempted gapping in prelim test: 5533 Number of HSP's gapped (non-prelim): 43 length of query: 124 length of database: 390,760,073 effective HSP length: 100 effective length of query: 24 effective length of database: 268,958,473 effective search space: 6455003352 effective search space used: 6455003352 T: 11 A: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 332 (132.5 bits) > > > Jason Stajich wrote: > >>ralf - can you send an example report - if I use your code and the >>t/data/ecolitst.bls report in the bioperl disto I get this >>jason@jason $ perl ralf_bug.pl >>AAC73113.1 >>AAC73113.1 >>AAC73113.1 >>AAC73113.1 >> >>also see below. >> >>-j >>On Wed, 17 Mar 2004, Ralf Schmid wrote: >> >> >> >>>Hi, >>> >>>I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my >>>blast parsing scripts. Using the following snippet of code on a blast output (3 >>>input sequences, -b 2 option for retrieving only two alignments, otherwise >>>standard) gives different results: >>> >>>=> code >>> >>>#!/usr/bin/perl -w >>>use strict; >>>use Bio::SearchIO; >>>my $in = new Bio::SearchIO( -format => 'blast', >>> -file => "test.out"); >>>my $prot = ''; >>>while( my $result = $in->next_result ) { >>> while (my $hit = $result->next_hit) { >>> $prot=$result->query_accession; >>> print"$prot\n"; >>> } >>>} >>> >>> >>>=> output bioperl 1.21: >>> >>>ZPP00163 >>>ZPP00163 >>>ZPP00036_1 >>>ZPP00036_1 >>>ZPP00157 >>>ZPP00157 >>> >>>- query accession is retrieved for each hit where there is an alignment >>> >>>=> output bioperl 1.4: >>> >>>ZPP00163. >>>ZPP00163. >>>ZPP00163. >>>ZPP00163. >>>ZPP00163. >>>ZPP00163. >>>ZPP00163. >>>... >>> >>>- query_accession is retrieved for each hit regardless whether there is an >>>alignment or not >>>- each query_accession ends with a "." >>> >>> >>>So far I have taken advantage of the blast -b option to set the number of hits >>>to be parsed by bioperl, but I can see the ratio in changing bioperl from >>>parsing every hit that has an alignment to parsing every hit. >>> >>> >>> >>This was a requested feature. You can add a little code which exists the >>hit loop if the hit doesn't have any hsps >>last if $hit->num_hsps == 0; >> >> >> >>>Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the >>>helpful comment in line 769 makes me believe that there is the change in parsing >>>coded, but I couldn't spot any reason for the "." at the end of each >>>query_accession. Not sure whether the two are related anyway. >>> >>> >>># This is for the case when we specify -b 0 (or B=0 for WU-BLAST) >>># and still want to construct minimal Hit objects >>>while(my $v = shift @hit_signifs) { >>>next unless defined $v; >>>$self->start_element({ 'Name' => 'Hit'}); >>>... >>> >>> >>>So far I'm fixing the "dot" issue by an s/\.$// , but ... >>> >>> >>>Cheers, >>> >>>Ralf >>> >>> >>> >>> >>> >>> >>>------------------------------------------------------------------------------ >>>Dr. Ralf Schmid >>>Nematode Bioinformatics >>>Blaxter Nematode Genomics Group >>>Institute of Cell, Animal and Population Biology >>>Ashworth Labs >>>University of Edinburgh >>>King's Buildings >>>Edinburgh >>>EH9 3JT >>>UK >>> >>>(+44)(0)131 650 7403 >>> >>> >>> >>> >>> >>>_______________________________________________ >>>Bioperl-l mailing list >>>Bioperl-l@portal.open-bio.org >>>http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >>-- >>Jason Stajich >>Duke University >>jason at cgt.mc.duke.edu >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> From james.wasmuth at ed.ac.uk Wed Mar 17 16:11:26 2004 From: james.wasmuth at ed.ac.uk (James Wasmuth) Date: Wed Mar 17 16:17:15 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing dot_at_the_end_of query_accession In-Reply-To: References: Message-ID: <4058BEFE.6030701@ed.ac.uk> Just noticed that what was required was $result->query_name rather than query_accession. Still, to me, its curious that the latter method should append the '.' . -james Jason Stajich wrote: >ralf - can you send an example report - if I use your code and the >t/data/ecolitst.bls report in the bioperl disto I get this >jason@jason $ perl ralf_bug.pl >AAC73113.1 >AAC73113.1 >AAC73113.1 >AAC73113.1 > >also see below. > >-j >On Wed, 17 Mar 2004, Ralf Schmid wrote: > > > >>Hi, >> >>I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my >>blast parsing scripts. Using the following snippet of code on a blast output (3 >>input sequences, -b 2 option for retrieving only two alignments, otherwise >>standard) gives different results: >> >>=> code >> >>#!/usr/bin/perl -w >>use strict; >>use Bio::SearchIO; >>my $in = new Bio::SearchIO( -format => 'blast', >> -file => "test.out"); >>my $prot = ''; >>while( my $result = $in->next_result ) { >> while (my $hit = $result->next_hit) { >> $prot=$result->query_accession; >> print"$prot\n"; >> } >>} >> >> >>=> output bioperl 1.21: >> >>ZPP00163 >>ZPP00163 >>ZPP00036_1 >>ZPP00036_1 >>ZPP00157 >>ZPP00157 >> >>- query accession is retrieved for each hit where there is an alignment >> >>=> output bioperl 1.4: >> >>ZPP00163. >>ZPP00163. >>ZPP00163. >>ZPP00163. >>ZPP00163. >>ZPP00163. >>ZPP00163. >>... >> >>- query_accession is retrieved for each hit regardless whether there is an >>alignment or not >>- each query_accession ends with a "." >> >> >>So far I have taken advantage of the blast -b option to set the number of hits >>to be parsed by bioperl, but I can see the ratio in changing bioperl from >>parsing every hit that has an alignment to parsing every hit. >> >> >> >This was a requested feature. You can add a little code which exists the >hit loop if the hit doesn't have any hsps >last if $hit->num_hsps == 0; > > > >>Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the >>helpful comment in line 769 makes me believe that there is the change in parsing >>coded, but I couldn't spot any reason for the "." at the end of each >>query_accession. Not sure whether the two are related anyway. >> >> >># This is for the case when we specify -b 0 (or B=0 for WU-BLAST) >># and still want to construct minimal Hit objects >>while(my $v = shift @hit_signifs) { >>next unless defined $v; >>$self->start_element({ 'Name' => 'Hit'}); >>... >> >> >>So far I'm fixing the "dot" issue by an s/\.$// , but ... >> >> >>Cheers, >> >>Ralf >> >> >> >> >> >> >>------------------------------------------------------------------------------ >>Dr. Ralf Schmid >>Nematode Bioinformatics >>Blaxter Nematode Genomics Group >>Institute of Cell, Animal and Population Biology >>Ashworth Labs >>University of Edinburgh >>King's Buildings >>Edinburgh >>EH9 3JT >>UK >> >>(+44)(0)131 650 7403 >> >> >> >> >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From jason at cgt.duhs.duke.edu Wed Mar 17 16:28:13 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 17 16:33:57 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing dot_at_the_end_of query_accession In-Reply-To: <4058BEFE.6030701@ed.ac.uk> References: <4058BEFE.6030701@ed.ac.uk> Message-ID: Agreed. The query_accession is a special method which will report the accession if it was properly parsed out. However, I think the problem is fixed post 1.4 as Hilmar made these changes below. The 1.4.0 release has revision 1.72 of SearchIO/blast.pm with the bug you are reporting so upgrading your copy to 1.76 version from CVS should take care of the problem I hope. On about line 515: my ($acc,$version) = &_get_accession_version($nm); + $version = defined($version) ? ".$version" : ""; $acc = '' unless defined($acc); $self->element({ 'Name' => 'BlastOutput_query-acc', 'Data' => "$acc$version"}); -jason On Wed, 17 Mar 2004, James Wasmuth wrote: > Just noticed that what was required was $result->query_name rather than > query_accession. Still, to me, its curious that the latter method > should append the '.' . > > > -james > > > Jason Stajich wrote: > > >ralf - can you send an example report - if I use your code and the > >t/data/ecolitst.bls report in the bioperl disto I get this > >jason@jason $ perl ralf_bug.pl > >AAC73113.1 > >AAC73113.1 > >AAC73113.1 > >AAC73113.1 > > > >also see below. > > > >-j > >On Wed, 17 Mar 2004, Ralf Schmid wrote: > > > > > > > >>Hi, > >> > >>I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my > >>blast parsing scripts. Using the following snippet of code on a blast output (3 > >>input sequences, -b 2 option for retrieving only two alignments, otherwise > >>standard) gives different results: > >> > >>=> code > >> > >>#!/usr/bin/perl -w > >>use strict; > >>use Bio::SearchIO; > >>my $in = new Bio::SearchIO( -format => 'blast', > >> -file => "test.out"); > >>my $prot = ''; > >>while( my $result = $in->next_result ) { > >> while (my $hit = $result->next_hit) { > >> $prot=$result->query_accession; > >> print"$prot\n"; > >> } > >>} > >> > >> > >>=> output bioperl 1.21: > >> > >>ZPP00163 > >>ZPP00163 > >>ZPP00036_1 > >>ZPP00036_1 > >>ZPP00157 > >>ZPP00157 > >> > >>- query accession is retrieved for each hit where there is an alignment > >> > >>=> output bioperl 1.4: > >> > >>ZPP00163. > >>ZPP00163. > >>ZPP00163. > >>ZPP00163. > >>ZPP00163. > >>ZPP00163. > >>ZPP00163. > >>... > >> > >>- query_accession is retrieved for each hit regardless whether there is an > >>alignment or not > >>- each query_accession ends with a "." > >> > >> > >>So far I have taken advantage of the blast -b option to set the number of hits > >>to be parsed by bioperl, but I can see the ratio in changing bioperl from > >>parsing every hit that has an alignment to parsing every hit. > >> > >> > >> > >This was a requested feature. You can add a little code which exists the > >hit loop if the hit doesn't have any hsps > >last if $hit->num_hsps == 0; > > > > > > > >>Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the > >>helpful comment in line 769 makes me believe that there is the change in parsing > >>coded, but I couldn't spot any reason for the "." at the end of each > >>query_accession. Not sure whether the two are related anyway. > >> > >> > >># This is for the case when we specify -b 0 (or B=0 for WU-BLAST) > >># and still want to construct minimal Hit objects > >>while(my $v = shift @hit_signifs) { > >>next unless defined $v; > >>$self->start_element({ 'Name' => 'Hit'}); > >>... > >> > >> > >>So far I'm fixing the "dot" issue by an s/\.$// , but ... > >> > >> > >>Cheers, > >> > >>Ralf > >> > >> > >> > >> > >> > >> > >>------------------------------------------------------------------------------ > >>Dr. Ralf Schmid > >>Nematode Bioinformatics > >>Blaxter Nematode Genomics Group > >>Institute of Cell, Animal and Population Biology > >>Ashworth Labs > >>University of Edinburgh > >>King's Buildings > >>Edinburgh > >>EH9 3JT > >>UK > >> > >>(+44)(0)131 650 7403 > >> > >> > >> > >> > >> > >>_______________________________________________ > >>Bioperl-l mailing list > >>Bioperl-l@portal.open-bio.org > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > >> > >> > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From R.Schmid at ed.ac.uk Wed Mar 17 16:42:47 2004 From: R.Schmid at ed.ac.uk (Ralf Schmid) Date: Wed Mar 17 18:04:44 2004 Subject: [Bioperl-l] Bio::SearchIO blast_parsing In-Reply-To: References: Message-ID: <1079559767.4058c657e88dd@staffmail.ed.ac.uk> Jason, see attached, > ralf - can you send an example report - if I use your code and the > t/data/ecolitst.bls report in the bioperl disto I get this > jason@jason $ perl ralf_bug.pl > AAC73113.1 > AAC73113.1 > AAC73113.1 > AAC73113.1 Just tried it for ecolitst.bls - it works fine ... > also see below. > > -j > This was a requested feature. makes perfectly sense (ie not having to fill up your disk with alignments if you just want to extract hit and e-value) You can add a little code which exists the > hit loop if the hit doesn't have any hsps > last if $hit->num_hsps == 0; > Thanks, Ralf ------------------------------------------------------------------------------- Dr. Ralf Schmid Nematode Bioinformatics Blaxter Nematode Genomics Group Institute of Cell, Animal and Population Biology Ashworth Labs University of Edinburgh King\'s Buildings Edinburgh EH9 3JT UK (+44)(0)131 650 7403 -------------- next part -------------- A non-text attachment was scrubbed... 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sdavis2 at mail.nih.gov Thu Mar 18 07:30:38 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Mar 18 07:28:18 2004 Subject: [Bioperl-l] GFF synopsis code question Message-ID: I have been learning to use Bio::DB::GFF and had a question about the synopsis code from Bio::DB::GFF. The section of code is: -------From Synopsis------- # pull out all transcript features my @transcripts = $segment->features('transcript'); # for each transcript, total the length of the introns my %totals; for my $t (@transcripts) { my @introns = $t->Intron; $totals{$t->name} += $_->length foreach @introns; } # Sort the exons of the first transcript by position my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon; # Get a region 1000 bp upstream of first exon my $upstream = $exons[0]->segment(-1000,0); # get its DNA my $dna = $upstream->dna; ------------------------------- It seems here that $exons[0] is a feature, so does not have a segment method? Instead, one can get the segment of interest by: my $upstream = $db->segment($exons[0],-1000=>0) Am I mistaken? I only bring it up as a documentation issue, as the code I give works for me. Sean From lstein at cshl.edu Thu Mar 18 09:05:25 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Thu Mar 18 10:56:56 2004 Subject: [Bioperl-l] GFF synopsis code question In-Reply-To: References: Message-ID: <200403180905.25264.lstein@cshl.edu> Thanks for catching that. This is a typo in the synopsis. It should read: my $upstream = $exons[0]->subseq(-1000,0); Lincoln On Thursday 18 March 2004 07:30 am, Sean Davis wrote: > I have been learning to use Bio::DB::GFF and had a question about > the synopsis code from Bio::DB::GFF. The section of code is: > > -------From Synopsis------- > # pull out all transcript features > my @transcripts = $segment->features('transcript'); > > # for each transcript, total the length of the introns > my %totals; > for my $t (@transcripts) { > my @introns = $t->Intron; > $totals{$t->name} += $_->length foreach @introns; > } > > # Sort the exons of the first transcript by position > my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon; > > # Get a region 1000 bp upstream of first exon > my $upstream = $exons[0]->segment(-1000,0); > > # get its DNA > my $dna = $upstream->dna; > ------------------------------- > > It seems here that $exons[0] is a feature, so does not have a > segment method? Instead, one can get the segment of interest by: > > my $upstream = $db->segment($exons[0],-1000=>0) > > Am I mistaken? I only bring it up as a documentation issue, as the > code I give works for me. > > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: signature Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040318/6f86592c/attachment.bin From MRBATESALANN at netscape.net Thu Mar 18 11:46:39 2004 From: MRBATESALANN at netscape.net (MRBATESALANN@netscape.net) Date: Thu Mar 18 11:44:36 2004 Subject: [Bioperl-l] REPLY SOON Message-ID: Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. Though I am very rich, I was never generous, I was always hostile to people and only focused on my business as that was the only thing I cared for. But now I regret all this as I now know that there is more to life than just wanting to have or make all the money in the world. I believe when God gives me a second chance to come to this world I would live my life a different way from how I have lived it. Now that God has called me, I have willed and given most of my property and assets to my immediate and extended family members as well as a few close friends. I want God to be merciful to me and accept my soul so, I have decided to give alms to charity organizations, as I want this to be one of the last good deeds I do on earth. So far, I have distributed money to some charity organizations in the U.A.E, Algeria and Malaysia. Now that my health has deteriorated so badly, I cannot do this myself anymore. I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From dobbo at thevillas.eclipse.co.uk Thu Mar 18 12:43:33 2004 From: dobbo at thevillas.eclipse.co.uk (rich) Date: Thu Mar 18 12:48:55 2004 Subject: [Bioperl-l] Bio::PopGen Message-ID: <1079631813.4059dfc57a3ff@webmail.eclipse.net.uk> Hi, i've been using a number of modules under Bio::PopGen. I have extended and added to suit my needs. I was wondering whether the modules/changes might be worth adding to the distro? Basically I have, 1) created two new Bio::PopGen::IO modules (based on csv.pm): Bio::PopGen::IO::ped.pm - takes ped format data (incl family, member, parentage, gender, affeted status). This module also has the option to look at family structure and create missing parents.This is required for using TRANSMIT Bio::PopGen::IO::phase.pm - deals with PHASE format data (I am also creating a Bio::PopGen::IO::hapmap.pm mod that deals with hapmap data) 2) I have changed Bio::PopGen::IO::csv.pm (and included within Bio::PopGen::IO::ped.pm) the ability to accept data where the field delim is the same as the allele delim (doesn't affect Bio::PopGen::IO::phase.pm) 3)In order to deal with the ped format I extended Bio::PopGen::Individual.pm so that an individual object will take ped data (fam id, member id,mother, father, sex, affected status) cheers Rich From vamsi at warta.bio.psu.edu Thu Mar 18 12:54:35 2004 From: vamsi at warta.bio.psu.edu (Vamsi) Date: Thu Mar 18 12:59:56 2004 Subject: [Bioperl-l] Bio::TreeIO::svggraph problems Message-ID: <200403181754.i2IHsZV05138@warta.bio.psu.edu> Hi, I am trying to use the Bio::TreeIO::svggraph module to display a newick format tree. Here is the tree: (a,b); and the code: ------------------------------------------- use Bio::TreeIO; my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); my $out = new Bio::TreeIO(-file => ">$ARGV[1]", -format => 'svggraph'); while( my $tree = $in->next_tree ) { my $svg_xml = $out->write_tree($tree); } ------------------------------------------- (which is from the documentation for Bio::TreeIO::svggraph) I have all the required SVG modules installed. But, I get the error Can't locate object method "new" via package "SVG::Graph::Glyph::tree" at /usr/perl5/site_perl/5.005/SVG/Graph/Frame.pm line 117, chunk 1. Any suggestions? Thanks, Vamsi From vamsi at warta.bio.psu.edu Thu Mar 18 13:05:54 2004 From: vamsi at warta.bio.psu.edu (Vamsi) Date: Thu Mar 18 13:11:16 2004 Subject: [Bioperl-l] Bio::TreeIO::svggraph problems Message-ID: <200403181805.i2II5sV05214@warta.bio.psu.edu> Hi, I am trying to use the Bio::TreeIO::svggraph module to display a newick format tree. Here is the tree: (a,b); and the code: ------------------------------------------- use Bio::TreeIO; my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); my $out = new Bio::TreeIO(-file => ">$ARGV[1]", -format => 'svggraph'); while( my $tree = $in->next_tree ) { my $svg_xml = $out->write_tree($tree); } ------------------------------------------- (which is from the documentation for Bio::TreeIO::svggraph) I have all the required SVG modules installed. But, I get the error Can't locate object method "new" via package "SVG::Graph::Glyph::tree" at /usr/perl5/site_perl/5.005/SVG/Graph/Frame.pm line 117, chunk 1. Any suggestions? Thanks, Vamsi From paulo.david at netvisao.pt Thu Mar 18 13:40:37 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Thu Mar 18 13:43:07 2004 Subject: [Bioperl-l] Bio::TreeIO::svggraph problems In-Reply-To: <200403181754.i2IHsZV05138@warta.bio.psu.edu> References: <200403181754.i2IHsZV05138@warta.bio.psu.edu> Message-ID: <4059ED25.6030503@netvisao.pt> Your code works for me, cut and pasted frome the e-mail, with the same tree. This is a long shot, but try enclosing '-file' and '-format' with single quotes, when you create $in and $out. I have perl 5.6.1, but I think earlier versions may have a problem with that. -Paulo Vamsi wrote: >I am trying to use the Bio::TreeIO::svggraph module to >display a newick format tree. Here is the tree: > >(a,b); > >and the code: > >------------------------------------------- >use Bio::TreeIO; > >my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); >my $out = new Bio::TreeIO(-file => ">$ARGV[1]", -format => 'svggraph'); > >while( my $tree = $in->next_tree ) { > my $svg_xml = $out->write_tree($tree); >} >------------------------------------------- > >(which is from the documentation for Bio::TreeIO::svggraph) > >I have all the required SVG modules installed. But, I get the error > >Can't locate object method "new" via package "SVG::Graph::Glyph::tree" at >/usr/perl5/site_perl/5.005/SVG/Graph/Frame.pm line 117, chunk 1. > From vamsi at warta.bio.psu.edu Thu Mar 18 14:03:24 2004 From: vamsi at warta.bio.psu.edu (Vamsi) Date: Thu Mar 18 14:09:07 2004 Subject: [Bioperl-l] Bio::TreeIO::svggraph problems In-Reply-To: <4059ED25.6030503@netvisao.pt> from "Paulo Almeida" at Mar 18, 2004 06:40:37 PM Message-ID: <200403181903.i2IJ3PO05521@warta.bio.psu.edu> No. That does not seem to be the problem since I can write out in other formats like 'tabtree' etc. The problem is with the SVG module but I have no idea where ... Thanks, Vamsi > > Your code works for me, cut and pasted frome the e-mail, with the same > tree. This is a long shot, but try enclosing '-file' and '-format' with > single quotes, when you create $in and $out. I have perl 5.6.1, but I > think earlier versions may have a problem with that. > > -Paulo > > Vamsi wrote: > > >I am trying to use the Bio::TreeIO::svggraph module to > >display a newick format tree. Here is the tree: > > > >(a,b); > > > >and the code: > > > >------------------------------------------- > >use Bio::TreeIO; > > > >my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); > >my $out = new Bio::TreeIO(-file => ">$ARGV[1]", -format => 'svggraph'); > > > >while( my $tree = $in->next_tree ) { > > my $svg_xml = $out->write_tree($tree); > >} > >------------------------------------------- > > > >(which is from the documentation for Bio::TreeIO::svggraph) > > > >I have all the required SVG modules installed. But, I get the error > > > >Can't locate object method "new" via package "SVG::Graph::Glyph::tree" at > >/usr/perl5/site_perl/5.005/SVG/Graph/Frame.pm line 117, chunk 1. > > > > > From jason at cgt.duhs.duke.edu Thu Mar 18 14:13:12 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Mar 18 14:18:39 2004 Subject: [Bioperl-l] Bio::PopGen In-Reply-To: <1079631813.4059dfc57a3ff@webmail.eclipse.net.uk> References: <1079631813.4059dfc57a3ff@webmail.eclipse.net.uk> Message-ID: Rich - Looks great. The ped info is incorporated into the bioperl-pedigree cvs module where I have father/mother/sibling information as well as a ped parser. Since the types of analyses are different for related individuals than for unrelated populations. If you send me your changes I can see about incorporating them - but you may want to look at the bioperl-pedigree dist first as well. -jason On Thu, 18 Mar 2004, rich wrote: > > Hi, > > i've been using a number of modules under Bio::PopGen. > > I have extended and added to suit my needs. I was > wondering whether the modules/changes might be worth > adding to the distro? > > Basically I have, > > 1) created two new Bio::PopGen::IO modules (based on > csv.pm): > > Bio::PopGen::IO::ped.pm - takes ped format data (incl > family, member, parentage, gender, affeted status). > > This module also has the option to look at family > structure and create missing parents.This is required > for using TRANSMIT > > Bio::PopGen::IO::phase.pm - deals with PHASE format data > > (I am also creating a Bio::PopGen::IO::hapmap.pm mod > that deals with hapmap data) > > 2) I have changed Bio::PopGen::IO::csv.pm (and included > within Bio::PopGen::IO::ped.pm) the ability to accept > data where the field delim is the same as the allele delim > (doesn't affect Bio::PopGen::IO::phase.pm) > > 3)In order to deal with the ped format I extended > Bio::PopGen::Individual.pm so that an individual object > will take ped data (fam id, member id,mother, father, > sex, affected status) > > > cheers > Rich > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From steve_chervitz at affymetrix.com Thu Mar 18 15:58:40 2004 From: steve_chervitz at affymetrix.com (Steve Chervitz) Date: Thu Mar 18 16:03:34 2004 Subject: [Bioperl-l] SearchIO::blast frac_aligned/identical/conserved bug fix Message-ID: <08C68436-791F-11D8-B56C-000A95765236@affymetrix.com> Just wanted to let folks know that I recently fixed a bug regarding the reporting of fraction aligned/identical/conserved for BLASTX, TBLASTX, and TBLASTN reports. For details, see http://bugzilla.bioperl.org/show_bug.cgi?id=1597 . This bug occurs when parsing these reports using SearchIO with -format=>'blast'. It is present in the 1.4 release (as well as 1.2.x and 1.3.x and possibly earlier). I fixed this in CVS on both branch-1-4 and bioperl-live. Steve -- Steve Chervitz AFFYMETRIX, INC. | 6550 Vallejo St. Ste 100 | Emeryville, CA 94608 Tel: 510-428-8530 | Fax: 510-428-8585 | Steve_Chervitz at affymetrix.com From bdirks at uclink.berkeley.edu Thu Mar 18 19:25:43 2004 From: bdirks at uclink.berkeley.edu (Bill Dirks) Date: Thu Mar 18 19:31:04 2004 Subject: [Bioperl-l] Bio::Tools::Genewise Message-ID: Hi, I believe there is an error in the synopsis section of Bioperl::Tools::Genewise The line that reads: my $gw = Bio::Tools::Genewise(-file=>"genewise.out"); It should be, I believe: my $gw = Bio::Tools::Genewise->new(-file=>"genewise.out"); I, however, still can't the synopsis to work. I put the output of the genewise example: genewise road.pep human.genomic > genewise.out and tried the synopsis sample script. However, $gw->next_prediction does not return anything. Does anyone have any ideas why? Thanks, Bill From shawnh at stanford.edu Thu Mar 18 19:41:31 2004 From: shawnh at stanford.edu (Shawn Hoon) Date: Thu Mar 18 19:46:52 2004 Subject: [Bioperl-l] Bio::Tools::Genewise In-Reply-To: References: Message-ID: <2AA8428F-793E-11D8-B0C2-000A95783436@stanford.edu> You would need to add the -genesf option when running genewise. Also, you can check out the wrapper for genewise in Bio::Tools::Run::Genewise in the bioperl-run package. cheers, shawn On Mar 18, 2004, at 4:25 PM, Bill Dirks wrote: > Hi, I believe there is an error in the synopsis section of > Bioperl::Tools::Genewise The line that reads: my $gw = > Bio::Tools::Genewise(-file=>"genewise.out"); It should be, I believe: > my $gw = Bio::Tools::Genewise->new(-file=>"genewise.out"); I, however, > still can't the synopsis to work. I put the output of the genewise > example: genewise road.pep human.genomic > genewise.out and tried the > synopsis sample script. However, $gw->next_prediction does not return > anything. Does anyone have any ideas why? Thanks, > Bill > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From birney at ebi.ac.uk Fri Mar 19 04:25:44 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Fri Mar 19 04:31:23 2004 Subject: [Bioperl-l] Bio::Tools::Genewise In-Reply-To: <2AA8428F-793E-11D8-B0C2-000A95783436@stanford.edu> Message-ID: On Thu, 18 Mar 2004, Shawn Hoon wrote: > You would need to add the -genesf option when running genewise. > > Also, you can check out the wrapper for genewise in > Bio::Tools::Run::Genewise in the bioperl-run package. I think -genesf is only available in the (now rather venerable) release candidate Genewise at http://www.sanger.ac.uk/Users/birney/wise2.2.3-rc7.tar.gz The reason for not releasing this is that actually I need to back out the changes made for the case of BLOSUM62.bla (it is in fact better to keep as backwardly compatible as possible) which all comes down to the case insanity that is Apple's HFS+ file system not playing nicely with cvs. (yup. That was too much detail right?) I will try to push the Wise2 package into some sort of sanity over this month wrt to these things and then make a proper release. For the moment, use the release candidate above... From gabriele.bucci at ieo-research.it Fri Mar 19 10:07:48 2004 From: gabriele.bucci at ieo-research.it (gabriele bucci) Date: Fri Mar 19 09:44:11 2004 Subject: [Bioperl-l] retrieving genomic sequence Message-ID: <200403191607.49531.gabriele.bucci@ieo-research.it> Hi everibody. Does anyone know if I could use BioPerl for retrieving DNA string from multiple specified genomic region? I mean, eg: from chromosome 1 starting 1598675 to 1689000, from chr 2 100.... to 101... ecc. I'm pretty sure it's possible but as a beginners as I'm I can't find the way trough the various perldocs.... Thanks to everybody in advance. Gabriele From kviel at emory.edu Fri Mar 19 09:48:43 2004 From: kviel at emory.edu (Kevin Roland Viel) Date: Fri Mar 19 09:54:02 2004 Subject: [Bioperl-l] ABI.pm and .ab1 files In-Reply-To: <200403191607.49531.gabriele.bucci@ieo-research.it> References: <200403191607.49531.gabriele.bucci@ieo-research.it> Message-ID: Is it possible to use the ABI.pm module to abstract the trace values from *.ab1 files? My inclination is that is not possible. Admittedly, I am quite weak in perl. Examining the module, I see only that it uses the binmode() function. I do not have an example of an *.abi file, but I cannot see where ABI.pm treats the file as anything different from a text file. I understand that the .ab1 file stores its data in Big Endian format. It could be that IO::File incorporates this, however. Thanks in advance, Kevin Kevin Viel Department of Epidemiology Rollins School of Public Health Emory University Atlanta, GA 30322 From skirov at utk.edu Fri Mar 19 10:40:15 2004 From: skirov at utk.edu (Stefan Kirov) Date: Fri Mar 19 10:45:55 2004 Subject: [Bioperl-l] retrieving genomic sequence In-Reply-To: <200403191607.49531.gabriele.bucci@ieo-research.it> References: <200403191607.49531.gabriele.bucci@ieo-research.it> Message-ID: <405B145F.1050505@utk.edu> You may want to try ensembl API: let's say you have a file like this: mychr.dat: 1,1598675,1689000 2,100,101 etc. open (CHR, ") { chomp $line; my ($chr, $start,$end)=split(/,/,$line); my $slice = $slice_adaptor->fetch_by_chr_start_end($chr,$start,$end); ................do something with it.... } To see how to work with ensembl go to http://www.ensembl.org/Docs/ and get the tutorial. It is based on Bioperl to some extent, and what you want is documented pretty well I believe. Also see http://www.ensembl.org/Docs/Pdoc/ensembl/. Hope this helps... amd have fun. Stefan gabriele bucci wrote: >Hi everibody. >Does anyone know if I could use BioPerl for retrieving DNA string from >multiple specified genomic region? >I mean, eg: from chromosome 1 starting 1598675 to 1689000, from chr 2 100.... >to 101... ecc. >I'm pretty sure it's possible but as a beginners as I'm I can't find the way >trough the various perldocs.... >Thanks to everybody in advance. > >Gabriele > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Stefan Kirov, Ph.D. University of Tennessee/Oak Ridge National Laboratory 1060 Commerce Park, Oak Ridge TN 37830-8026 USA tel +865 576 5120 fax +865 241 1965 e-mail: skirov@utk.edu sao@ornl.gov From Anthony.Underwood at hpa.org.uk Fri Mar 19 10:37:27 2004 From: Anthony.Underwood at hpa.org.uk (SRMD, Col - Underwood, Anthony) Date: Fri Mar 19 10:49:41 2004 Subject: [Bioperl-l] ABI.pm and .ab1 files Message-ID: <427DA33A6101484BA7A72934AF90DF73051AA853@exchange1.phls.org.uk> Hi Kevin As far as I am aware the ABI module doesn't allow this. However if you run an abi file through phred (available free to academic/non-profit-http://www.phrap.org/) with the -c option (e.g phred -c trace.abi) this will write out an scf file which can have the trace values extracted using the BioPerl SCF IO module. I hope that this helps. Anthony Dr Anthony Underwood Bioinformatics Group Genomics, Proteomic and Bioinformatics Unit Central Public Health Laboratory Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 2004400 ext. 3618 f: 0208 3583138 e: anthony.underwood@hpa.org.uk > -----Original Message----- > From: Kevin Roland Viel [mailto:kviel@emory.edu] > Sent: 19 March 2004 14:49 > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] ABI.pm and .ab1 files > > > Is it possible to use the ABI.pm module to abstract the trace > values from > *.ab1 files? My inclination is that is not possible. > Admittedly, I am > quite weak in perl. Examining the module, I see only that it uses the > binmode() function. I do not have an example of an *.abi file, but I > cannot see where ABI.pm treats the file as anything different > from a text > file. I understand that the .ab1 file stores its data in Big Endian > format. It could be that IO::File incorporates this, however. > > Thanks in advance, > > Kevin > > > Kevin Viel > Department of Epidemiology > Rollins School of Public Health > Emory University > Atlanta, GA 30322 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason at cgt.duhs.duke.edu Fri Mar 19 12:14:02 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 19 12:19:31 2004 Subject: [Bioperl-l] Bio::Tools::Genewise In-Reply-To: References: Message-ID: I think it is 2.2.0. Note the ! lines. For those of you on linux biolinux.org provides a nice rpm install of wise 2.2.0 -j [jason@lugano jason]$ genewise -help genewise ($Name: wise2-2-0 $) genewise in fasta format Dna sequence options -u start position in dna -v end position in dna -trev Compare on the reverse strand -tfor [default] Compare on the forward strand -both Both strands -tabs Report positions as absolute to truncated/reverse sequence -fembl File is an EMBL file native format Protein comparison options -s start position in protein -t end position in protein -[g]ap [ 12] gap penalty -[e]xt [ 2] extension penalty -[m]atrix [blosum62.bla] Comparison matrix HMM options -hmmer Protein file is HMMer file (version 2 compatible) -hname Use this as the name of the HMM, not filename Gene Model options -init [default] [default/global/local/wing/endbias] startend policy for the HMM/protein -codon [codon.table] Codon file -gene [human.gf] Gene parameter file -subs [1e-05] Substitution error rate -indel [1e-05] Insertion/deletion error rate -cfreq [model/flat] Using codon bias or not? [default flat] -splice [model/flat] Using splice model or GT/AG? [default model] -intron [model/tied] Use tied model for introns [default tied] -null [syn/flat] Random Model as synchronous or flat [default syn] -pg Potential Gene file (heurestic for speeding alignments) -alln [1.0] Probability of matching a NNN codon -insert [model/flat] Use protein insert model [default flat] Algorithm options -alg [623/623L/2193/2193L] Algorithm used [default 623/623L] Output options [default -pretty -para] -pretty show pretty ascii output -pseudo Mark genes with frameshifts as pseudogenes -genes show gene structure ! ! -genesf show gene structure with supporting evidence ! -embl show EMBL feature format with CDS key -diana show EMBL feature format with misc_feature key (for diana) -para show parameters -sum show summary output -cdna show cDNA -trans show protein translation, breaking at frameshifts -pep show protein translation, splicing frameshifts -ace ace file gene structure -gff Gene Feature Format file -gener raw gene structure -alb show logical AlnBlock alignment -pal show raw matrix alignment -block [50] Length of main block in pretty output -divide [//] divide string for multiple outputs New gene model statistics -splice_max_collar [5.0] maximum Bits value for a splice site -splice_min_collar [-5.0] minimum Bits value for a splice site -splice_score_offset [4.5] score offset for splice sites -genestats [gene.stat] Dynamic programming matrix implementation -dymem memory style [default/linear/explicit] -kbyte memory amount to use [4000] -dydebug drop into dynamite dp matrix debugger Standard options -help help -version show version and compile info -silent No messages on stderr -quiet No report on stderr -erroroffstd No warning messages to stderr -errorlog [file] Log warning messages to file See WWW help at http://www.sanger.ac.uk/Software/Wise2/ On Fri, 19 Mar 2004, Ewan Birney wrote: > > > On Thu, 18 Mar 2004, Shawn Hoon wrote: > > > You would need to add the -genesf option when running genewise. > > > > Also, you can check out the wrapper for genewise in > > Bio::Tools::Run::Genewise in the bioperl-run package. > > I think -genesf is only available in the (now rather venerable) release > candidate Genewise at > > http://www.sanger.ac.uk/Users/birney/wise2.2.3-rc7.tar.gz > > > The reason for not releasing this is that actually I need to back out the > changes made for the case of BLOSUM62.bla (it is in fact better to keep as > backwardly compatible as possible) which all comes down to the case > insanity that is Apple's HFS+ file system not playing nicely with cvs. > > (yup. That was too much detail right?) > > > I will try to push the Wise2 package into some sort of sanity over this > month wrt to these things and then make a proper release. For the moment, > use the release candidate above... > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Fri Mar 19 12:16:17 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 19 12:21:40 2004 Subject: [Bioperl-l] retrieving genomic sequence In-Reply-To: <200403191607.49531.gabriele.bucci@ieo-research.it> References: <200403191607.49531.gabriele.bucci@ieo-research.it> Message-ID: See Bio::DB::Fasta for a fast and easy way to do this for a local copy of the genome you are interested in. Bio::DB::GFF will also do this for you if you want to load the data into a relational database. -jason On Fri, 19 Mar 2004, gabriele bucci wrote: > Hi everibody. > Does anyone know if I could use BioPerl for retrieving DNA string from > multiple specified genomic region? > I mean, eg: from chromosome 1 starting 1598675 to 1689000, from chr 2 100.... > to 101... ecc. > I'm pretty sure it's possible but as a beginners as I'm I can't find the way > trough the various perldocs.... > Thanks to everybody in advance. > > Gabriele > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From bdirks at uclink.berkeley.edu Fri Mar 19 12:28:21 2004 From: bdirks at uclink.berkeley.edu (Bill Dirks) Date: Fri Mar 19 12:33:42 2004 Subject: [Bioperl-l] Bio::Tools::Genewise In-Reply-To: Message-ID: Thanks for your help. I have wise 2.2.0 and the flag worked. Now, I'm going to check out Bio::Tools::Run::Genewise. Bill On Fri, 19 Mar 2004 12:14:02 -0500 (EST) Jason Stajich wrote: >I think it is 2.2.0. Note the ! lines. > >For those of you on linux biolinux.org provides a nice rpm install of wise >2.2.0 > >-j >[jason@lugano jason]$ genewise -help >genewise ($Name: wise2-2-0 $) >genewise in fasta format >Dna sequence options > -u start position in dna > -v end position in dna > -trev Compare on the reverse strand > -tfor [default] Compare on the forward strand > -both Both strands > -tabs Report positions as absolute to truncated/reverse >sequence > -fembl File is an EMBL file native format >Protein comparison options > -s start position in protein > -t end position in protein > -[g]ap [ 12] gap penalty > -[e]xt [ 2] extension penalty > -[m]atrix [blosum62.bla] Comparison matrix >HMM options > -hmmer Protein file is HMMer file (version 2 compatible) > -hname Use this as the name of the HMM, not filename >Gene Model options > -init [default] [default/global/local/wing/endbias] startend policy >for the HMM/protein > -codon [codon.table] Codon file > -gene [human.gf] Gene parameter file > -subs [1e-05] Substitution error rate > -indel [1e-05] Insertion/deletion error rate > -cfreq [model/flat] Using codon bias or not? [default flat] > -splice [model/flat] Using splice model or GT/AG? [default model] > -intron [model/tied] Use tied model for introns [default tied] > -null [syn/flat] Random Model as synchronous or flat [default syn] > -pg Potential Gene file (heurestic for speeding >alignments) > -alln [1.0] Probability of matching a NNN codon > -insert [model/flat] Use protein insert model [default flat] >Algorithm options > -alg [623/623L/2193/2193L] Algorithm used [default 623/623L] >Output options [default -pretty -para] > -pretty show pretty ascii output > -pseudo Mark genes with frameshifts as pseudogenes > -genes show gene structure >! >! -genesf show gene structure with supporting evidence >! > -embl show EMBL feature format with CDS key > -diana show EMBL feature format with misc_feature key (for >diana) > -para show parameters > -sum show summary output > -cdna show cDNA > -trans show protein translation, breaking at frameshifts > -pep show protein translation, splicing frameshifts > -ace ace file gene structure > -gff Gene Feature Format file > -gener raw gene structure > -alb show logical AlnBlock alignment > -pal show raw matrix alignment > -block [50] Length of main block in pretty output > -divide [//] divide string for multiple outputs >New gene model statistics > -splice_max_collar [5.0] maximum Bits value for a splice site > -splice_min_collar [-5.0] minimum Bits value for a splice site > -splice_score_offset [4.5] score offset for splice sites > -genestats [gene.stat] >Dynamic programming matrix implementation > -dymem memory style [default/linear/explicit] > -kbyte memory amount to use [4000] > -dydebug drop into dynamite dp matrix debugger >Standard options > -help help > -version show version and compile info > -silent No messages on stderr > -quiet No report on stderr > -erroroffstd No warning messages to stderr > -errorlog [file] Log warning messages to file > >See WWW help at http://www.sanger.ac.uk/Software/Wise2/ > > > > >On Fri, 19 Mar 2004, Ewan Birney wrote: > >> >> >> On Thu, 18 Mar 2004, Shawn Hoon wrote: >> >> > You would need to add the -genesf option when running genewise. >> > >> > Also, you can check out the wrapper for genewise in >> > Bio::Tools::Run::Genewise in the bioperl-run package. >> >> I think -genesf is only available in the (now rather venerable) release >> candidate Genewise at >> >> http://www.sanger.ac.uk/Users/birney/wise2.2.3-rc7.tar.gz >> >> >> The reason for not releasing this is that actually I need to back out the >> changes made for the case of BLOSUM62.bla (it is in fact better to keep as >> backwardly compatible as possible) which all comes down to the case >> insanity that is Apple's HFS+ file system not playing nicely with cvs. >> >> (yup. That was too much detail right?) >> >> >> I will try to push the Wise2 package into some sort of sanity over this >> month wrt to these things and then make a proper release. For the moment, >> use the release candidate above... >> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu From wstrauss at genwaybio.com Fri Mar 19 16:59:25 2004 From: wstrauss at genwaybio.com (William Strauss) Date: Fri Mar 19 17:05:35 2004 Subject: [Bioperl-l] bioperl installation advice needed Message-ID: I download from cpan the Bundle::BioPerl module and I did the installation of it but it says that IO::String isn't available on cpan. Do you know where I can get the IO::String or how I can properly download it from cpan? From jason at cgt.duhs.duke.edu Fri Mar 19 17:26:00 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Fri Mar 19 17:31:24 2004 Subject: [Bioperl-l] bioperl installation advice needed In-Reply-To: References: Message-ID: Did you just try cpan> install IO::String It should be on there, maybe something is not working with your cpan configuration? You did do cpan> install Bundle::BioPerl I have found problems with Net::FTP and needing to use FTP passive mode depending on your local network setup. Otherwise you can always grab it here (or at any CPAN mirror) ftp://ftp.duke.edu/pub/perl/modules/by-module/IO/IO-String-1.04.tar.gz -jason On Fri, 19 Mar 2004, William Strauss wrote: > I download from cpan the Bundle::BioPerl module and I did the installation > of it but it says that IO::String isn't available on cpan. Do you know > where I can get the IO::String or how I can properly download it from cpan? > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mcipriano at mbl.edu Sun Mar 21 20:19:51 2004 From: mcipriano at mbl.edu (Michael Cipriano) Date: Sun Mar 21 20:25:18 2004 Subject: [Bioperl-l] alignio Message-ID: <000201c40fab$c67e0b70$c1c01543@Ripley> If I have a string that is the text that is inside a nexus file, can I get that to an AlignIO object without creating a temp file? Michael Cipriano (mcipriano@mbl.edu) Research Assistant I, Global Infectious Diseases From jason at cgt.duhs.duke.edu Sun Mar 21 21:26:57 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Sun Mar 21 21:32:24 2004 Subject: [Bioperl-l] alignio In-Reply-To: <000201c40fab$c67e0b70$c1c01543@Ripley> References: <000201c40fab$c67e0b70$c1c01543@Ripley> Message-ID: use IO::String to make a filehandle and pass the fh in. See the FAQ - analagous information for how to do this for SeqIO. -j On Sun, 21 Mar 2004, Michael Cipriano wrote: > If I have a string that is the text that is inside a nexus file, can I > get that to an AlignIO object without creating a temp file? > > Michael Cipriano (mcipriano@mbl.edu) > Research Assistant I, Global Infectious Diseases > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mpjfb at usc.es Mon Mar 22 04:08:21 2004 From: mpjfb at usc.es (mpjfb@usc.es) Date: Mon Mar 22 04:13:50 2004 Subject: [Bioperl-l] Can't run bioperl from java Message-ID: <1079946501.405ead053c2e2@correoweb.usc.es> Hello. I don't know if this is of topic but I have some problems trying to run Bioperl from Java. My problem comes as follows: I wrote a perl script tha perform multiple blast alignments and parses them. As this programs needs to be run in text mode (and it can be really painfull when you have to add many arguments) I decided to write a GUI using JAVA. When I run my perl script directly it works fine and if I run other perl scripts (that don't use bioperl) from the GUI everything works fine. Does anyone have any advice of what can be the problem???? I thought that it can be some error with my bioperl install (I move from OSX 10.1 to 10.3). Any help would be apprecited. thanks a lot, Julio From ak at ebi.ac.uk Mon Mar 22 04:31:12 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Mon Mar 22 04:36:39 2004 Subject: [Bioperl-l] Can't run bioperl from java In-Reply-To: <1079946501.405ead053c2e2@correoweb.usc.es> References: <1079946501.405ead053c2e2@correoweb.usc.es> Message-ID: <20040322093112.GA27094@ebi.ac.uk> On Mon, Mar 22, 2004 at 10:08:21AM +0100, mpjfb@usc.es wrote: > Hello. > I don't know if this is of topic but I have some problems trying to run Bioperl > from Java. > My problem comes as follows: > I wrote a perl script tha perform multiple blast alignments and parses them. > As this programs needs to be run in text mode (and it can be really painfull > when you have to add many arguments) I decided to write a GUI using JAVA. > When I run my perl script directly it works fine and if I run other perl scripts > (that don't use bioperl) from the GUI everything works fine. > Does anyone have any advice of what can be the problem???? I thought that it can > be some error with my bioperl install (I move from OSX 10.1 to 10.3). > Any help would be apprecited. > thanks a lot, Julio Do you get any error messages whatsoever? (Is there a reason you don't want to use BioJava for the whole application? It should be able to handle blast parsing I would have thougth.) Andreas -- |[][]| Andreas K?h?ri |=][=| | [] | EMBL, European Bioinformatics Institute |[==]| |[][]| Wellcome Trust Genome Campus |=][=| | [] | Hinxton, Cambridgeshire, CB10 1SD |[==]| |[][]| United Kingdom |=][=| From gert.thijs at esat.kuleuven.ac.be Mon Mar 22 05:06:04 2004 From: gert.thijs at esat.kuleuven.ac.be (Gert Thijs) Date: Mon Mar 22 05:11:38 2004 Subject: [Bioperl-l] Can't run bioperl from java In-Reply-To: <1079946501.405ead053c2e2@correoweb.usc.es> References: <1079946501.405ead053c2e2@correoweb.usc.es> Message-ID: <1079949962.3103.43.camel@sista-08.esat.kuleuven.ac.be> Julio, As far as I understand the problem from your description, I guess the problem stems from the way java runs system calls. We had a similar problem here a while ago. I do not remember the details of the problem/solution, but I remember that part of the problems was that some SHELL variables are not the same in the java system call compared to running it on the command line. If I am not mistaken, I think that you can add extra arguments to the java system call to set these shell variables like PATH, PERL5LIB. Gert On Mon, 2004-03-22 at 10:08, mpjfb@usc.es wrote: > Hello. > I don't know if this is of topic but I have some problems trying to run Bioperl > from Java. > My problem comes as follows: > I wrote a perl script tha perform multiple blast alignments and parses them. > As this programs needs to be run in text mode (and it can be really painfull > when you have to add many arguments) I decided to write a GUI using JAVA. > When I run my perl script directly it works fine and if I run other perl scripts > (that don't use bioperl) from the GUI everything works fine. > Does anyone have any advice of what can be the problem???? I thought that it can > be some error with my bioperl install (I move from OSX 10.1 to 10.3). > Any help would be apprecited. > thanks a lot, Julio > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- + Gert Thijs + Postdoctoral Researcher + K.U.Leuven + ESAT-SCD + Kasteelpark Arenberg 10 + B-3001 Leuven-Heverlee + Belgium + + Tel : +32 16 327928 + Fax : +32 16 321970 + email: gert.thijs@esat.kuleuven.ac.be + + http://www.esat.kuleuven.ac.be/~thijs + http://www.esat.kuleuven.ac.be/~dna/BioI/ + From Oliver.Wafzig at axaron.com Mon Mar 22 05:44:59 2004 From: Oliver.Wafzig at axaron.com (Oliver Wafzig) Date: Mon Mar 22 05:47:49 2004 Subject: [Bioperl-l] Can't run bioperl from java In-Reply-To: <1079946501.405ead053c2e2@correoweb.usc.es> References: <1079946501.405ead053c2e2@correoweb.usc.es> Message-ID: <200403221144.59601.Oliver.Wafzig@axaron.com> Hi Julio, if you are using one string (containing all your perl commandline args and whitespaces) to call 'runtime().exec()', try it using a string array. It might help. Oliver On Monday 22 March 2004 10:08, mpjfb@usc.es wrote: > Hello. > I don't know if this is of topic but I have some problems trying to run > Bioperl from Java. > My problem comes as follows: > I wrote a perl script tha perform multiple blast alignments and parses > them. As this programs needs to be run in text mode (and it can be really > painfull when you have to add many arguments) I decided to write a GUI > using JAVA. When I run my perl script directly it works fine and if I run > other perl scripts (that don't use bioperl) from the GUI everything works > fine. > Does anyone have any advice of what can be the problem???? I thought that > it can be some error with my bioperl install (I move from OSX 10.1 to > 10.3). Any help would be apprecited. > thanks a lot, Julio > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From mpjfb at usc.es Mon Mar 22 06:08:40 2004 From: mpjfb at usc.es (mpjfb@usc.es) Date: Mon Mar 22 06:14:07 2004 Subject: [Bioperl-l] Can't run bioperl from java In-Reply-To: <200403221144.59601.Oliver.Wafzig@axaron.com> References: <1079946501.405ead053c2e2@correoweb.usc.es> <200403221144.59601.Oliver.Wafzig@axaron.com> Message-ID: <1079953720.405ec938b5cb5@correoweb.usc.es> Hello. Thanks for your fast answers. I tryied both writting the commands in a single string and in an array and in both cases I have he same problem. I'm not getting any error message. What it happens is that the perl scripts starts and when it comes to analize the first sequence it seems that the perl script ends and the java programs goes to the next task as if everything went well. Maybe the problem is not with bioperl but with the programs bioperl calls (blast in this case) as the program finishes working when it's supposed to start with the first blast. I check both the console and the java error log and there are no error messages in any of them. I will try to test a bioperl script were I don't call any other external program like blast to check if this is the problem. Thanks again, Julio. Mensaje citado por Oliver Wafzig : > Hi Julio, > if you are using one string (containing all your perl commandline args and > whitespaces) to call 'runtime().exec()', try it using a string array. > It might help. > > Oliver > > > On Monday 22 March 2004 10:08, mpjfb@usc.es wrote: > > Hello. > > I don't know if this is of topic but I have some problems trying to run > > Bioperl from Java. > > My problem comes as follows: > > I wrote a perl script tha perform multiple blast alignments and parses > > them. As this programs needs to be run in text mode (and it can be really > > painfull when you have to add many arguments) I decided to write a GUI > > using JAVA. When I run my perl script directly it works fine and if I run > > other perl scripts (that don't use bioperl) from the GUI everything works > > fine. > > Does anyone have any advice of what can be the problem???? I thought that > > it can be some error with my bioperl install (I move from OSX 10.1 to > > 10.3). Any help would be apprecited. > > thanks a lot, Julio > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From zhouyuwhu at hotmail.com Mon Mar 22 01:42:14 2004 From: zhouyuwhu at hotmail.com (=?gb2312?B?1twg0+4=?=) Date: Mon Mar 22 09:08:29 2004 Subject: [Bioperl-l] How to extract intron's exon sequences? Message-ID: Hi, everyone, Is there any module to esaily extract intron's upstream and downstream exon sequences? Thanks. Yu Zhou _________________________________________________________________ ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger: http://messenger.msn.com/cn From jason at cgt.duhs.duke.edu Mon Mar 22 09:35:36 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Mar 22 09:41:04 2004 Subject: [Bioperl-l] How to extract intron's exon sequences? In-Reply-To: References: Message-ID: Really depends on the data you are working with. Where are your annotations coming from. What Species? Ensembl has made this easy to do for species in the ensembl system. You can also write code to do this based on annotated sequence records using Bio::SeqIO to parse and manipulating sequences and their annotations. See the Feature-Annotation HOWTO on the bioperl HOWTO page for some more examples. -jason On Mon, 22 Mar 2004, [gb2312] ÖÜ Óî wrote: > Hi, everyone, > > Is there any module to esaily extract intron's upstream and downstream exon > sequences? Thanks. > > > Yu Zhou > > _________________________________________________________________ > ÓëÁª»úµÄÅóÓѽøÐн»Á÷£¬ÇëʹÓà MSN Messenger: http://messenger.msn.com/cn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From antivirus at unito.it Mon Mar 22 11:09:41 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Mon Mar 22 11:15:09 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0322170932678] Message-ID: <200403221609.i2MG9gIj032711@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: tvenesio@unito.it Inflex ID: 0322170932678 Report Details ----------------------------------------------- AntiVirus Results... File NAME/TYPE Scan Results MS-DOS executable (EXE), OS/2 or MS Windows 0322170932678 from:bioperl-l@bioperl.org to: tvenesio@unito.it END OF MESSAGE. End. . From chauser at duke.edu Mon Mar 22 11:29:51 2004 From: chauser at duke.edu (Charles Hauser) Date: Mon Mar 22 11:35:24 2004 Subject: [Bioperl-l] Identifying bla(s)t hits which overlap Message-ID: <1079972990.19558.30.camel@pandorina> I'm interested in identifying assembled EST contigs which span genomic scaffolds as a means of tying scaffolds together. So, I would like to find blast or blat hits which overlap: schematic of bla(s)t hits: contig 1.xxx --------------------------------------------- scaffold 1 ----------------[-- scaffold N --]----------- It appears I need to use Bio::SimpleAlign but thought I'd ask if there are other approaches? Charles From cdwan at mail.ahc.umn.edu Mon Mar 22 12:16:34 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Mon Mar 22 12:22:03 2004 Subject: [Bioperl-l] Correct values for "strand?" Message-ID: There is some debate in my little group of programmers about the correct values to indicate the strand of a feature. I'm wondering if there is any agreed standard that we should work towards...and if (failing that) there is a preference among the members of this list. These seem to be the options that I find in the code: '1' : forward strand (Watson) '0' : unknown, or not meaninful '-1' : reverse strand (Crick) ** OR ** '+' : forward strand '-' : reverse strand I lean towards the first because of the many statements like this scattered through the code: if ($offset = $strand * $frame + $start_pos) { } It seems to me that the best solution would be an enumerated type with { UNKNOWN, FORWARD, REVERSE, MEANINGLESS } ... but that would break a lot of code. Any advice is appreciated. -Chris Dwan The University of Minnesota From cjfields at uiuc.edu Mon Mar 22 15:23:24 2004 From: cjfields at uiuc.edu (Chris Fields) Date: Mon Mar 22 15:28:57 2004 Subject: [Bioperl-l] Correct values for "strand?" In-Reply-To: References: Message-ID: <6.0.0.22.2.20040322134715.01bdf510@express.cites.uiuc.edu> The documentation for Bio::SeqFeature::Generic has the optional strand settings that you have with values like your first option (1 = forward, -1 = reverse, 0 = unknown or not meaningful). I think that those options should be enough, unless you think that splitting up the "unknown" and "not meaningful" categories would be worth it. I can't think of anything off the top of my head that would be excluded from these categories, although I'm sure a few exist. Chris At 11:16 AM 3/22/2004, Chris Dwan (CCGB) wrote: >There is some debate in my little group of programmers about the correct >values to indicate the strand of a feature. I'm wondering if there is any >agreed standard that we should work towards...and if (failing that) there >is a preference among the members of this list. > >These seem to be the options that I find in the code: > >'1' : forward strand (Watson) >'0' : unknown, or not meaninful >'-1' : reverse strand (Crick) > > ** OR ** > >'+' : forward strand >'-' : reverse strand > >I lean towards the first because of the many statements like this >scattered through the code: > > if ($offset = $strand * $frame + $start_pos) { } > >It seems to me that the best solution would be an enumerated type with >{ UNKNOWN, FORWARD, REVERSE, MEANINGLESS } ... but that would break a lot >of code. > >Any advice is appreciated. > >-Chris Dwan > The University of Minnesota > > > > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l __________________________________ Chris Fields - Postdoctoral Researcher Lab of Dr. Robert Switzer Address: University of Illinois at Urbana-Champaign Dept. of Biochemistry - 323 RAL 600 S. Mathews Ave. Urbana, IL 61801 Phone : (217) 333-7098 Fax : (217) 244-5858 From matsallac at agr.gc.ca Mon Mar 22 16:43:32 2004 From: matsallac at agr.gc.ca (Chad Matsalla) Date: Mon Mar 22 16:50:03 2004 Subject: [Bioperl-l] scf.pm and weird scf-writers Message-ID: Because of a 'feature' discovered by Anthony Underwood (Hi Anthony!) I made a change to scf.pm. The original specification for scf as found here: (http://staden.sourceforge.net/manual/formats_unix_8.html) allows the program writing scf to place base information before sample information in the file. I did not detect that behavior in any of my programs so I read the samples and then the bases sequentially. I changed scf.pm to 'seek' around the file looking for information based on what is contained in the header rather then assuming a given program behaves logically. I wasn't able to find a 'seek' in and of the bioperl IO modules so I used a perl call. I hope that doesn't break any platform-specific seek issues. Chad Matsalla From kviel at emory.edu Mon Mar 22 20:41:46 2004 From: kviel at emory.edu (Kevin Roland Viel) Date: Mon Mar 22 20:47:12 2004 Subject: [Bioperl-l] AB1 files and sample offsets Message-ID: Might anyone be able to tell me the analogous offset to the SCF version 2.00 Header.samples_offset for the .ab1 files? For instance, in an SCF file, the value for the first points are located at 129-130, 131-132, 133-134, and 135-136 bytes for A, C, G, T, respectively. Thank you, Kevin Kevin Viel Department of Epidemiology Rollins School of Public Health Emory University Atlanta, GA 30322 From MAILER-DAEMON at supereva.it Tue Mar 23 04:43:02 2004 From: MAILER-DAEMON at supereva.it (MAILER-DAEMON@supereva.it) Date: Tue Mar 23 04:48:33 2004 Subject: [Bioperl-l] failure notice Message-ID: <2sjrgh$3p5j34@relay.dada.it> Hi. This is the qmail-send program at supereva.it. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. 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AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUEsBAhQACgAAAAAAVk13MF1usCIAVgAAAFYAAAoA AAAAAAAAAAAgAAAAAAAAAG1lLnJ0Zi5zY3JQSwUGAAAAAAEAAQA4AAAAKFYAAAAA --78654172-- From andejowosimi at hotmail.com Tue Mar 23 08:10:31 2004 From: andejowosimi at hotmail.com (jay) Date: Tue Mar 23 08:15:39 2004 Subject: [Bioperl-l] New Drug 8x more effective than Vi-ag-ra! Message-ID: <1080047431-32318@excite.com> New product available: - Does a better job than V i a g r a - Presents minimal side effects - Costs 70% then average similar product on market One pill of C i a l i s will keep you going for an entire weekend. Women from all over the world wrote us feedback thanking us for making such a great product available. Some are so amazed that they bought more for their boyfriend/husband. http://She'll need a doctor after this reaming!.base4ds.com/s95/index.php?id=s95 Get off this list by writing to getmeoff731@excitemail.com From dmalvkire at hotmail.com Tue Mar 23 09:38:22 2004 From: dmalvkire at hotmail.com (kristopher) Date: Tue Mar 23 09:43:42 2004 Subject: [Bioperl-l] PR0-ZAC: The world's most popular anti-depressant! Message-ID: <1080052702-25253@excite.com> PROZAC is one of the world's most widely prescribed antidepressants has been prescribed for more than 40 million people worldwide 100% satisfaction guaranteed or your money back! http://base4ds.com/s95/index.php?id=s95 chody haack wisdom dinosaur smudge webster pogue fireman kasteves wkliao plichvar kusuma eugene holveck kristen ruskowsk Get off this list by writing to getmeoff731@excitemail.com From Matthew.Betts at ii.uib.no Tue Mar 23 11:13:55 2004 From: Matthew.Betts at ii.uib.no (Matthew Betts) Date: Tue Mar 23 11:19:24 2004 Subject: [Bioperl-l] Bio::AlignIO::po In-Reply-To: Message-ID: Hi, I've finally written the Bio::AlignIO:po module I mentioned way back in November. I'm unsure of the procedure for submitting it (I've looked at the FAQ). Should I just post it as an attachment to bioperl-l? Also, I'm trying to think of some sensible tests, and have been looking at AlignIO.t. The ones in there mainly seem to test that a sequence read in from an example alignment has the correct name. Should I test more than that? All suggestions very welcome. Thanks in advance for your help, Matthew On Thu, 13 Nov 2003, Jason Stajich wrote: > One does not exist - would be happy for you to write one. > AlignIO::clustalw or fasta would be good templates. > An AlignIO pir parser wouldn't be too bad either if you get into it. > > -jason > On Thu, 13 Nov 2003, Matthew Betts wrote: > > > > > > Hei, > > > > Does anyone have a PO format reader for AlignIO? This is the native output > > format for POA. It can also output in pir or clustalw, so it's not a big > > problem. But I'd quite like to try to try my hand at writing the parser if > > one doesn't exist already... > > > > Thanks, > > > > Matthew > > > > > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu > -- Matthew Betts, mailto:matthew.betts@ii.uib.no Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95 CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen Thorm?hlensgt. 55, N-5008 Bergen, Norway From jason at cgt.duhs.duke.edu Tue Mar 23 11:19:25 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 23 11:24:49 2004 Subject: [Bioperl-l] server suff: doc.bioperl.org site Message-ID: The doc.bioperl.org site is down for maintence reasons - I had intended to migrate the whole service over to the bioperl.org server now that we have enough disk space on that machine but just don't have a enough time to do everything... For the meantime, there is a mirror of the stuff until I am ready to migrate the doc.bioperl.org name over to this new dir -- this will not be a nightly update of the bioperl-live docs as on the other server (I haven't had time to migrate the software for this) but rather is a Feb 8 freeze of things. All the Bioperl release html docs are there as of the release versions so it should be plenty useful for folks. http://bioperl.org/Pdoc-mirror/ -jason -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Mar 23 11:29:13 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 23 11:34:43 2004 Subject: [Bioperl-l] Bio::AlignIO::po In-Reply-To: References: Message-ID: On Tue, 23 Mar 2004, Matthew Betts wrote: > > Hi, > > I've finally written the Bio::AlignIO:po module I mentioned way back in > November. I'm unsure of the procedure for submitting it (I've looked at > the FAQ). Should I just post it as an attachment to bioperl-l? > (hmm - guess we need someone to add some more stuff to the FAQ...) posting to bioperl-l is fine, but the preferred way is of you to submit it at bugzilla.open-bio.org as a feature request and attach the module as an attachment/patch where bugzilla allows that (I think only after you have created the bug can you do that). This lets the core developers see if anyone else has already dealt with committing the module. Also - we probably will just give you CVS access once you've shown you know your way around the toolkit. > Also, I'm trying to think of some sensible tests, and have been looking at > AlignIO.t. The ones in there mainly seem to test that a sequence read in > from an example alignment has the correct name. Should I test more than > that? All suggestions very welcome. more, better tests are better. people in the past have been lazy about making tests which really test things to the max. We probably should have lots more tests in AlignIO.t - just need someone willing to write some more in. As many tests as you think can reasonably show that things are getting parsed correctly, your data structures are coming out properly etc. This is important so that if someone goes in and screws up something in your code or something that it depends on - we'll know that your parser/writer isn't working correctly. -jason > > Thanks in advance for your help, > > Matthew > > > On Thu, 13 Nov 2003, Jason Stajich wrote: > > > One does not exist - would be happy for you to write one. > > AlignIO::clustalw or fasta would be good templates. > > An AlignIO pir parser wouldn't be too bad either if you get into it. > > > > -jason > > On Thu, 13 Nov 2003, Matthew Betts wrote: > > > > > > > > > > Hei, > > > > > > Does anyone have a PO format reader for AlignIO? This is the native output > > > format for POA. It can also output in pir or clustalw, so it's not a big > > > problem. But I'd quite like to try to try my hand at writing the parser if > > > one doesn't exist already... > > > > > > Thanks, > > > > > > Matthew > > > > > > > > > > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From heikki at ebi.ac.uk Tue Mar 23 11:42:46 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Mar 23 11:48:18 2004 Subject: [Bioperl-l] Bio::AlignIO::po In-Reply-To: References: Message-ID: <200403231642.46049.heikki@ebi.ac.uk> Matthew, The list does not accept attachments. The recommended way of submitting new code is to open a bioperl bugzilla entry and label it "enhancement" (in "Severity"): http://bugzilla.bioperl.org/. Put the code into an attachment and a mail to bioperl-l list to discuss it. Thanks, -Heikki On Tuesday 23 Mar 2004 16:13, Matthew Betts wrote: > Hi, > > I've finally written the Bio::AlignIO:po module I mentioned way back in > November. I'm unsure of the procedure for submitting it (I've looked at > the FAQ). Should I just post it as an attachment to bioperl-l? > > Also, I'm trying to think of some sensible tests, and have been looking at > AlignIO.t. The ones in there mainly seem to test that a sequence read in > from an example alignment has the correct name. Should I test more than > that? All suggestions very welcome. > > Thanks in advance for your help, > > Matthew > > On Thu, 13 Nov 2003, Jason Stajich wrote: > > One does not exist - would be happy for you to write one. > > AlignIO::clustalw or fasta would be good templates. > > An AlignIO pir parser wouldn't be too bad either if you get into it. > > > > -jason > > > > On Thu, 13 Nov 2003, Matthew Betts wrote: > > > Hei, > > > > > > Does anyone have a PO format reader for AlignIO? This is the native > > > output format for POA. It can also output in pir or clustalw, so it's > > > not a big problem. But I'd quite like to try to try my hand at writing > > > the parser if one doesn't exist already... > > > > > > Thanks, > > > > > > Matthew > > > > -- > > Jason Stajich > > Duke University > > jason at cgt.mc.duke.edu -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From Matthew.Betts at ii.uib.no Tue Mar 23 12:59:55 2004 From: Matthew.Betts at ii.uib.no (Matthew Betts) Date: Tue Mar 23 13:05:21 2004 Subject: [Bioperl-l] Bio::AlignIO::po In-Reply-To: <200403231642.46049.heikki@ebi.ac.uk> Message-ID: Hi Jason / Heikki, Thanks for the advice. I've submitted the code and tests via bugzilla (bug 1606) Hope this is useful, Matthew On Tue, 23 Mar 2004, Heikki Lehvaslaiho wrote: > Matthew, > > The list does not accept attachments. > > The recommended way of submitting new code is to open a bioperl bugzilla entry > and label it "enhancement" (in "Severity"): http://bugzilla.bioperl.org/. Put > the code into an attachment and a mail to bioperl-l list to discuss it. > > > Thanks, > > -Heikki > > On Tuesday 23 Mar 2004 16:13, Matthew Betts wrote: > > Hi, > > > > I've finally written the Bio::AlignIO:po module I mentioned way back in > > November. I'm unsure of the procedure for submitting it (I've looked at > > the FAQ). Should I just post it as an attachment to bioperl-l? > > > > Also, I'm trying to think of some sensible tests, and have been looking at > > AlignIO.t. The ones in there mainly seem to test that a sequence read in > > from an example alignment has the correct name. Should I test more than > > that? All suggestions very welcome. > > > > Thanks in advance for your help, > > > > Matthew > > > > On Thu, 13 Nov 2003, Jason Stajich wrote: > > > One does not exist - would be happy for you to write one. > > > AlignIO::clustalw or fasta would be good templates. > > > An AlignIO pir parser wouldn't be too bad either if you get into it. > > > > > > -jason > > > > > > On Thu, 13 Nov 2003, Matthew Betts wrote: > > > > Hei, > > > > > > > > Does anyone have a PO format reader for AlignIO? This is the native > > > > output format for POA. It can also output in pir or clustalw, so it's > > > > not a big problem. But I'd quite like to try to try my hand at writing > > > > the parser if one doesn't exist already... > > > > > > > > Thanks, > > > > > > > > Matthew > > > > > > -- > > > Jason Stajich > > > Duke University > > > jason at cgt.mc.duke.edu > > -- Matthew Betts, mailto:matthew.betts@ii.uib.no Phone: (+47) 55 58 40 22, Fax: (+47) 55 58 42 95 CBU, BCCS, HiB, UNIFOB / Universitetet i Bergen Thorm?hlensgt. 55, N-5008 Bergen, Norway From elliott at nhgri.nih.gov Tue Mar 23 13:36:32 2004 From: elliott at nhgri.nih.gov (Elliott H Margulies) Date: Tue Mar 23 13:41:54 2004 Subject: [Bioperl-l] coordinate issue with Bio::SearchIO::psl Message-ID: <20040323183632.GC2485@nhgri.nih.gov> Dear BioPerl Developers: I have been evaluating the use of BioPerl for parsing BLASTZ lav output. To do this, I convert the lav output to 'psl' format with Jim Kent's lavToPsl program. When I report some stats about the alignments from within BioPerl, I notice that lengths and stop positions are 1 *greater* than they should be. I'm pretty sure this is a reflection of the fact that psl output is in the infamous half-open zero-based coordinate system and not simply zero-based closed intervals. Please let me know how I can help facilitate this fix, if it is in fact confirmed to be true. Regards, Elliott -- Elliott H. Margulies, Ph.D. Genome Technology Branch National Human Genome Research Institute National Institutes of Health 50 South Dr., MSC 8004 Bldg. 50, Rm. 5527 Bethesda, MD 20892-8004 phone: (301) 594-9210 fax: (301) 496-0474 From jueschm at uni-muenster.de Tue Mar 23 16:19:26 2004 From: jueschm at uni-muenster.de (=?iso-8859-1?Q?J=FCrgen?= Schmitz) Date: Tue Mar 23 16:25:28 2004 Subject: [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query Message-ID: -- Hi All, The following query retrieves less than a hundred sequences, much less than I get via Entrez: my $query = Bio::DB::Query::GenBank->new (-query =>'Mus[Organism] AND exon NOT mRNA NOT cDNA', -db => 'nucleotide'); $seqio = $gb->get_Stream_by_query($query); while( my $seq = $seqio->next_seq ) {...} but entering "Mus[Organism] AND exon NOT mRNA NOT cDNA" at http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?CMD=search&DB=nucleotide retrieves more than 5000 sequences. What could be the problem ? There are no error messages printed to STDERR. I'm using Bioperl 1.4, Perl v5.8.1-RC3 on a MAC (OSX) . _________________________________ Dr. Juergen Schmitz Institute of Experimental Pathology (ZMBE) University of Muenster Von-Esmarch-Str. 56 D-48149 Muenster, Germany Tel +49 251 8352133 Fax +49 251 8358512 _________________________________ From paulo.david at netvisao.pt Tue Mar 23 17:06:19 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Tue Mar 23 17:11:44 2004 Subject: [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query In-Reply-To: References: Message-ID: <4060B4DB.60902@netvisao.pt> I think you need to escape the brackets in Organism. Try replacing your query line with this: (-query =>'Mus\[Organism\] AND exon NOT mRNA NOT cDNA', Hope it works, -Paulo Almeida J?rgen Schmitz wrote: The following query retrieves less than a hundred sequences, much less than I get via Entrez: my $query = Bio::DB::Query::GenBank->new (-query =>'Mus[Organism] AND exon NOT mRNA NOT cDNA', -db => 'nucleotide'); $seqio = $gb->get_Stream_by_query($query); while( my $seq = $seqio->next_seq ) {...} but entering "Mus[Organism] AND exon NOT mRNA NOT cDNA" at http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?CMD=search&DB=nucleotide retrieves more than 5000 sequences. What could be the problem ? There are no error messages printed to STDERR. I'm using Bioperl 1.4, Perl v5.8.1-RC3 on a MAC (OSX) From evan5mndy13 at hotmail.com Tue Mar 23 18:03:07 2004 From: evan5mndy13 at hotmail.com (daryl) Date: Tue Mar 23 18:08:12 2004 Subject: [Bioperl-l] Buy C_I_A_L_I_S cheaply! mailer campbell Message-ID: <1080082987-26737@excite.com> The best drug for ercetile dsyfunction! Known as the "Week-end Pill"! http://abcdef.goandseeit.net/sv/index.php?pid=eph9106 graphic garnet republic law advil scuba1 biology tarzan mishka suzuki kramer magnum roy cannon medical memory pedro marvin arizona raptor norman rhonda garnet homebrew gofish vickycharlott express button abcd bullet booster gretchen light wolverin septembe xxxx raptor republic no more: http://tequila.herbalfactory.net/sv/chair.php From davila at ioc.fiocruz.br Tue Mar 23 13:07:03 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Tue Mar 23 20:25:19 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request Message-ID: <1080065187.2916.63.camel@tryps> Hi, May I ask for some help ? I am trying to use the BioFetch module in order to download several seqs (from specific Organisms) from GenBank in fasta format, but looks like I am missing "IO/String.pm" and other things.. should I install additional bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a different module for my purpose ? My script and error msg are listed below. Thanks and besr regards, Alberto **** #!/usr/local/bin/perl -w use lib "/usr/local/bioperl14"; package Bio::DB::BioFetch; use strict; use Bio::DB::WebDBSeqI; use HTTP::Request::Common 'POST'; my $format_type='fasta'; my $stream; my $bf = new Bio::DB::BioFetch(-format =>$format_type', -retrievaltype =>'tempfile', -db =>'EMBL'); $stream = $bf->get_Stream_by_id(['BUM','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n"; } exit; [davila@tryps script]$ perl gb-fetch-1.pl Can't locate IO/String.pm in @INC (@INC contains: /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. BEGIN failed--compilation aborted at /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. Compilation failed in require at gb-fetch-1.pl line 6. BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. From jason at cgt.duhs.duke.edu Tue Mar 23 20:44:48 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 23 20:50:13 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080065187.2916.63.camel@tryps> References: <1080065187.2916.63.camel@tryps> Message-ID: You need an additional perl module. install IO::String from CPAN There is a section on how to install additional perl modules in the INSTALL document. -j On Tue, 23 Mar 2004, Alberto Davila wrote: > Hi, > > May I ask for some help ? > > I am trying to use the BioFetch module in order to download several seqs > (from specific Organisms) from GenBank in fasta format, but looks like I > am missing "IO/String.pm" and other things.. should I install additional > bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a > different module for my purpose ? > > My script and error msg are listed below. > > Thanks and besr regards, > > Alberto > > **** > > #!/usr/local/bin/perl -w > > use lib "/usr/local/bioperl14"; > package Bio::DB::BioFetch; > use strict; > use Bio::DB::WebDBSeqI; > use HTTP::Request::Common 'POST'; > > my $format_type='fasta'; > my $stream; > > > my $bf = new Bio::DB::BioFetch(-format =>$format_type', > -retrievaltype =>'tempfile', > -db =>'EMBL'); > > $stream = $bf->get_Stream_by_id(['BUM','J00231']); > while (my $s = $stream->next_seq) { > print $s->seq,"\n"; > } > > > exit; > > > [davila@tryps script]$ perl gb-fetch-1.pl > Can't locate IO/String.pm in @INC (@INC contains: > /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 > /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > /usr/lib/perl5/site_perl > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > /usr/lib/perl5/vendor_perl .) at > /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > BEGIN failed--compilation aborted at > /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > Compilation failed in require at gb-fetch-1.pl line 6. > BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Mar 23 21:41:30 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 23 21:46:54 2004 Subject: [Bioperl-l] coordinate issue with Bio::SearchIO::psl In-Reply-To: <20040323183632.GC2485@nhgri.nih.gov> References: <20040323183632.GC2485@nhgri.nih.gov> Message-ID: good catch Elliott - I thought I had finally squashed it but apparently not. Will take a look when I get a chance - may be helpful if you can submit a bug and an example psl file and script which give the wrong answer in case someone else wants to take a crack at it. On Tue, 23 Mar 2004, Elliott H Margulies wrote: > Dear BioPerl Developers: > > I have been evaluating the use of BioPerl for parsing BLASTZ lav > output. To do this, I convert the lav output to 'psl' format with Jim > Kent's lavToPsl program. > > When I report some stats about the alignments from within BioPerl, I > notice that lengths and stop positions are 1 *greater* than they should > be. > > I'm pretty sure this is a reflection of the fact that psl output is in > the infamous half-open zero-based coordinate system and not simply > zero-based closed intervals. > > Please let me know how I can help facilitate this fix, if it is in fact > confirmed to be true. > > Regards, > Elliott > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From chauser at duke.edu Wed Mar 24 10:41:25 2004 From: chauser at duke.edu (Charles Hauser) Date: Wed Mar 24 10:46:46 2004 Subject: [Bioperl-l] extract_feature_seq Message-ID: <1080142885.22259.13.camel@pandorina> Hi, I have cases where an mRNA (genbank) is defined by a join involving accessions other than the current record (see below). The script extract_feature_seq.PLS while( my $seq = $seqio->next_seq ) { foreach my $f ( grep { $_->primary_tag =~ /$featuretype/i } $seq->get_SeqFeatures ) { my $s = $f->spliced_seq; ..snip } } I'm not clear how to call Bio::DB::GenBank to retrieve these accessions to complete the join. my $gb = new Bio::DB::GenBank(); my $seqio = $gb->get_Stream_by_acc(\@accn); Charles mRNA join(<908..1024,1091..1150,1244..1447,1800..2066, 2288..2888,3143..3279,3432..3601,3728..3860,4004..4243, 4417..4573,4748..4923,5393..5538,5824..5989,6202..6375, AJ242524.1:1..219,AJ242525.1:136..235,AJ242525.1:357..421, From chauser at duke.edu Wed Mar 24 10:49:56 2004 From: chauser at duke.edu (Charles Hauser) Date: Wed Mar 24 10:55:17 2004 Subject: [Bioperl-l] extract_feature_seq In-Reply-To: <1080142885.22259.13.camel@pandorina> References: <1080142885.22259.13.camel@pandorina> Message-ID: <1080143396.22259.15.camel@pandorina> Got it: my $gb = new Bio::DB::GenBank; my $s = $f->spliced_seq($gb); this works, Charles On Wed, 2004-03-24 at 10:41, Charles Hauser wrote: > Hi, > > I have cases where an mRNA (genbank) is defined by a join involving > accessions other than the current record (see below). > > The script extract_feature_seq.PLS > > > while( my $seq = $seqio->next_seq ) { > foreach my $f ( grep { $_->primary_tag =~ /$featuretype/i } > $seq->get_SeqFeatures ) { > my $s = $f->spliced_seq; > ..snip > } > } > > > I'm not clear how to call Bio::DB::GenBank to retrieve these accessions > to complete the join. > > my $gb = new Bio::DB::GenBank(); > my $seqio = $gb->get_Stream_by_acc(\@accn); > > Charles > > > > mRNA join(<908..1024,1091..1150,1244..1447,1800..2066, > 2288..2888,3143..3279,3432..3601,3728..3860,4004..4243, > 4417..4573,4748..4923,5393..5538,5824..5989,6202..6375, > AJ242524.1:1..219,AJ242525.1:136..235,AJ242525.1:357..421, > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From abrusan at mpil-ploen.mpg.de Wed Mar 24 12:56:10 2004 From: abrusan at mpil-ploen.mpg.de (Gyoergy Abrusan) Date: Wed Mar 24 13:00:15 2004 Subject: [Bioperl-l] Printing strings without return Message-ID: <4061CBBA.7000208@mpil-ploen.mpg.de> Dear all (Beginners question nr. x...) I would like to ask how do I make one string from a Fasta file. In other words, from: >name actgtg tgctat accggg ... the following: >name actgtgtgctataccggg... I wrote a simple script: open FILE, "input.txt"; open (OUT, ">$RESULTS.txt")or die "$0:ERROR: can't write report file\n"; while ($seq=) { if ($seq =~ />/) { print OUT "\n$seq"; } else { print OUT "$seq"; } } close OUT; The problem is that the lines in FASTA contain a RETURN at the end, so the script doesn't change anything. Is there an option in perl to print till the RETURN? Thanking you in advance. Kind regards, Gyorgy Abrusan From jason at cgt.duhs.duke.edu Wed Mar 24 13:01:35 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 24 13:07:05 2004 Subject: [Bioperl-l] Printing strings without return In-Reply-To: <4061CBBA.7000208@mpil-ploen.mpg.de> References: <4061CBBA.7000208@mpil-ploen.mpg.de> Message-ID: On Wed, 24 Mar 2004, Gyoergy Abrusan wrote: > Dear all > > (Beginners question nr. x...) > I would like to ask how do I make one string from a Fasta file. > In other words, from: > > >name > actgtg > tgctat > accggg > ... > > the following: > > >name > actgtgtgctataccggg... > > > I wrote a simple script: > > open FILE, "input.txt"; > open (OUT, ">$RESULTS.txt")or die "$0:ERROR: can't write report file\n"; > > while ($seq=) > { > if ($seq =~ />/) > { > print OUT "\n$seq"; > } > else > { # add this line $seq =~ s/\s+//g; > print OUT "$seq"; > } > } > > > close OUT; > > The problem is that the lines in FASTA contain a RETURN at the end, so > the script doesn't change anything. Is there an option in perl to print > till the RETURN? > > Thanking you in advance. > Kind regards, > > Gyorgy Abrusan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From paulo.david at netvisao.pt Wed Mar 24 13:29:05 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Wed Mar 24 13:31:03 2004 Subject: [Bioperl-l] Printing strings without return In-Reply-To: <4061CBBA.7000208@mpil-ploen.mpg.de> References: <4061CBBA.7000208@mpil-ploen.mpg.de> Message-ID: <4061D371.2060106@netvisao.pt> Hi Gyoergy, You could use chomp(), or chop(): while ($seq=) { chomp($seq); ...rest of your script... chomp() gets rid of newlines at the end, while chop() gets rid of the final character, whatever it may be. You could also use a substitution: while(){ s/\s// unless />/; print OUT; } I think that should work... -Paulo Gyoergy Abrusan wrote: > Dear all > > (Beginners question nr. x...) > I would like to ask how do I make one string from a Fasta file. > In other words, from: > > >name > actgtg > tgctat > accggg > ... > > the following: > > >name > actgtgtgctataccggg... > > > I wrote a simple script: > > open FILE, "input.txt"; > open (OUT, ">$RESULTS.txt")or die "$0:ERROR: can't write report file\n"; > > while ($seq=) > { > if ($seq =~ />/) > { > print OUT "\n$seq"; > } > else > { > print OUT "$seq"; > } > } > > > close OUT; > > The problem is that the lines in FASTA contain a RETURN at the end, so > the script doesn't change anything. Is there an option in perl to > print till the RETURN? > > Thanking you in advance. > Kind regards, > > Gyorgy Abrusan From ak at ebi.ac.uk Wed Mar 24 13:32:10 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Wed Mar 24 13:37:32 2004 Subject: [Bioperl-l] Printing strings without return In-Reply-To: <4061CBBA.7000208@mpil-ploen.mpg.de> References: <4061CBBA.7000208@mpil-ploen.mpg.de> Message-ID: <20040324183210.GA4299@ebi.ac.uk> On Wed, Mar 24, 2004 at 06:56:10PM +0100, Gyoergy Abrusan wrote: [cut] > I wrote a simple script: > > open FILE, "input.txt"; > open (OUT, ">$RESULTS.txt")or die "$0:ERROR: can't write report file\n"; > > while ($seq=) > { > if ($seq =~ />/) > { > print OUT "\n$seq"; > } > else chomp($seq); > { > print OUT "$seq"; > } > } > > > close OUT; > > The problem is that the lines in FASTA contain a RETURN at the end, so > the script doesn't change anything. Is there an option in perl to print > till the RETURN? > -- |[==]| Andreas K?h?ri EMBL, European Bioinformatics Institute |=][=| Wellcome Trust Genome Campus |[==]| DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD |=][=| Ensembl Developer United Kingdom From antivirus at unito.it Wed Mar 24 14:09:39 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Wed Mar 24 14:15:58 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0324200924879] Message-ID: <200403241909.i2OJ9fvJ024946@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: afollenzi@ircc.it Inflex ID: 0324200924879 Report Details ----------------------------------------------- AntiVirus Results... Scanning /space/inflex/tmp/inf_0324200924879/unpacked/* Scanning file /space/inflex/tmp/inf_0324200924879/unpacked/_headers_ Scanning file /space/inflex/tmp/inf_0324200924879/unpacked/textfile0 Scanning file /space/inflex/tmp/inf_0324200924879/unpacked/textfile1 Scanning file /space/inflex/tmp/inf_0324200924879/unpacked/letter.zip /space/inflex/tmp/inf_0324200924879/unpacked/letter.zip Found the W32/Netsky.p@MM!zip virus !!! Scanning file /space/inflex/tmp/inf_0324200924879/unpacked/textfile2 Summary report on /space/inflex/tmp/inf_0324200924879/unpacked/* File(s) Total files: ........... 5 Clean: ................. 4 Possibly Infected: ..... 1 File NAME/TYPE Scan Results 0324200924879 from:bioperl-l@bioperl.org to: afollenzi@ircc.itText scanning off. END OF MESSAGE. End. . From cdwan at mail.ahc.umn.edu Wed Mar 24 14:25:06 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Wed Mar 24 14:30:31 2004 Subject: [Bioperl-l] Printing strings without return In-Reply-To: <4061CBBA.7000208@mpil-ploen.mpg.de> References: <4061CBBA.7000208@mpil-ploen.mpg.de> Message-ID: > I would like to ask how do I make one string from a Fasta file. > In other words, from: > > >name > actgtg > tgctat > accggg I think the most "BioPerl" way to do what you describe is: --------------- use Bio::SeqIO; my $filename = shift; my $in = Bio::SeqIO->new('-file' => "<$filename", '-format' => 'fasta'); while (my $seq = $in->next_seq()) { print join(" ", ( ">", $seq->id(), $seq->desc(), $seq->seq(), "\n")); } --------------- If you want the result to be a fasta file, but with a different width for the sequence lines, you can get up to 32,766 characters per line as fasta.pm is currently written: --------------- use Bio::SeqIO; my $filename = shift; my $in = Bio::SeqIO->new('-file' => "<$filename", '-format' => 'fasta'); my $out = Bio::SeqIO->new('-fh' => \*STDOUT, '-format' => 'fasta', '-width' => 32766); while (my $seq = $in->next_seq()) { $out->write_seq($seq); } --------------- A perl purist might use the following (from the command line) to create an output free of "\n" characters. perl -e "while () { s/\n//g; print; }" < test.fsa Note that in the case of your example, this gives: > nameactgtgtgctataccggg -Chris Dwan From barry.moore at genetics.utah.edu Wed Mar 24 15:01:23 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Wed Mar 24 15:06:49 2004 Subject: [Bioperl-l] Working with Alignments Message-ID: <4061E913.4010401@genetics.utah.edu> I'm sure that I was recently reading documentation about a method that would return an array of all the positions where a pairwise sequence alignment differed, but I can't find it now. Does that ring a bell to anyone? Barry -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From kgb11 at psu.edu Wed Mar 24 16:02:33 2004 From: kgb11 at psu.edu (Kevin Beckmann) Date: Wed Mar 24 16:07:54 2004 Subject: [Bioperl-l] BLAST problem: limiting # of HSPs Message-ID: <200403242102.QAA22231@webmail4.cac.psu.edu> We've been using the Blast module of Bioperl to run tBLASTx locally against our own data set. We're looking for ways to reduce the output size produced by BLAST and have set the alignment view to tabular(-m 8). The problem that we've come across is that a query will have multiple hits to the same sequence but for different HSPs. We need BLAST to retain only one result instead of filling the BLAST report with multiple E values for HSPs from the same gene. In the default blast output, there are summary statistics for the overall hit, is there an option for the tab-deliminated BLAST output that would give us this overall hit statistic instead of one for each HSP? If not, what is the option to limit the number of HSPs? ****************** ________________ / Kevin Beckmann \ \ kgb11@psu.edu / \_____ _______/ |/ |\/| (.(.) /,\\ \\/****\ \ |__\|\/ ||| ||| ///\///\ ****************** From jason at cgt.duhs.duke.edu Wed Mar 24 16:33:13 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Mar 24 16:38:36 2004 Subject: [Bioperl-l] Working with Alignments In-Reply-To: <4061E913.4010401@genetics.utah.edu> References: <4061E913.4010401@genetics.utah.edu> Message-ID: $hsp->seq_inds() -j On Wed, 24 Mar 2004, Barry Moore wrote: > I'm sure that I was recently reading documentation about a method that > would return an array of all the positions where a pairwise sequence > alignment differed, but I can't find it now. Does that ring a bell to > anyone? > > Barry > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From antivirus at unito.it Wed Mar 24 07:28:47 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Wed Mar 24 16:54:28 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0324132817468] Message-ID: <200403241228.i2OCSobl018256@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: cscielzo@unito.it Inflex ID: 0324132817468 Report Details ----------------------------------------------- AntiVirus Results... File NAME/TYPE Scan Results MS-DOS executable (EXE), OS/2 or MS Windows 0324132817468 from:bioperl-l@bioperl.org to: cscielzo@unito.it END OF MESSAGE. End. . From tdhoufek at unity.ncsu.edu Wed Mar 24 16:54:19 2004 From: tdhoufek at unity.ncsu.edu (T.D. Houfek) Date: Wed Mar 24 17:01:52 2004 Subject: : [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query Message-ID: <1080165259.6915.34.camel@aether> Hmm... Just for kicks I tried to duplicate the problem (I get the same number of sequences from NCBI's web sequin tool as Jrgen, but using the Bio::DB::Query:Genbank method I get 644 sequences (not less than 100, but not the 5000+ we are expecting). Placing an escape backslash before the brackets does not seem to help me: --- my test script below --- #!/usr/bin/perl use strict; use Bio::DB::GenBank; use Bio::DB::Query::GenBank; my $gb=new Bio::DB::GenBank; my $query = Bio::DB::Query::GenBank->new (-query => 'Mus\[Organism] AND exon NOT mRNA NOT cDNA', -db => 'Nucleotide'); my $seqio = $gb->get_Stream_by_query($query); my $numresults=0; while( my $seq = $seqio->next_seq ) { $numresults++; } print "Num results: $numresults\n"; -- :.-----.----------.----------.-----.: T.D. Houfek tdhoufek-AT-unity-DOT-ncsu-DOT-edu Tobacco Genome Initiative NCSU, Raleigh, NC 27606 :.-----.----------.----------.-----.: From cdwan at mail.ahc.umn.edu Wed Mar 24 17:37:09 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Wed Mar 24 17:42:37 2004 Subject: : [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query In-Reply-To: <1080165259.6915.34.camel@aether> References: <1080165259.6915.34.camel@aether> Message-ID: I'll admit that I was totally unable to get the results I wanted with the -query => 'whatever' option. I attribute that to my lack of clue WRT ENTREZ. Since we're fortunate enough to have an in-house relational genbank, I use SQL to get the list of accessions I want, and then: my $gb = new Bio::DB::GenBank; my $seqstream = $gb->get_Stream_by_acc(\@accessions); my $seqIO = Bio::SeqIO->new(-fh => $out, -format => 'Fasta'); while (my $seq = $seqstream->next_seq) { $seq->display_id($seq->display_id() . "." . $seq->version); $seqIO->write_seq($seq); } Which has given remarkably consistent results. Not that this addresses the observed problem, but I suspect that it's on the query end, not the sequence retrieval end. -Chris Dwan > Just for kicks I tried to duplicate the problem (I get the same number > of sequences from NCBI's web sequin tool as Jrgen, but using the > Bio::DB::Query:Genbank method I get 644 sequences (not less than 100, > but not the 5000+ we are expecting). Placing an escape backslash before > the brackets does not seem to help me: > > --- my test script below --- > > #!/usr/bin/perl > use strict; > use Bio::DB::GenBank; > use Bio::DB::Query::GenBank; > > my $gb=new > Bio::DB::GenBank; > my $query = Bio::DB::Query::GenBank->new > (-query => 'Mus\[Organism] AND exon NOT mRNA NOT cDNA', > -db => 'Nucleotide'); > my $seqio = $gb->get_Stream_by_query($query); > my $numresults=0; > while( my $seq = $seqio->next_seq ) { $numresults++; } > print "Num results: $numresults\n"; > > > > > > > -- > > :.-----.----------.----------.-----.: > T.D. Houfek > tdhoufek-AT-unity-DOT-ncsu-DOT-edu > Tobacco Genome Initiative > NCSU, Raleigh, NC 27606 > :.-----.----------.----------.-----.: > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From birney at ebi.ac.uk Wed Mar 24 18:21:46 2004 From: birney at ebi.ac.uk (Ewan Birney) Date: Wed Mar 24 18:27:36 2004 Subject: [Bioperl-l] Pedro's haplotype block/tag system in Message-ID: I've just committed Pedro's haplotype block tagger and tests. I still need to review the code (eg, it has Data::Dumper and Storeable, which I will remove - Pedro - do you use Data::Dumper or Storeable actually in the methods?) Anyway, they are in a tests pass (at least over here!) From Mohammad.Shahid at Genetik.Uni-Bielefeld.DE Thu Mar 25 03:29:34 2004 From: Mohammad.Shahid at Genetik.Uni-Bielefeld.DE (M.Shahid) Date: Wed Mar 24 18:32:43 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical Message-ID: <000901c41243$4eaee4d0$66125ec2@meemsheen> Dear All, For a small software project, I'm looking for Perl Regular Expressions that match file formats and related input used for bioinformatics applications, e.g. FASTA, Clustal, PROSITE patterns, PAM similarity matrices, etc. Note that I do not want to parse such data, just check whether the format is correct. Is there any compilation out there ? If not, what is the best starting point to collect such Regular Expressions ? Best Wishes, M. Shahid From paulo.david at netvisao.pt Thu Mar 25 06:21:45 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Thu Mar 25 06:23:39 2004 Subject: : [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query Message-ID: <4062C0C9.1030204@netvisao.pt> Yes, escaping characters doesn't seem to have anything to do with this problem. I suggested it because it worked for me in a different situation. However, if you use the count method, instead of cycling through all the results, to get the number of returned sequences, you get 5066, as it should be: #!/usr/bin/perl use strict; use Bio::DB::GenBank; use Bio::DB::Query::GenBank; my $gb=new Bio::DB::GenBank; my $query = Bio::DB::Query::GenBank->new (-query => 'Mus[Organism] exon NOT mRNA NOT cDNA', -db => 'Nucleotide'); my $seqio = $gb->get_Stream_by_query($query); print "Num results:" , $query->count , "\n"; I'm looking into it further, but I don't know what the problem could be. -Paulo Almeida T.D. Houfek wrote: >Hmm... > >Just for kicks I tried to duplicate the problem (I get the same number >of sequences from NCBI's web sequin tool as Jrgen, but using the >Bio::DB::Query:Genbank method I get 644 sequences (not less than 100, >but not the 5000+ we are expecting). Placing an escape backslash before >the brackets does not seem to help me: > >--- my test script below --- > >#!/usr/bin/perl >use strict; >use Bio::DB::GenBank; >use Bio::DB::Query::GenBank; > >my $gb=new >Bio::DB::GenBank; >my $query = Bio::DB::Query::GenBank->new > (-query => 'Mus\[Organism] AND exon NOT mRNA NOT cDNA', > -db => 'Nucleotide'); >my $seqio = $gb->get_Stream_by_query($query); >my $numresults=0; >while( my $seq = $seqio->next_seq ) { $numresults++; } >print "Num results: $numresults\n"; > From karesncatalia at hotmail.com Thu Mar 25 07:15:54 2004 From: karesncatalia at hotmail.com (elijah) Date: Thu Mar 25 07:21:12 2004 Subject: [Bioperl-l] As Seen on CNN, the Winningest CAS1N0! groovy stingray Message-ID: <1080216954-8998@excite.com> Come and play at the world's PREMIERE ONLINE CASINOn! We are happy to offer you, in an elegant atmosphere, a 50% BONUSz for your first deposit as a New Player. Sign=up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically credeit your account with a 50% BONrUS of extra chcips, to wagcr in our caseno. Don't hesitate and try your luck! CLICK HERE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ cardinal chevystrawber dude chiquita shawn trek yvonne shawn skidoorambo1 petunia safety shit cosmos fiona REoMOVE un_subvan@hotmail.com From jason at cgt.duhs.duke.edu Thu Mar 25 08:03:33 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Mar 25 08:09:01 2004 Subject: [Bioperl-l] Re: asking for a help In-Reply-To: <1080180541.40623f3d3e041@webmail.uoguelph.ca> References: <1080180541.40623f3d3e041@webmail.uoguelph.ca> Message-ID: Joshua - You can translate sequence within bioperl directly (if they are spliced and you know their frame) with the method $seq->translate(). If they are annotations in genbank/embl format you can use the $feature->splice_seq to get the spliced exons out of the sequence, but you will probably have to read more about the Sequences and Features before this will make sense. You should read the bioperl Feature and Sequence HOWTO first linked off the HOWTO page on the bioperl website. Bio::Factory and Bio::Tools::Run modules are in bioperl-run package which is available from the bioperl distribution directory (http://bioperl.org/DIST) -jason On Wed, 24 Mar 2004 szhan@uoguelph.ca wrote: > Hello, Jason: > I have got a list of genes (nucleotides sequences), I want to translate them > using a program (transeq) in EMBOSS and compare their function similarity > using blastp of bl2seq in BLAST. I read FAQ in bioperl web site and it said > that I can find a module: Bio::Factory::EMBOSS to do that, but I could not > find it. Could you please give me a guide to do this job? > Your help will be highly appreciated! > Joshua > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From antivirus at unito.it Thu Mar 25 08:22:56 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Thu Mar 25 08:28:17 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0325142225336] Message-ID: <200403251322.i2PDMu6Q025417@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: mando@unito.it Inflex ID: 0325142225336 Report Details ----------------------------------------------- AntiVirus Results... File NAME/TYPE Scan Results MS-DOS executable (EXE), OS/2 or MS Windows 0325142225336 from:bioperl-l@bioperl.org to: mando@unito.it END OF MESSAGE. End. . From Pedro.X.Gomez-Fabre at gsk.com Thu Mar 25 04:10:42 2004 From: Pedro.X.Gomez-Fabre at gsk.com (Pedro.X.Gomez-Fabre@gsk.com) Date: Thu Mar 25 08:30:54 2004 Subject: [Bioperl-l] Re: Pedro's haplotype block/tag system in In-Reply-To: Message-ID: "Ewan Birney" wrote on 24/03/2004 23:21:46: > > > I've just committed Pedro's haplotype block tagger and tests. I still need > to review the code (eg, it has Data::Dumper and Storeable, which I will > remove - Pedro - do you use Data::Dumper or Storeable actually in the > methods?) > I have removed Data::Dumper from the modules. I used it for testing. I do use Storable to copy (clone) some structures (i.e. list of lists) in HtSNP.pm on: use Storable qw(dclone); $self -> {'w_pop_freq'} = dclone ( $self ->pattern_freq() ); $self->{snp_type}->{useful_snp} = dclone ( $self ->snp_ids() ); $self -> {'split_hap'} = dclone ($out); @$arr= @{dclone(\@outValues)}; @$hap = @{dclone $out}; If there any other module I should be using instead I'll be glad to know. Thanks Ewan and Jason for review. Pedro > > Anyway, they are in a tests pass (at least over here!) > > > > From davila at ioc.fiocruz.br Thu Mar 25 07:40:07 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Thu Mar 25 08:30:57 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: References: <1080065187.2916.63.camel@tryps> Message-ID: <1080218407.3118.8.camel@tryps> Thanks Jason, I installed the IO::String, then it is working fine now. However I have a doubt, the "get_Stream_by_id" is returning me more than the "sequence per se", what is it ? My script and results are listed below. Finally I would like to save (in my local disk) the retrieved sequences as fasta files... is there any argument for that ? Thanks again, Alberto #!/usr/local/bin/perl -w use lib "/usr/local/bioperl14"; use Bio::DB::BioFetch; use strict; use Bio::DB::WebDBSeqI; use HTTP::Request::Common 'POST'; my $format_type='fasta'; my $stream; my $bf = new Bio::DB::BioFetch(-format =>$format_type, -retrievaltype =>'tempfile', -db =>'EMBL'); $stream = $bf->get_Stream_by_id(['BUM','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n\n\n"; } exit; [davila@tryps script]$ perl gb-fetch-1.pl agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgcat gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtgaa gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatgggt cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttgg tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggtg cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacacc tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaacc caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagaccc nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagca gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagta caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagcc cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacctg cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaacta caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaagag caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcagaa gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtcg cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagcg ctgccctgg On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: > You need an additional perl module. > > > install IO::String from CPAN > > There is a section on how to install additional perl modules in the > INSTALL document. > > -j > > On Tue, 23 Mar 2004, Alberto Davila wrote: > > > Hi, > > > > May I ask for some help ? > > > > I am trying to use the BioFetch module in order to download several seqs > > (from specific Organisms) from GenBank in fasta format, but looks like I > > am missing "IO/String.pm" and other things.. should I install additional > > bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a > > different module for my purpose ? > > > > My script and error msg are listed below. > > > > Thanks and besr regards, > > > > Alberto > > > > **** > > > > #!/usr/local/bin/perl -w > > > > use lib "/usr/local/bioperl14"; > > package Bio::DB::BioFetch; > > use strict; > > use Bio::DB::WebDBSeqI; > > use HTTP::Request::Common 'POST'; > > > > my $format_type='fasta'; > > my $stream; > > > > > > my $bf = new Bio::DB::BioFetch(-format =>$format_type', > > -retrievaltype =>'tempfile', > > -db =>'EMBL'); > > > > $stream = $bf->get_Stream_by_id(['BUM','J00231']); > > while (my $s = $stream->next_seq) { > > print $s->seq,"\n"; > > } > > > > > > exit; > > > > > > [davila@tryps script]$ perl gb-fetch-1.pl > > Can't locate IO/String.pm in @INC (@INC contains: > > /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 > > /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > /usr/lib/perl5/site_perl > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > /usr/lib/perl5/vendor_perl .) at > > /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > BEGIN failed--compilation aborted at > > /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > Compilation failed in require at gb-fetch-1.pl line 6. > > BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. From sanges at biogem.it Thu Mar 25 08:46:24 2004 From: sanges at biogem.it (Remo Sanges) Date: Thu Mar 25 08:51:54 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080218407.3118.8.camel@tryps> References: <1080065187.2916.63.camel@tryps> <1080218407.3118.8.camel@tryps> Message-ID: Hi Alberto, you are getting 2 sequences because you are querying for 2 id: BUM and J00231. With the get stream by id method you can ask for a large number of id, you need only write id separated by ',' in the array ref ['id1','id2','id3','id4',...]. Remo On Mar 25, 2004, at 1:40 PM, Alberto Davila wrote: > Thanks Jason, > > I installed the IO::String, then it is working fine now. However I have > a doubt, the "get_Stream_by_id" is returning me more than the "sequence > per se", what is it ? My script and results are listed below. Finally I > would like to save (in my local disk) the retrieved sequences as fasta > files... is there any argument for that ? > > Thanks again, Alberto > > > #!/usr/local/bin/perl -w > > use lib "/usr/local/bioperl14"; > use Bio::DB::BioFetch; > use strict; > use Bio::DB::WebDBSeqI; > use HTTP::Request::Common 'POST'; > > my $format_type='fasta'; > my $stream; > > > my $bf = new Bio::DB::BioFetch(-format =>$format_type, > -retrievaltype =>'tempfile', > -db =>'EMBL'); > > $stream = $bf->get_Stream_by_id(['BUM','J00231']); > while (my $s = $stream->next_seq) { > print $s->seq,"\n\n\n"; > } > > > exit; > > > > > [davila@tryps script]$ perl gb-fetch-1.pl > agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgca > t > gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtga > a > gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > > > cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatggg > t > cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttg > g > tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggt > g > cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacac > c > tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaac > c > caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagacc > c > nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagc > a > gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagt > a > caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagc > c > cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacct > g > cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaact > a > caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaaga > g > caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcaga > a > gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtc > g > cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagc > g > ctgccctgg > > > > > On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: >> You need an additional perl module. >> >> >> install IO::String from CPAN >> >> There is a section on how to install additional perl modules in the >> INSTALL document. >> >> -j >> >> On Tue, 23 Mar 2004, Alberto Davila wrote: >> >>> Hi, >>> >>> May I ask for some help ? >>> >>> I am trying to use the BioFetch module in order to download several >>> seqs >>> (from specific Organisms) from GenBank in fasta format, but looks >>> like I >>> am missing "IO/String.pm" and other things.. should I install >>> additional >>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a >>> different module for my purpose ? >>> >>> My script and error msg are listed below. >>> >>> Thanks and besr regards, >>> >>> Alberto >>> >>> **** >>> >>> #!/usr/local/bin/perl -w >>> >>> use lib "/usr/local/bioperl14"; >>> package Bio::DB::BioFetch; >>> use strict; >>> use Bio::DB::WebDBSeqI; >>> use HTTP::Request::Common 'POST'; >>> >>> my $format_type='fasta'; >>> my $stream; >>> >>> >>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', >>> -retrievaltype =>'tempfile', >>> -db =>'EMBL'); >>> >>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); >>> while (my $s = $stream->next_seq) { >>> print $s->seq,"\n"; >>> } >>> >>> >>> exit; >>> >>> >>> [davila@tryps script]$ perl gb-fetch-1.pl >>> Can't locate IO/String.pm in @INC (@INC contains: >>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 >>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 >>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 >>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 >>> /usr/lib/perl5/site_perl >>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 >>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 >>> /usr/lib/perl5/vendor_perl .) at >>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>> BEGIN failed--compilation aborted at >>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>> Compilation failed in require at gb-fetch-1.pl line 6. >>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From sdavis2 at mail.nih.gov Thu Mar 25 09:12:23 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Mar 25 09:14:05 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080218407.3118.8.camel@tryps> Message-ID: Alberto, This code will output your sequences in fasta to a file called outfile.fa. Sean #!/usr/local/bin/perl -w use lib "/usr/local/bioperl14"; use Bio::DB::BioFetch; use strict; use Bio::DB::WebDBSeqI; use HTTP::Request::Common 'POST'; my $format_type='fasta';my $stream; my $bf = new Bio::DB::BioFetch(-format =>$format_type, -retrievaltype =>'tempfile', -db =>'EMBL'); #open a seqio handle for writing to outfile.fa my $seqio = new Bio::SeqIO(-format=>'fasta', -file=>'>outfile.fa'); $stream = $bf->get_Stream_by_id(['BUM','J00231']); while (my $s = $stream->next_seq) { print $s->seq,"\n\n\n"; #write the fasta $seqio->write_seq($s); } On 3/25/04 7:40 AM, "Alberto Davila" wrote: > Thanks Jason, > > I installed the IO::String, then it is working fine now. However I have > a doubt, the "get_Stream_by_id" is returning me more than the "sequence > per se", what is it ? My script and results are listed below. Finally I > would like to save (in my local disk) the retrieved sequences as fasta > files... is there any argument for that ? > > Thanks again, Alberto > > > #!/usr/local/bin/perl -w > > use lib "/usr/local/bioperl14"; > use Bio::DB::BioFetch; > use strict; > use Bio::DB::WebDBSeqI; > use HTTP::Request::Common 'POST'; > > my $format_type='fasta'; > my $stream; > > > my $bf = new Bio::DB::BioFetch(-format =>$format_type, > -retrievaltype =>'tempfile', > -db =>'EMBL'); > > $stream = $bf->get_Stream_by_id(['BUM','J00231']); > while (my $s = $stream->next_seq) { > print $s->seq,"\n\n\n"; > } > > > exit; > > > > > [davila@tryps script]$ perl gb-fetch-1.pl > agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgcat > gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtgaa > gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > > > cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatgggt > cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttgg > tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggtg > cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacacc > tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaacc > caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagaccc > nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagca > gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagta > caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagcc > cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacctg > cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaacta > caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaagag > caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcagaa > gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtcg > cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagcg > ctgccctgg > > > > > On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: >> You need an additional perl module. >> >> >> install IO::String from CPAN >> >> There is a section on how to install additional perl modules in the >> INSTALL document. >> >> -j >> >> On Tue, 23 Mar 2004, Alberto Davila wrote: >> >>> Hi, >>> >>> May I ask for some help ? >>> >>> I am trying to use the BioFetch module in order to download several seqs >>> (from specific Organisms) from GenBank in fasta format, but looks like I >>> am missing "IO/String.pm" and other things.. should I install additional >>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a >>> different module for my purpose ? >>> >>> My script and error msg are listed below. >>> >>> Thanks and besr regards, >>> >>> Alberto >>> >>> **** >>> >>> #!/usr/local/bin/perl -w >>> >>> use lib "/usr/local/bioperl14"; >>> package Bio::DB::BioFetch; >>> use strict; >>> use Bio::DB::WebDBSeqI; >>> use HTTP::Request::Common 'POST'; >>> >>> my $format_type='fasta'; >>> my $stream; >>> >>> >>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', >>> -retrievaltype =>'tempfile', >>> -db =>'EMBL'); >>> >>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); >>> while (my $s = $stream->next_seq) { >>> print $s->seq,"\n"; >>> } >>> >>> >>> exit; >>> >>> >>> [davila@tryps script]$ perl gb-fetch-1.pl >>> Can't locate IO/String.pm in @INC (@INC contains: >>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 >>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 >>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 >>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 >>> /usr/lib/perl5/site_perl >>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 >>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 >>> /usr/lib/perl5/vendor_perl .) at >>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>> BEGIN failed--compilation aborted at >>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>> Compilation failed in require at gb-fetch-1.pl line 6. >>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From gocougs21sally at hotmail.com Thu Mar 25 22:33:33 2004 From: gocougs21sally at hotmail.com (donnie) Date: Thu Mar 25 09:37:54 2004 Subject: [Bioperl-l] GOD in the sack? No? Here's how! lulu new rhonda Message-ID: <1080272013-13686@excite.com> Greatest offers on VIAGRzxA and CIzALcIS (rufus sugar) As low as three dollars a dose! Super deals, 80 pcneert off! Ship-ped straight to your doorstep! (barry amanda1) Clik Here: http://test2.mypersonalmeds.net/sv/index.php?pid=eph9106 reynolds angels johnson goblue yvonne strawber medical mikael tintin nimrod impala dodgers mailman marvin river cosmos isaac aspen speedo zeppelin rambo1 tattoo smiths chance josh From pvh at egenetics.com Thu Mar 25 10:05:18 2004 From: pvh at egenetics.com (Peter van Heusden) Date: Thu Mar 25 10:10:46 2004 Subject: [Bioperl-l] hash key for SeqFeatureI Message-ID: <4062F52E.5000705@egenetics.com> Hi Bioperlers I'm adding hash_key methods to various classes (part of my work in making Bioperl object comparable), and for SeqFeatureI, I was wondering whether the following is adaquate: primary_tag(), display_id(), location->start(), location->end()? The point of a hash_key() method is to return a string which uniquely identifies the object - i.e. if two hash keys are identical, then the objects are equivalent. And related to this, where is the strandedness of Bioperl SeqFeatures stored? Peter From cdwan at mail.ahc.umn.edu Thu Mar 25 10:25:52 2004 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Thu Mar 25 10:31:17 2004 Subject: [Bioperl-l] hash key for SeqFeatureI In-Reply-To: <4062F52E.5000705@egenetics.com> References: <4062F52E.5000705@egenetics.com> Message-ID: > And related to this, where is the strandedness of Bioperl SeqFeatures > stored? Bio::SeqFeature::Generic has a member "location" which is a Bio::Location::Simple. Bio::Location::Simple inherits the strand method from Bio::Location::Atomic. Really, under the hood, it's: seqfeature->location()->{'_strand')} Which may be accessed as seqfeature->strand() Allowed values are -1 (or '-'), 1 (or '+') and 0 (or '.'). -Chris Dwan From antivirus at unito.it Thu Mar 25 10:27:19 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Thu Mar 25 10:32:40 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0325162716542] Message-ID: <200403251527.i2PFRJiv016573@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: mapiccol@unito.it Inflex ID: 0325162716542 Report Details ----------------------------------------------- AntiVirus Results... File NAME/TYPE Scan Results MS-DOS executable (EXE), OS/2 or MS Windows 0325162716542 from:bioperl-l@bioperl.org to: mapiccol@unito.it END OF MESSAGE. End. . From ra1ywrite at hotmail.com Thu Mar 25 10:41:03 2004 From: ra1ywrite at hotmail.com (levi) Date: Thu Mar 25 10:47:23 2004 Subject: [Bioperl-l] hi there! dundeec zhongguop soccer1c Message-ID: <1080229263-32314@excite.com> PR0ZoAC, XANAtX, VIAGRsA, CIALInS, ZYBAlN & more!! Stop depresfsion, quit smokinvg, increase erectuions! Drugc at HUGE DISCOuNTS!!!! http://aofg.base4ds.com/s95/index.php?id=s95 steph soccer1 supra justin1 beautifu jeanette suzuki button percy metallicapolo shawn petunia buttons magnum chiquita baskeT ruth alfred philip montreal dude campbell mantra josh From jason at cgt.duhs.duke.edu Thu Mar 25 11:07:53 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Mar 25 11:13:53 2004 Subject: [Bioperl-l] hash key for SeqFeatureI In-Reply-To: References: <4062F52E.5000705@egenetics.com> Message-ID: actually it is not always a Location::Simple but instead is always a Bio::LocationI object Which can be Peter the (somewhat old) object diagram on the bioperl website might be helpful. Split locations won't have strands but will delegate to their internal components which are a list of Bio::LocationI objects. Fuzzy and Split locations will try and return a sensible summary value for start/end/strand. The method $location->to_FTstring() will return a string which should be comparable (although sets of locations in different orders stored in a SplitLocation will not be equivalent). -j On Thu, 25 Mar 2004, Chris Dwan (CCGB) wrote: > > > And related to this, where is the strandedness of Bioperl SeqFeatures > > stored? > > Bio::SeqFeature::Generic has a member "location" which is a > Bio::Location::Simple. Bio::Location::Simple inherits the strand method > from Bio::Location::Atomic. > > Really, under the hood, it's: > seqfeature->location()->{'_strand')} > > Which may be accessed as > seqfeature->strand() > > Allowed values are -1 (or '-'), 1 (or '+') and 0 (or '.'). > > -Chris Dwan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From pftfroms1 at yahoo.co.uk Thu Mar 25 20:02:36 2004 From: pftfroms1 at yahoo.co.uk (Post Budget) Date: Thu Mar 25 14:06:33 2004 Subject: [Bioperl-l] Tobacco-Offer Message-ID: <200403251906.i2PJ6Tg2026463@portal.open-bio.org> Hi All, if you are a smoker in the UK or anywhere else please just take a few minutes of your time to read this, if not please accept my apologies for this E mail, it is not my intention to upset anyone. Smokers - are you still paying high street prices for your cigarettes, cigars or rolling/pipe tobacco. For instance, I can send you by registered post, 800 cigarettes for 180 euros. This works out to about ?3.10 a packet (depending on exchange rate). For this price, and it includes all brands they will be sent by registered post direct to your door. Just click on the link below:- http://www.geocities.com/cheapuk1tobacco Yours faithfully A believer in the rights of the British Smokers P.S. If this E at all offends you mail - that is not my intention ---- YOU WILL NOT BE E MAILED AGAIN http://www.geocities.com/cheapuk1tobacco If you would like to be removed from our database please email pftrems2@yahoo.co.uk with REMOVES in the subject line From barry.moore at genetics.utah.edu Thu Mar 25 12:43:21 2004 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Thu Mar 25 14:22:07 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080218407.3118.8.camel@tryps> References: <1080065187.2916.63.camel@tryps> <1080218407.3118.8.camel@tryps> Message-ID: <40631A39.9000205@genetics.utah.edu> Alberto- You said, "the 'get_Stream_by_id' is returning me more than the 'sequence per se'". I'm not sure if this is what your asking, but I'll take a shot. Since your are retrieving your two sequences in EMBL format, you get all the associated information that you would see if you downloaded that same file from the web interface. Your sequences are stored by BioPerl as RichSeq objects which inherits a PrimarySeq objects. So that EMBL file data is stored in the RichSeq object and the associated PrimarySeq object it inherited. Of course when you save that locally as a fasta file, that extra information is lost. If you decide you need to use that data have a look at the documentation for Bio::Seq::RichSeq and Bio::PrimarySeq and the SeqIO and Feature Annotation HOW TOs to learn more. Barry Alberto Davila wrote: >Thanks Jason, > >I installed the IO::String, then it is working fine now. However I have >a doubt, the "get_Stream_by_id" is returning me more than the "sequence >per se", what is it ? My script and results are listed below. Finally I >would like to save (in my local disk) the retrieved sequences as fasta >files... is there any argument for that ? > >Thanks again, Alberto > > >#!/usr/local/bin/perl -w > >use lib "/usr/local/bioperl14"; >use Bio::DB::BioFetch; >use strict; >use Bio::DB::WebDBSeqI; >use HTTP::Request::Common 'POST'; > >my $format_type='fasta'; >my $stream; > > >my $bf = new Bio::DB::BioFetch(-format =>$format_type, > -retrievaltype =>'tempfile', > -db =>'EMBL'); > > $stream = $bf->get_Stream_by_id(['BUM','J00231']); > while (my $s = $stream->next_seq) { > print $s->seq,"\n\n\n"; > } > > > exit; > > > > >[davila@tryps script]$ perl gb-fetch-1.pl >agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgcat >gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtgaa >gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > > >cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatgggt >cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttgg >tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggtg >cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacacc >tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaacc >caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagaccc >nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagca >gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagta >caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagcc >cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacctg >cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaacta >caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaagag >caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcagaa >gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtcg >cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagcg >ctgccctgg > > > > >On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: > > >>You need an additional perl module. >> >> >>install IO::String from CPAN >> >>There is a section on how to install additional perl modules in the >>INSTALL document. >> >>-j >> >>On Tue, 23 Mar 2004, Alberto Davila wrote: >> >> >> >>>Hi, >>> >>>May I ask for some help ? >>> >>>I am trying to use the BioFetch module in order to download several seqs >>>(from specific Organisms) from GenBank in fasta format, but looks like I >>>am missing "IO/String.pm" and other things.. should I install additional >>>bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a >>>different module for my purpose ? >>> >>>My script and error msg are listed below. >>> >>>Thanks and besr regards, >>> >>>Alberto >>> >>>**** >>> >>>#!/usr/local/bin/perl -w >>> >>>use lib "/usr/local/bioperl14"; >>>package Bio::DB::BioFetch; >>>use strict; >>>use Bio::DB::WebDBSeqI; >>>use HTTP::Request::Common 'POST'; >>> >>>my $format_type='fasta'; >>>my $stream; >>> >>> >>>my $bf = new Bio::DB::BioFetch(-format =>$format_type', >>> -retrievaltype =>'tempfile', >>> -db =>'EMBL'); >>> >>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); >>> while (my $s = $stream->next_seq) { >>> print $s->seq,"\n"; >>> } >>> >>> >>> exit; >>> >>> >>>[davila@tryps script]$ perl gb-fetch-1.pl >>>Can't locate IO/String.pm in @INC (@INC contains: >>>/usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 >>>/usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 >>>/usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >>>/usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >>>/usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>>/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 >>>/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 >>>/usr/lib/perl5/site_perl >>>/usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >>>/usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >>>/usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>>/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 >>>/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 >>>/usr/lib/perl5/vendor_perl .) at >>>/usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>>BEGIN failed--compilation aborted at >>>/usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>>Compilation failed in require at gb-fetch-1.pl line 6. >>>BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. >>> >>> > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- Barry Moore Dept. of Human Genetics University of Utah Salt Lake City, UT From sdavis2 at mail.nih.gov Thu Mar 25 14:37:13 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Thu Mar 25 14:42:31 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <40631A39.9000205@genetics.utah.edu> Message-ID: Alberto, I would second that. If are doing more with this than retrieving raw sequence (if you care at all), maybe you could let Barry and I know what you are trying to do more generally. Bioperl is quite powerful, but it does take some direction to get started. Sean On 3/25/04 12:43 PM, "Barry Moore" wrote: > Alberto- > > You said, "the 'get_Stream_by_id' is returning me more than the > 'sequence per se'". I'm not sure if this is what your asking, but I'll > take a shot. Since your are retrieving your two sequences in EMBL > format, you get all the associated information that you would see if you > > downloaded that same file from the web interface. Your sequences are > stored by BioPerl as RichSeq objects which inherits a PrimarySeq > objects. So that EMBL file data is stored in the RichSeq object and the > > associated PrimarySeq object it inherited. Of course when you save > that locally as a fasta file, that extra information is lost. If you > decide you need to use that data have a look at the documentation for > Bio::Seq::RichSeq and Bio::PrimarySeq and the SeqIO and Feature > Annotation HOW TOs to learn more. > > Barry > > Alberto Davila wrote: > >> Thanks Jason, >> >> I installed the IO::String, then it is working fine now. However I have >> a doubt, the "get_Stream_by_id" is returning me more than the "sequence >> per se", what is it ? My script and results are listed below. Finally I >> would like to save (in my local disk) the retrieved sequences as fasta >> files... is there any argument for that ? >> >> Thanks again, Alberto >> >> >> #!/usr/local/bin/perl -w >> >> use lib "/usr/local/bioperl14"; >> use Bio::DB::BioFetch; >> use strict; >> use Bio::DB::WebDBSeqI; >> use HTTP::Request::Common 'POST'; >> >> my $format_type='fasta'; >> my $stream; >> >> >> my $bf = new Bio::DB::BioFetch(-format =>$format_type, >> -retrievaltype =>'tempfile', >> -db =>'EMBL'); >> >> $stream = $bf->get_Stream_by_id(['BUM','J00231']); >> while (my $s = $stream->next_seq) { >> print $s->seq,"\n\n\n"; >> } >> >> >> exit; >> >> >> >> >> [davila@tryps script]$ perl gb-fetch-1.pl >> agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgca > t >> gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtga > a >> gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca >> > >> > >> cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatggg > t >> cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttg > g >> tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggt > g >> cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacac > c >> tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaac > c >> caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagacc > c >> nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagc > a >> gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagt > a >> caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagc > c >> cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacct > g >> cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaact > a >> caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaaga > g >> caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcaga > a >> gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtc > g >> cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagc > g >> ctgccctgg >> >> >> >> >> On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: >> >> >>> You need an additional perl module. >>> >>> >>> install IO::String from CPAN >>> >>> There is a section on how to install additional perl modules in the >>> INSTALL document. >>> >>> -j >>> >>> On Tue, 23 Mar 2004, Alberto Davila wrote: >>> >>> >>> >>>> Hi, >>>> >>>> May I ask for some help ? >>>> >>>> I am trying to use the BioFetch module in order to download several > seqs >>>> (from specific Organisms) from GenBank in fasta format, but looks > like I >>>> am missing "IO/String.pm" and other things.. should I install > additional >>>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a >>>> different module for my purpose ? >>>> >>>> My script and error msg are listed below. >>>> >>>> Thanks and besr regards, >>>> >>>> Alberto >>>> >>>> **** >>>> >>>> #!/usr/local/bin/perl -w >>>> >>>> use lib "/usr/local/bioperl14"; >>>> package Bio::DB::BioFetch; >>>> use strict; >>>> use Bio::DB::WebDBSeqI; >>>> use HTTP::Request::Common 'POST'; >>>> >>>> my $format_type='fasta'; >>>> my $stream; >>>> >>>> >>>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', >>>> -retrievaltype =>'tempfile', >>>> -db =>'EMBL'); >>>> >>>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); >>>> while (my $s = $stream->next_seq) { >>>> print $s->seq,"\n"; >>>> } >>>> >>>> >>>> exit; >>>> >>>> >>>> [davila@tryps script]$ perl gb-fetch-1.pl >>>> Can't locate IO/String.pm in @INC (@INC contains: >>>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 >>>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 >>>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi >>>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi >>>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi >>>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi >>>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 >>>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 >>>> /usr/lib/perl5/site_perl >>>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi >>>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 >>>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 >>>> /usr/lib/perl5/vendor_perl .) at >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>>> BEGIN failed--compilation aborted at >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. >>>> Compilation failed in require at gb-fetch-1.pl line 6. >>>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. >>>> >>>> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> From davila at ioc.fiocruz.br Thu Mar 25 15:38:32 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Thu Mar 25 16:37:03 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: References: Message-ID: <1080247112.7333.23.camel@tryps> Hi Sean, Thanks for your valuable help ! I solved the problem using "Bio::DB::Query::GenBank", my goal was to retrieve 2 types of sequences (mitochondrial and ribosomal) from specific organism (eg Bothrops spp)... I am listing my script for those interested to do something similar.. the only warning I get is: [davila@tryps script]$ perl fetch2contaminant.pl Useless use of a constant in void context at fetch2contaminant.pl line 10. I was not sure in which field (eg keyword or feature) I should look for ribosomal and mitochondrial genes, but leaving blank gave some good results. Indeed Bioperl is powerful... a bit confusing for beginners too. Thanks and best regards, Alberto #!/usr/local/bin/perl -w use lib "/usr/local/bioperl14"; use strict; use Bio::DB::Query::GenBank; use Bio::SeqIO; use Bio::DB::GenBank; my $query_string = ('Bothrops[Organism] AND ribosomal','Bothrops[Organism] AND mitochondrial'); my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide', -query=>$query_string, -mindate => '1985', -maxdate => '2004'); my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query); #open a seqio handle for writing the outputfile in fasta my $outfile = new Bio::SeqIO(-format=>'fasta', -file=>'>contaminant.bothrops'); while (my $s = $seqio->next_seq) { #write the fasta $outfile->write_seq($s); } exit; On Thu, 2004-03-25 at 16:37, Sean Davis wrote: > Alberto, > > I would second that. If are doing more with this than retrieving raw > sequence (if you care at all), maybe you could let Barry and I know what you > are trying to do more generally. Bioperl is quite powerful, but it does > take some direction to get started. > > Sean > > On 3/25/04 12:43 PM, "Barry Moore" wrote: > > > Alberto- > > > > You said, "the 'get_Stream_by_id' is returning me more than the > > 'sequence per se'". I'm not sure if this is what your asking, but I'll > > take a shot. Since your are retrieving your two sequences in EMBL > > format, you get all the associated information that you would see if you > > > > downloaded that same file from the web interface. Your sequences are > > stored by BioPerl as RichSeq objects which inherits a PrimarySeq > > objects. So that EMBL file data is stored in the RichSeq object and the > > > > associated PrimarySeq object it inherited. Of course when you save > > that locally as a fasta file, that extra information is lost. If you > > decide you need to use that data have a look at the documentation for > > Bio::Seq::RichSeq and Bio::PrimarySeq and the SeqIO and Feature > > Annotation HOW TOs to learn more. > > > > Barry > > > > Alberto Davila wrote: > > > >> Thanks Jason, > >> > >> I installed the IO::String, then it is working fine now. However I have > >> a doubt, the "get_Stream_by_id" is returning me more than the "sequence > >> per se", what is it ? My script and results are listed below. Finally I > >> would like to save (in my local disk) the retrieved sequences as fasta > >> files... is there any argument for that ? > >> > >> Thanks again, Alberto > >> > >> > >> #!/usr/local/bin/perl -w > >> > >> use lib "/usr/local/bioperl14"; > >> use Bio::DB::BioFetch; > >> use strict; > >> use Bio::DB::WebDBSeqI; > >> use HTTP::Request::Common 'POST'; > >> > >> my $format_type='fasta'; > >> my $stream; > >> > >> > >> my $bf = new Bio::DB::BioFetch(-format =>$format_type, > >> -retrievaltype =>'tempfile', > >> -db =>'EMBL'); > >> > >> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > >> while (my $s = $stream->next_seq) { > >> print $s->seq,"\n\n\n"; > >> } > >> > >> > >> exit; > >> > >> > >> > >> > >> [davila@tryps script]$ perl gb-fetch-1.pl > >> agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgca > > t > >> gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtga > > a > >> gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > >> > > > >> > > > >> cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatggg > > t > >> cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttg > > g > >> tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggt > > g > >> cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacac > > c > >> tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaac > > c > >> caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagacc > > c > >> nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagc > > a > >> gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagt > > a > >> caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagc > > c > >> cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacct > > g > >> cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaact > > a > >> caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaaga > > g > >> caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcaga > > a > >> gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtc > > g > >> cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagc > > g > >> ctgccctgg > >> > >> > >> > >> > >> On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: > >> > >> > >>> You need an additional perl module. > >>> > >>> > >>> install IO::String from CPAN > >>> > >>> There is a section on how to install additional perl modules in the > >>> INSTALL document. > >>> > >>> -j > >>> > >>> On Tue, 23 Mar 2004, Alberto Davila wrote: > >>> > >>> > >>> > >>>> Hi, > >>>> > >>>> May I ask for some help ? > >>>> > >>>> I am trying to use the BioFetch module in order to download several > > seqs > >>>> (from specific Organisms) from GenBank in fasta format, but looks > > like I > >>>> am missing "IO/String.pm" and other things.. should I install > > additional > >>>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a > >>>> different module for my purpose ? > >>>> > >>>> My script and error msg are listed below. > >>>> > >>>> Thanks and besr regards, > >>>> > >>>> Alberto > >>>> > >>>> **** > >>>> > >>>> #!/usr/local/bin/perl -w > >>>> > >>>> use lib "/usr/local/bioperl14"; > >>>> package Bio::DB::BioFetch; > >>>> use strict; > >>>> use Bio::DB::WebDBSeqI; > >>>> use HTTP::Request::Common 'POST'; > >>>> > >>>> my $format_type='fasta'; > >>>> my $stream; > >>>> > >>>> > >>>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', > >>>> -retrievaltype =>'tempfile', > >>>> -db =>'EMBL'); > >>>> > >>>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > >>>> while (my $s = $stream->next_seq) { > >>>> print $s->seq,"\n"; > >>>> } > >>>> > >>>> > >>>> exit; > >>>> > >>>> > >>>> [davila@tryps script]$ perl gb-fetch-1.pl > >>>> Can't locate IO/String.pm in @INC (@INC contains: > >>>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 > >>>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 > >>>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > >>>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > >>>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > >>>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > >>>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > >>>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > >>>> /usr/lib/perl5/site_perl > >>>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > >>>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > >>>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > >>>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > >>>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > >>>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > >>>> /usr/lib/perl5/vendor_perl .) at > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > >>>> BEGIN failed--compilation aborted at > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > >>>> Compilation failed in require at gb-fetch-1.pl line 6. > >>>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. From rfsouza at citri.iq.usp.br Thu Mar 25 20:48:51 2004 From: rfsouza at citri.iq.usp.br (Robson Francisco de Souza) Date: Thu Mar 25 20:51:48 2004 Subject: [Bioperl-l] Sequence IDs Message-ID: <20040326014851.GG23629@genoma4.iq.usp.br> Hi, This is not quite a bioperl question, but maybe there is some useful code in bioperl that can easy the task below. I'm trying to automatically track GI changes for a sequence in Genbank, so that I can list all GI numbers associated to a gene in a complete genome from Genbank, EMBL or Kegg. I need this to compare results from Kegg Orthologs database (GenomeNet), COG database (NCBI) and the String server from EMBL. Although I was able to download Kegg release 29, GI numbers for genes in this release are outdated and do not agree with COG GIs. Does anybody know of a way to retrive all GIs (PID) for every genes in complete genomes? Also, what is the unique ID or accession key for protein/dna sequence that is used by all main sequence databases (Genbank, SP/TrEMBL, DDBJ), if there is any? I couldn't find an easy way to cross results from analysis that employ identifications from different databases. Thanks for any help. Robson From lavwson_24 at hotmail.com Thu Mar 25 21:56:46 2004 From: lavwson_24 at hotmail.com (thad) Date: Thu Mar 25 22:01:42 2004 Subject: [Bioperl-l] Buy C_I_A_L_I_S cheaply! cuddles playboy Message-ID: <1080269806-22450@excite.com> This drug puts Vi-ag-ra to shame! One pill, all weekend! http://happyday.wehavecheap.com/sv/index.php?pid=eph9106 politics glenn saskia jan biology japan cosmos director jkm lamer snuffy jkm sarah1 ssssss redwing fireball cardinal skidoo dodgers tiffany electric dragonfl slacker laddie hornet lovevalhalla tina valhalla daddy benoit wolfMan mookie sherry swimming ruby buttons cynthia bozo get off the list here: http://mimi.mybestchoice.net/mm/chair.php From Mohammad.Shahid at Genetik.Uni-Bielefeld.DE Fri Mar 26 15:36:33 2004 From: Mohammad.Shahid at Genetik.Uni-Bielefeld.DE (M.Shahid) Date: Fri Mar 26 06:39:33 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical bioinformatics applications input data Message-ID: <000c01c41372$07675af0$66125ec2@meemsheen> Dear All, For a small software project, I'm looking for Perl Regular Expressions that match file formats and related input used for bioinformatics applications, e.g. FASTA, Clustal, PROSITE patterns, PAM similarity matrices, etc. Note that I do not want to parse such data, just check whether the format is correct. Is there any compilation out there ? If not, what is the best starting point to collect such Regular Expressions ? Best Wishes, M. Shahid From ak at ebi.ac.uk Fri Mar 26 07:01:49 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri Mar 26 07:07:07 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical bioinformatics applications input data In-Reply-To: <000c01c41372$07675af0$66125ec2@meemsheen> References: <000c01c41372$07675af0$66125ec2@meemsheen> Message-ID: <20040326120149.GA3578@ebi.ac.uk> On Fri, Mar 26, 2004 at 12:36:33PM -0800, M.Shahid wrote: > Dear All, > For a small software project, I'm looking for Perl Regular > Expressions that match file formats and related input used > for bioinformatics applications, e.g. FASTA, Clustal, > PROSITE patterns, PAM similarity matrices, etc. Note > that I do not want to parse such data, just check whether > the format is correct. Is there any compilation out there ? > If not, what is the best starting point to collect such Regular > Expressions ? I'm wondering wheather regular expression really would be the best thing to use. It is common knowledge that it is *very* hard to validate formats such as for example HTML using regular expressions (one needs a proper validating parser). Detecting is another matter. There is a module called Bio::Tools::GuessSeqFormat in BioPerl that, I originally wrote. It doesn't claim to validate the various input formats or even that it will deliver a correct answer. It will only apply regular expressions to the header lines of data files and try to determine the format of the file (or string). I don't know what the best approach to format validation would be, but it is my belief that regular expression can not be used alone. Regards, Andreas -- | {} | Andreas K?h?ri EMBL, European Bioinformatics Institute |{}{}| Wellcome Trust Genome Campus | {} | DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD |{}{}| Ensembl Developer United Kingdom From Zhongwu.Lai at ari.altanapharma.com Thu Mar 25 18:28:19 2004 From: Zhongwu.Lai at ari.altanapharma.com (Zhongwu.Lai@ari.altanapharma.com) Date: Fri Mar 26 08:37:59 2004 Subject: [Bioperl-l] A question about Bio::Graphics Message-ID: Hi, I'm wondering whether someone can help me on how to show a description in Bio::Graphics on left, or right side of the Glyph, instead of below. I'm using following code: my $track = $panel->add_track(-glyph => 'graded_segments', -label => 1, -connector => 'dashed', -bgcolor => 'blue', -font2color => 'red', -sort_order => 'high_score', -description => sub { my $feature = shift; return unless $feature->has_tag('description'); my ($description) = $feature->each_tag_value('description'); my $score = $feature->score; "$description, score=$score"; }); However, the description is by default always below the glyph. As UCSC genome browser has demonstrated, it can be put on side. But I couldn't find the right option. Your time and help is greatly appreciated! Zhongwu From khoueiry at ibsm.cnrs-mrs.fr Fri Mar 26 07:14:10 2004 From: khoueiry at ibsm.cnrs-mrs.fr (KHOUEIRY pierre) Date: Fri Mar 26 08:38:02 2004 Subject: [Bioperl-l] coloring subseq Message-ID: <40641E92.4080803@ibsm.cnrs-mrs.fr> Hello, Anybody can help me to color a subseq in Bioperl.. Per example, I have a subseq of "NPYCEWKCPVHNYIPNWLKLA" in wich i like to color H and C in blue and P and K in red... Any suggestions would be appreciated Thanks... -- --------------------------------- Pierre Khoueiry khoueiry@ibsm.cnrs-mrs.fr LCB - CNRS 31, Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France --------------------------------- TIP : When the cup is half empty, make it half full From ak at ebi.ac.uk Fri Mar 26 08:52:46 2004 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri Mar 26 08:58:12 2004 Subject: [Bioperl-l] coloring subseq In-Reply-To: <40641E92.4080803@ibsm.cnrs-mrs.fr> References: <40641E92.4080803@ibsm.cnrs-mrs.fr> Message-ID: <20040326135246.GA5053@ebi.ac.uk> On Fri, Mar 26, 2004 at 01:14:10PM +0100, KHOUEIRY pierre wrote: > Hello, > Anybody can help me to color a subseq in Bioperl.. Per example, I have a > subseq of "NPYCEWKCPVHNYIPNWLKLA" in wich i like to color > H and C in blue and P and K in red... > Any suggestions would be appreciated > Thanks... This would be colors in a Unix console window, in HTML, in a PNG file, or where? Here's a short way of doing it by applying HTML tags with a color attribute (I'm not sure this is the correct usage of the tag in HTML, but it shouldn't be hard to modify): my $seq = 'NPYCEWKCPVHNYIPNWLKLA'; $seq =~ s/([NC])/\1<\/font>/g; $seq =~ s/([PK])/\1<\/font>/g; print "$seq\n"; -- |(==)| Andreas K?h?ri EMBL, European Bioinformatics Institute |=)(=| Wellcome Trust Genome Campus |(==)| DAS Project Leader Hinxton, Cambridgeshire, CB10 1SD |=)(=| Ensembl Developer United Kingdom From heikki at ebi.ac.uk Fri Mar 26 09:55:17 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Fri Mar 26 10:00:46 2004 Subject: [Bioperl-l] Sequence IDs In-Reply-To: <20040326014851.GG23629@genoma4.iq.usp.br> References: <20040326014851.GG23629@genoma4.iq.usp.br> Message-ID: <200403261455.17296.heikki@ebi.ac.uk> Robson, In my best knowledge there is not yet a global system for gene idenfiers, so I can not help you there. GenBank, EMBL and DDBJ have agreed on using accession numbers (AC line) as unique, global identifiers. All other IDs are unique only within a single database. -Heikki On Friday 26 Mar 2004 01:48, Robson Francisco de Souza wrote: > Hi, > > This is not quite a bioperl question, but maybe there is some useful > code in bioperl that can easy the task below. > > I'm trying to automatically track GI changes for a sequence in Genbank, > so that I can list all GI numbers associated to a gene in a complete > genome from Genbank, EMBL or Kegg. I need this to compare results from > Kegg Orthologs database (GenomeNet), COG database (NCBI) and the String > server from EMBL. > Although I was able to download Kegg release 29, GI numbers for genes in > this release are outdated and do not agree with COG GIs. Does anybody > know of a way to retrive all GIs (PID) for every genes in complete genomes? > > Also, what is the unique ID or accession key for protein/dna > sequence that is used by all main sequence databases (Genbank, > SP/TrEMBL, DDBJ), if there is any? I couldn't find an easy way to cross > results from analysis that employ identifications from different > databases. > > Thanks for any help. > Robson > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From rnilsson at clarku.edu Fri Mar 26 10:55:22 2004 From: rnilsson at clarku.edu (henrik nilsson) Date: Fri Mar 26 11:01:12 2004 Subject: [Bioperl-l] Fetching > 500 sequences Message-ID: <200403261055.22737.rnilsson@clarku.edu> Hi, Thank you very much for your help. I went through and took out any references to "retmax" in both Bio::DB::Query::GenBank and Bio::DB::GenBank and Bio::DB::NCBIHelper. Our script first sends a query through Bio::DB::Query::GenBank and that works fine (it only returns the count found, and that count is > 7000). However, we then actually query GenBank with Bio::DB::GenBank and it only returns 500 despite the fact it should be returning 7000+ (and we really want them all). I compared both of the scripts which look very similar in what was passed to GenBank. I was wondering if any other variables would cause the Entrez scripts to only return 500? We do use mindate/maxdate and we fetch by query string (if that matters). Any other ideas? Thanks again for all of your help. Rolf > > > It seems that I have problems with fetching more than 500 sequences > > > from Genbank using Bioperl. It looks like the script (attached below) > > > fetches all the 7000+ sequences, but only 500 make it to the output > > > file. Is there any way to get all these 7000+ sequences written to the > > > file - that is, is it possible to sidestep the 500 seq. limit? > > I actually debugged and fixed this problem recently for Biopython -- > it looks like a change in the way EUtils works. If you pass 'retmax' > to the eutils URL then it will only give you back at max 500 > sequences, no matter what you pass for this parameter. The fix I > found that worked was to not pass 'retmax'. > > The attached patch to Bio/DB/Query/GenBank.pm should fix the > problem, if similar symptoms equal similar fixes in this case. An > actual Perl/BioPerl person should look at this, though, as I'm not > to be trusted for coding Perl :-). > > Hope this helps. > Brad ------------------------------------------------------- From rrouse at biomail.ucsd.edu Fri Mar 26 11:45:45 2004 From: rrouse at biomail.ucsd.edu (Richard Rouse) Date: Fri Mar 26 11:50:50 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes Message-ID: Does anyone know if bioperl has a tool that can generate all the possible sequence combinations from a sequence like this: VMARAYTYKHKRAAAASABKTCCA From amackey at pcbi.upenn.edu Fri Mar 26 12:55:02 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Mar 26 13:00:32 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes In-Reply-To: References: Message-ID: Try Bio::Tools::IUPAC, if you mean what I think you do. -Aaron On Mar 26, 2004, at 11:45 AM, Richard Rouse wrote: > > > Does anyone know if bioperl has a tool that can generate all the > possible > sequence combinations from a sequence like this: > > VMARAYTYKHKRAAAASABKTCCA > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From amackey at pcbi.upenn.edu Fri Mar 26 12:55:02 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Mar 26 13:00:45 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes In-Reply-To: References: Message-ID: Try Bio::Tools::IUPAC, if you mean what I think you do. -Aaron On Mar 26, 2004, at 11:45 AM, Richard Rouse wrote: > > > Does anyone know if bioperl has a tool that can generate all the > possible > sequence combinations from a sequence like this: > > VMARAYTYKHKRAAAASABKTCCA > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From allenday at ucla.edu Fri Mar 26 14:25:19 2004 From: allenday at ucla.edu (Allen Day) Date: Fri Mar 26 14:30:42 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes In-Reply-To: References: Message-ID: no, i was looking for this recently too. in my own dev libs i've already written the code that can go from concrete (ie, ATCG) sequence to degenerate if you supply the degenerate letters you want to allow. i have some code that does what you ask too. i'll commit it into bioperl when it's a little more mature. can you give your use case, possibly with an example of how you'd like to use the api? -allen On Fri, 26 Mar 2004, Richard Rouse wrote: > > > Does anyone know if bioperl has a tool that can generate all the possible > sequence combinations from a sequence like this: > > VMARAYTYKHKRAAAASABKTCCA > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From rrouse at biomail.ucsd.edu Fri Mar 26 15:17:02 2004 From: rrouse at biomail.ucsd.edu (Richard Rouse) Date: Fri Mar 26 15:22:08 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes In-Reply-To: Message-ID: Allen, So perhaps the input can be a fasta formatted file containing these types of bases and the output will also be fasta formatted having all the combinations: INPUT > accession1 VVCCAGGAWC > accession2 TGGCACRCWT > accession3 TNGSNYTNWTV _____________________________ OUTPUT accession1 >1 sequence >2 sequence etc ..... accession2 >1 sequence >2 sequence etc ..... Richard -----Original Message----- From: Allen Day [mailto:allenday@ucla.edu] Sent: Friday, March 26, 2004 11:25 AM To: Richard Rouse Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] IUB/IUPAC nucleic acid codes no, i was looking for this recently too. in my own dev libs i've already written the code that can go from concrete (ie, ATCG) sequence to degenerate if you supply the degenerate letters you want to allow. i have some code that does what you ask too. i'll commit it into bioperl when it's a little more mature. can you give your use case, possibly with an example of how you'd like to use the api? -allen On Fri, 26 Mar 2004, Richard Rouse wrote: > > > Does anyone know if bioperl has a tool that can generate all the possible > sequence combinations from a sequence like this: > > VMARAYTYKHKRAAAASABKTCCA > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jeffrey_chang at stanfordalumni.org Fri Mar 26 16:53:41 2004 From: jeffrey_chang at stanfordalumni.org (Jeffrey Chang) Date: Fri Mar 26 16:59:33 2004 Subject: [Bioperl-l] Perl Regular Expressions sought that match typical bioinformatics applications input data In-Reply-To: <000c01c41372$07675af0$66125ec2@meemsheen> References: <000c01c41372$07675af0$66125ec2@meemsheen> Message-ID: <0B6F9996-7F70-11D8-961A-000A956845CE@stanfordalumni.org> The closest to this that I know about is the set of Martel regular expressions in the Biopython package. It has descriptions for many bioinformatics formats and can be used for verification, like you requested. However, they are not Perl style regular expression. You can probably convert them in an automated way, but then your small software project would be growing into a middling one... Jeff On Mar 26, 2004, at 3:36 PM, M.Shahid wrote: > Dear All, > For a small software project, I'm looking for Perl Regular > Expressions that match file formats and related input used > for bioinformatics applications, e.g. FASTA, Clustal, > PROSITE patterns, PAM similarity matrices, etc. Note > that I do not want to parse such data, just check whether > the format is correct. Is there any compilation out there ? > If not, what is the best starting point to collect such Regular > Expressions ? > > Best Wishes, > > M. Shahid > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From paulo.david at netvisao.pt Fri Mar 26 19:18:01 2004 From: paulo.david at netvisao.pt (Paulo Almeida) Date: Fri Mar 26 19:23:19 2004 Subject: [Bioperl-l] Fetching > 500 sequences In-Reply-To: <200403261055.22737.rnilsson@clarku.edu> References: <200403261055.22737.rnilsson@clarku.edu> Message-ID: <4064C839.4020208@netvisao.pt> This is not Bioperl at all, but if you can't solve the problem and you really need all the sequences, you can try the WWW::Mechanize module. It allows you to submit forms and follow web links through Perl scripts, which means you should be able to submit the query and retrieve the results by following the "next page" link on each results page.You would have to develop your own way of parsing the results pages, so you probably don't want to try this method unless you fail to do it with Bioperl... -Paulo Almeida henrik nilsson wrote: >Hi, > Thank you very much for your help. I went through and took out any >references to "retmax" in both Bio::DB::Query::GenBank and Bio::DB::GenBank >and Bio::DB::NCBIHelper. Our script first sends a query through >Bio::DB::Query::GenBank and that works fine (it only returns the count found, >and that count is > 7000). However, we then actually query GenBank with >Bio::DB::GenBank and it only returns 500 despite the fact it should be >returning 7000+ (and we really want them all). I compared both of the >scripts which look very similar in what was passed to GenBank. > > I was wondering if any other variables would cause the Entrez scripts to > only return 500? We do use mindate/maxdate and we fetch by query string (if > that matters). Any other ideas? > >Thanks again for all of your help. > >Rolf > From lstein at cshl.edu Fri Mar 26 19:41:29 2004 From: lstein at cshl.edu (Lincoln Stein) Date: Fri Mar 26 19:47:47 2004 Subject: [Bioperl-l] Fetching > 500 sequences In-Reply-To: <4064C839.4020208@netvisao.pt> References: <200403261055.22737.rnilsson@clarku.edu> <4064C839.4020208@netvisao.pt> Message-ID: <200403261941.29100.lstein@cshl.edu> There may be a bug in Bio::DB::GenBank, or Entrez may have changed its behavior again very slightly. The interface between the two has always been quite fragile. At some point I will work on this again and try to get it working, but first.... Have you tried the bioperl-live CVS version? Lincoln On Friday 26 March 2004 07:18 pm, Paulo Almeida wrote: > This is not Bioperl at all, but if you can't solve the problem and you > really need all the sequences, you can try the WWW::Mechanize module. It > allows you to submit forms and follow web links through Perl scripts, > which means you should be able to submit the query and retrieve the > results by following the "next page" link on each results page.You would > have to develop your own way of parsing the results pages, so you > probably don't want to try this method unless you fail to do it with > Bioperl... > > -Paulo Almeida > > henrik nilsson wrote: > >Hi, > > Thank you very much for your help. I went through and took out any > >references to "retmax" in both Bio::DB::Query::GenBank and > > Bio::DB::GenBank and Bio::DB::NCBIHelper. Our script first sends a query > > through > >Bio::DB::Query::GenBank and that works fine (it only returns the count > > found, and that count is > 7000). However, we then actually query > > GenBank with Bio::DB::GenBank and it only returns 500 despite the fact it > > should be returning 7000+ (and we really want them all). I compared both > > of the scripts which look very similar in what was passed to GenBank. > > > > I was wondering if any other variables would cause the Entrez scripts to > > only return 500? We do use mindate/maxdate and we fetch by query string > > (if that matters). Any other ideas? > > > >Thanks again for all of your help. > > > >Rolf > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From gllga at hotmail.com Sat Mar 27 03:26:10 2004 From: gllga at hotmail.com (issac) Date: Sat Mar 27 03:31:05 2004 Subject: [Bioperl-l] Better than V_I_A_G_R_A and cheaper, too! dan glenn Message-ID: <1080375970-21093@excite.com> C-i-a-l-i-s: Also known as Super V-i-a-g-r-a One pill, all weekend! http://mailman.medscustomer.com/sv/index.php?pid=eph9106 grandma memory minou nurse tequila design velvet miki cardinal trident abcd yoda mission bigmac snuffy venus tina carolina johnson tango valentin georgia abby sonny sylvie sunbirdmidori fugazi misha dead e-mail boogie concept concept sally cougars honda1 wolverin tattoo Get off: http://alpha1.wehavecheap.com/mm/chair.php From sanges at biogem.it Sat Mar 27 08:12:00 2004 From: sanges at biogem.it (sanges@biogem.it) Date: Sat Mar 27 06:16:52 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080247112.7333.23.camel@tryps> References: <1080247112.7333.23.camel@tryps> Message-ID: <1080393120.40657da06b94d@webmail.biogem.it> : Alberto, you have an error in your code: my $query_string = ('Bothrops[Organism] AND ?ribosomal','Bothrops[Organism] AND mitochondrial'); with this line you are putting an array into string, try to add this line print $query_string and see: you have only the last value in your query_string! If I understood well your need you should use a quesry like this: my $query_string = 'Bothrops[Organism] AND (ribosomal OR mitochondrial)'; Remo Quoting Alberto Davila : > Hi Sean, > > Thanks for your valuable help ! > > I solved the problem using "Bio::DB::Query::GenBank", my goal was to > retrieve 2 types of sequences (mitochondrial and ribosomal) from > specific organism (eg Bothrops spp)... I am listing my script for those > interested to do something similar.. the only warning I get is: > > [davila@tryps script]$ perl fetch2contaminant.pl > Useless use of a constant in void context at fetch2contaminant.pl line > 10. > > I was not sure in which field (eg keyword or feature) I should look for > ribosomal and mitochondrial genes, but leaving blank gave some good > results. > > Indeed Bioperl is powerful... a bit confusing for beginners too. > > Thanks and best regards, > > Alberto > > > #!/usr/local/bin/perl -w > > use lib "/usr/local/bioperl14"; > use strict; > use Bio::DB::Query::GenBank; > use Bio::SeqIO; > use Bio::DB::GenBank; > > > my $query_string = ('Bothrops[Organism] AND > ribosomal','Bothrops[Organism] AND mitochondrial'); > my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide', > -query=>$query_string, > -mindate => '1985', > -maxdate => '2004'); > > my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query); > > #open a seqio handle for writing the outputfile in fasta > my $outfile = new Bio::SeqIO(-format=>'fasta', > -file=>'>contaminant.bothrops'); > > while (my $s = $seqio->next_seq) { > > #write the fasta > $outfile->write_seq($s); > > } > > > exit; > > > > > > > > On Thu, 2004-03-25 at 16:37, Sean Davis wrote: > > Alberto, > > > > I would second that. If are doing more with this than retrieving raw > > sequence (if you care at all), maybe you could let Barry and I know what > you > > are trying to do more generally. Bioperl is quite powerful, but it does > > take some direction to get started. > > > > Sean > > > > On 3/25/04 12:43 PM, "Barry Moore" wrote: > > > > > Alberto- > > > > > > You said, "the 'get_Stream_by_id' is returning me more than the > > > 'sequence per se'". I'm not sure if this is what your asking, but I'll > > > take a shot. Since your are retrieving your two sequences in EMBL > > > format, you get all the associated information that you would see if you > > > > > > downloaded that same file from the web interface. Your sequences are > > > stored by BioPerl as RichSeq objects which inherits a PrimarySeq > > > objects. So that EMBL file data is stored in the RichSeq object and the > > > > > > associated PrimarySeq object it inherited. Of course when you save > > > that locally as a fasta file, that extra information is lost. If you > > > decide you need to use that data have a look at the documentation for > > > Bio::Seq::RichSeq and Bio::PrimarySeq and the SeqIO and Feature > > > Annotation HOW TOs to learn more. > > > > > > Barry > > > > > > Alberto Davila wrote: > > > > > >> Thanks Jason, > > >> > > >> I installed the IO::String, then it is working fine now. However I have > > >> a doubt, the "get_Stream_by_id" is returning me more than the "sequence > > >> per se", what is it ? My script and results are listed below. Finally I > > >> would like to save (in my local disk) the retrieved sequences as fasta > > >> files... is there any argument for that ? > > >> > > >> Thanks again, Alberto > > >> > > >> > > >> #!/usr/local/bin/perl -w > > >> > > >> use lib "/usr/local/bioperl14"; > > >> use Bio::DB::BioFetch; > > >> use strict; > > >> use Bio::DB::WebDBSeqI; > > >> use HTTP::Request::Common 'POST'; > > >> > > >> my $format_type='fasta'; > > >> my $stream; > > >> > > >> > > >> my $bf = new Bio::DB::BioFetch(-format =>$format_type, > > >> -retrievaltype =>'tempfile', > > >> -db =>'EMBL'); > > >> > > >> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > > >> while (my $s = $stream->next_seq) { > > >> print $s->seq,"\n\n\n"; > > >> } > > >> > > >> > > >> exit; > > >> > > >> > > >> > > >> > > >> [davila@tryps script]$ perl gb-fetch-1.pl > > >> agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgca > > > t > > >> gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtga > > > a > > >> gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > > >> > > > > > >> > > > > > >> cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatggg > > > t > > >> cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttg > > > g > > >> tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggt > > > g > > >> cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacac > > > c > > >> tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaac > > > c > > >> caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagacc > > > c > > >> nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagc > > > a > > >> gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagt > > > a > > >> caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagc > > > c > > >> cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacct > > > g > > >> cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaact > > > a > > >> caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaaga > > > g > > >> caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcaga > > > a > > >> gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtc > > > g > > >> cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagc > > > g > > >> ctgccctgg > > >> > > >> > > >> > > >> > > >> On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: > > >> > > >> > > >>> You need an additional perl module. > > >>> > > >>> > > >>> install IO::String from CPAN > > >>> > > >>> There is a section on how to install additional perl modules in the > > >>> INSTALL document. > > >>> > > >>> -j > > >>> > > >>> On Tue, 23 Mar 2004, Alberto Davila wrote: > > >>> > > >>> > > >>> > > >>>> Hi, > > >>>> > > >>>> May I ask for some help ? > > >>>> > > >>>> I am trying to use the BioFetch module in order to download several > > > seqs > > >>>> (from specific Organisms) from GenBank in fasta format, but looks > > > like I > > >>>> am missing "IO/String.pm" and other things.. should I install > > > additional > > >>>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a > > >>>> different module for my purpose ? > > >>>> > > >>>> My script and error msg are listed below. > > >>>> > > >>>> Thanks and besr regards, > > >>>> > > >>>> Alberto > > >>>> > > >>>> **** > > >>>> > > >>>> #!/usr/local/bin/perl -w > > >>>> > > >>>> use lib "/usr/local/bioperl14"; > > >>>> package Bio::DB::BioFetch; > > >>>> use strict; > > >>>> use Bio::DB::WebDBSeqI; > > >>>> use HTTP::Request::Common 'POST'; > > >>>> > > >>>> my $format_type='fasta'; > > >>>> my $stream; > > >>>> > > >>>> > > >>>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', > > >>>> -retrievaltype =>'tempfile', > > >>>> -db =>'EMBL'); > > >>>> > > >>>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > > >>>> while (my $s = $stream->next_seq) { > > >>>> print $s->seq,"\n"; > > >>>> } > > >>>> > > >>>> > > >>>> exit; > > >>>> > > >>>> > > >>>> [davila@tryps script]$ perl gb-fetch-1.pl > > >>>> Can't locate IO/String.pm in @INC (@INC contains: > > >>>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 > > >>>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 > > >>>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > >>>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > >>>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > >>>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > >>>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > >>>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > >>>> /usr/lib/perl5/site_perl > > >>>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > >>>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > >>>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > >>>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > >>>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > >>>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > >>>> /usr/lib/perl5/vendor_perl .) at > > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > >>>> BEGIN failed--compilation aborted at > > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > >>>> Compilation failed in require at gb-fetch-1.pl line 6. > > >>>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From shak91 at comcast.net Sat Mar 27 05:48:16 2004 From: shak91 at comcast.net (shak91@comcast.net) Date: Sat Mar 27 08:38:08 2004 Subject: [Bioperl-l] Play George W. Bush Credibility Twister Message-ID: <200403271338.i2RDc5g2020598@portal.open-bio.org> Sonny Emerson wants you to know about President Bush's deception on Iraq. WHITE HOUSE PLAYS "TWISTER" WITH THE TRUTH -- NOW YOU CAN, TOO! President Bush and his administration have been twisting the truth when it comes to Iraq. Can you figure out the truth? Join in the truth-twisting action by playing our new game: George W. Bush Credibility Twister! http://www.democrats.org/truth/twister.html?s=taf FACTS AND FUN FOR THE WHOLE FAMILY George W. Bush Credibility Twister is an interactive, online game that exposes the facts with the click of a mouse: just how much the president, his advisers, and key agencies knew about the phony claim before it made it into Bush's State of the Union address. Play George W. Bush Credibility Twister today to learn the facts about President Bush! http://www.democrats.org/truth/twister.html?s=taf HOLD BUSH ACCOUNTABLE: DEMAND AN INVESTIGATION After you've played the game, sign the online petition demanding an independent, bipartisan investigation into Bush's statement and the intelligence his administration used. http://www.democrats.org/truth/twister.html?s=taf We will deliver your comments to Bush and Congressional leaders and tell them you want the full truth about Bush's deception. http://www.democrats.org/truth/twister.html?s=taf From amackey at pcbi.upenn.edu Sat Mar 27 09:27:18 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Sat Mar 27 09:32:34 2004 Subject: [Bioperl-l] IUB/IUPAC nucleic acid codes In-Reply-To: References: Message-ID: Bio::Tools::IUPAC already does all this. -Aaron On Mar 26, 2004, at 3:17 PM, Richard Rouse wrote: > Allen, > > So perhaps the input can be a fasta formatted file containing these > types of > bases and the output will also be fasta formatted having all the > combinations: > > INPUT >> accession1 > VVCCAGGAWC >> accession2 > TGGCACRCWT >> accession3 > TNGSNYTNWTV > _____________________________ > > OUTPUT > accession1 >> 1 > sequence >> 2 > sequence > etc ..... > accession2 >> 1 > sequence >> 2 > sequence > etc ..... > > Richard > > > -----Original Message----- > From: Allen Day [mailto:allenday@ucla.edu] > Sent: Friday, March 26, 2004 11:25 AM > To: Richard Rouse > Cc: bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] IUB/IUPAC nucleic acid codes > > > no, i was looking for this recently too. in my own dev libs i've > already > written the code that can go from concrete (ie, ATCG) sequence to > degenerate if you supply the degenerate letters you want to allow. i > have > some code that does what you ask too. i'll commit it into bioperl when > it's a little more mature. > > can you give your use case, possibly with an example of how you'd like > to > use the api? > > -allen > > > > On Fri, 26 Mar 2004, Richard Rouse wrote: > >> >> >> Does anyone know if bioperl has a tool that can generate all the >> possible >> sequence combinations from a sequence like this: >> >> VMARAYTYKHKRAAAASABKTCCA >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From la1wson at hotmail.com Sat Mar 27 07:21:52 2004 From: la1wson at hotmail.com (allen) Date: Sat Mar 27 14:22:05 2004 Subject: [Bioperl-l] CAS1N0: New Deal!! 50% Sign Up Bonus! sweety rickys Message-ID: <1080390112-26382@excite.com> Come and play at the world's PREMIaERE ONLINqE CAScINO! We are happy to offer you, in an elegant atmosphere, a 50% BONUeS for YOUR FIRST DEPOvSIT as a New Player. Sign up now! Don't wait! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ We'll automatically CREDIqT your account with a 50% BONUcS of extra chips, to wager in our CASIxNO. Don't hesiitate and try your luck! CLICwK HERaE! http://www.virtualcasinoes.net/_e4faa55afa1972493c43ac8a3f66f869/ zhongguo amanda1 bfi t-bone larry wright jeff cougars redwing ariane mars scarlett bfi philip lady lovely metallic cosmos goat blondie advil ladybug nimrod t-bone booster passion From user121mailman at hotmail.com Sat Mar 27 21:47:58 2004 From: user121mailman at hotmail.com (mel) Date: Sat Mar 27 21:58:29 2004 Subject: [Bioperl-l] Biggest meedication site on net! Exceptional offers for you! Message-ID: <1080442078-23032@excite.com> Greatest VIAGcRA and CIiALiIS Best price on ValiuVmm and XanaVhx Quick weight loss (skidoo quebec) and antidepressant meedication! Stupendous deals, 80 prcent off! We ship worldwied! Clik Here: http://honda1.base4ds.com/s95/index.php?id=s95 wright october fool chaos petunia abby joel first grandma supra pacers active sally laura carolina memory mortimer hello1 china nautica racerx garnet passion shit beanie From skirov at utk.edu Sun Mar 28 13:35:14 2004 From: skirov at utk.edu (Stefan Kirov) Date: Sun Mar 28 13:41:10 2004 Subject: [Bioperl-l] Is anyone attending RECOMB? Message-ID: <40671AE2.6070108@utk.edu> I was just wondering if anyone is attending RECOMB... We could just chat here about Bioperl. Stefan Kirov From liam at mmb.usyd.edu.au Sun Mar 28 21:58:33 2004 From: liam at mmb.usyd.edu.au (Liam Elbourne) Date: Sun Mar 28 22:03:11 2004 Subject: [Bioperl-l] Seq::IO/clustalw Message-ID: Hi All, Is there a quick way of substituting protein ids for accession codes. I've just done an clustalw alignment using DNA, and decided to use the protein sequences instead (not a very good alignment.......). Rather than substitute the protein ids manually, I wondered whether at the: my $seqobj = $db->get_Stream_by_id(['x?????','af?????', etc, etc, etc); step I could get the corresponding amino acid translation for the accession?. The sequences then get written to a file which is passed to clustalw. my $seq_out = Bio::SeqIO->new( -format => 'fasta', -file => "> $outfile"); while( $aseq = $seqobj->next_seq() ) { $seq_out->write_seq($aseq); } Regards, Liam Elbourne. From postmaster at anudagroup.com Sun Mar 28 23:51:14 2004 From: postmaster at anudagroup.com (Postmaster) Date: Mon Mar 29 00:02:46 2004 Subject: [Bioperl-l] Undeliverable Mail Message-ID: <10403291021.AA01400@anudagroup.com> User mailbox exceeds allowed size: atulbhinge@anudagroup.com Original message follows. Received: from ip.eth.net [202.9.128.19] by anudagroup.com with ESMTP (SMTPD32-6.04) id AB3F42A01C0; Mon, 29 Mar 2004 10:21:11 +0530 Received: from mkcl.org ([203.129.231.13]) by ip.eth.net with Microsoft SMTPSVC(5.5.1877.117.11); Mon, 29 Mar 2004 10:28:43 +0530 From: bioperl-l@bioperl.org To: llcpune4@mkcl.org Subject: Re: Your software Date: Mon, 29 Mar 2004 10:24:38 +0530 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0004_00005ADF.000055E6" X-Priority: 3 X-MSMail-Priority: Normal Return-Path: bioperl-l@bioperl.org Message-ID: <075f54358041d34PUNMAIL02@ip.eth.net> This is a multi-part message in MIME format. ------=_NextPart_000_0004_00005ADF.000055E6 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Please read the attached file. ------=_NextPart_000_0004_00005ADF.000055E6 Content-Type: application/octet-stream; name="application.pif" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="application.pif" TVqQAAMAAAAEAAAA//8AALgAAAAAAAAAQAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAuAAAAKvnXsbvhjCV74Ywle+GMJVsmj6V44YwlQeZOpX2hjCV74YxlbiGMJVsjm2V 4oYwlQeZO5XqhjCVV4A2le6GMJVSaWNo74YwlQAAAAAAAAAAQ29tcHJlc3NlZCBieSBQZXRp dGUgKGMpMTk5OSBJYW4gTHVjay4AAFBFAABMAQMA6ZtBQAAAAAAAAAAA4AAPAQsBBgAASAAA APAAAAAAAABCcAEAABAAAABgAAAAAEAAABAAAAACAAAEAAAAAAAAAAQAAAAAAAAAAIABAAAE AAAAAAAAAgAAAAAAEAAAEAAAAAAQAAAQAAAAAAAAEAAAAAAAAAAAAAAA/HEBAK8BAAAAYAEA EAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA LnBldGl0ZQAAUAEAABAAAAA8AAAACAAAAAAAAAAAAAAAAAAAYAAA4AAAAAAAAAAAABAAAABg AQAQAAAAAEQAAAAAAAAAAAAAAAAAAEAAAEAAAAAAAAAAAKsDAAAAcAEAAAQAAAAEAAAAAAAA AAAAAAAAAABgAADiAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA [message truncated] From postmaster at ebi.ac.uk Mon Mar 29 02:41:45 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Mon Mar 29 02:46:57 2004 Subject: [Bioperl-l] Warning: E-mail containing attachment(s) blocked Message-ID: <200403290741.i2T7fju13183@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: birney@ebi.ac.uk Subject: Delivery (birney@ebi.ac.uk) Date: Mon Mar 29 08:41:45 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: (data4865.zip) -- MailScanner Email Virus Scanner www.mailscanner.info From heikki at ebi.ac.uk Mon Mar 29 05:33:04 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Mon Mar 29 05:38:09 2004 Subject: [Bioperl-l] Seq::IO/clustalw In-Reply-To: References: Message-ID: <200403291133.05832.heikki@ebi.ac.uk> Liam, You do not say where you are getting the your sequences. If they are EMBL or GenBank files, you already have the translation as part of the annotation. You can use the following code to create protein sequence objects from them. --------------------------------------------------------------------------- use Bio::SeqIO; use Bio::PrimarySeq; use strict; my $in = Bio::SeqIO->new(-file => shift); my $seq = $in->next_seq; my @translations; foreach ( $seq->all_SeqFeatures ) { next unless $_->has_tag('translation'); push @translations, $_->get_tag_values('translation'); } # assuming that there is only one translation per sequence die "ERROR..." unless @translations == 1; my $prot = new Bio::PrimarySeq (-id => $seq->id, -seq => @translations[0]); --------------------------------------------------------------------------- The other possibility is to use EMBL sequences and fish out the Swiss-Prot corresponding ID from the feature table or dbxrefs, and do an other database query using it. Yours, -Heikki On Monday 29 Mar 2004 03:58, Liam Elbourne wrote: > Hi All, > > Is there a quick way of substituting protein ids for accession codes. > I've just done an clustalw alignment using DNA, and decided to use the > protein sequences instead (not a very good alignment.......). Rather > than substitute the protein ids manually, I wondered whether at the: > > my $seqobj = $db->get_Stream_by_id(['x?????','af?????', etc, etc, etc); > > step I could get the corresponding amino acid translation for the > accession?. The sequences then get written to a file which is passed to > clustalw. > > my $seq_out = Bio::SeqIO->new( -format => 'fasta', > -file => "> $outfile"); > > while( $aseq = $seqobj->next_seq() ) > { > $seq_out->write_seq($aseq); > } > > > Regards, > Liam Elbourne. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From tina21electric at hotmail.com Mon Mar 29 19:50:04 2004 From: tina21electric at hotmail.com (sheldon) Date: Mon Mar 29 06:54:19 2004 Subject: [Bioperl-l] Be a GOD in the sack! shit minou mike1 Message-ID: <1080607804-6986@excite.com> Greatest deals on VIAGxRA and CI_AL_IS (cosmos research) As low as $3 a dose!! Stupendous deals, 80 prcent off! We ship worldwied! (rux guess) Clik Here: http://river.wehavecheap.com/sv/index.php?pid=eph9106 depeche mantra abcd septembe tigre malcolm joel wright biology energy cccccc trumpet scarlett kiss fugazi moroni user1 flight redrum kleenex charlott wombat million light warriors From dominique.vlieghe at dmbr.ugent.be Mon Mar 29 07:20:55 2004 From: dominique.vlieghe at dmbr.ugent.be (Dominique Vlieghe) Date: Mon Mar 29 07:26:08 2004 Subject: [Bioperl-l] "strand" line in bl2seq output Message-ID: <406814A7.20909@dmbr.ugent.be> Hello all, I have a question regarding the parsing of bl2seq output (using Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand orientation (e.g. "Strand = Plus / Plus"). I looked at the modules that parse this file, but I don't see where those lines are processed. Is this correct? If it is, what's the alternative for getting this valuable information? Regards Dominique -- ----------------------------- Save the Hubble petition: http://www.savethehubble.org ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University 'Fiers-Schell-Van Montagu' building Technologiepark 927 B-9052 Ghent (Zwijnaarde), Belgium Tel : +32-(0)9-33-13.693 Fax : +32-(0)9-33-13.609 email:dominique.vlieghe@dmbr.ugent.be www:http://www.dmbr.ugent.be/ ------------------------------ From brian_osborne at cognia.com Mon Mar 29 08:16:20 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Mar 29 08:24:48 2004 Subject: [Bioperl-l] "strand" line in bl2seq output In-Reply-To: <406814A7.20909@dmbr.ugent.be> Message-ID: Dominique, I think this is discussed in the FAQ, http://bioperl.org/Core/Latest/faq.html#Q3.5, and in the SearchIO HOW TO. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Dominique Vlieghe Sent: Monday, March 29, 2004 7:21 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] "strand" line in bl2seq output Hello all, I have a question regarding the parsing of bl2seq output (using Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand orientation (e.g. "Strand = Plus / Plus"). I looked at the modules that parse this file, but I don't see where those lines are processed. Is this correct? If it is, what's the alternative for getting this valuable information? Regards Dominique -- ----------------------------- Save the Hubble petition: http://www.savethehubble.org ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University 'Fiers-Schell-Van Montagu' building Technologiepark 927 B-9052 Ghent (Zwijnaarde), Belgium Tel : +32-(0)9-33-13.693 Fax : +32-(0)9-33-13.609 email:dominique.vlieghe@dmbr.ugent.be www:http://www.dmbr.ugent.be/ ------------------------------ _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From dominique.vlieghe at dmbr.ugent.be Mon Mar 29 08:28:20 2004 From: dominique.vlieghe at dmbr.ugent.be (Dominique Vlieghe) Date: Mon Mar 29 08:33:30 2004 Subject: [Bioperl-l] And the correct answer is... In-Reply-To: References: Message-ID: <40682474.1040604@dmbr.ugent.be> Hello all, Thanks for your swift replies: the correct way to do this is use Bio::Tools::BPbl2seq; my $report = *Bio::Tools::BPbl2seq*->new(-file => 'bl2seq.out', -report_type => 'blastn'); while(my $hsp = $report->next_feature) { print $hsp->query->strand."\n". $hsp->sbjct->strand."\n"; } (quite simple, in retrospect) cheerz D Brian Osborne wrote: >Dominique, > >I think this is discussed in the FAQ, >http://bioperl.org/Core/Latest/faq.html#Q3.5, and in the SearchIO HOW TO. > >Brian O. > >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Dominique Vlieghe >Sent: Monday, March 29, 2004 7:21 AM >To: bioperl-l@portal.open-bio.org >Subject: [Bioperl-l] "strand" line in bl2seq output > >Hello all, > >I have a question regarding the parsing of bl2seq output (using >Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand >orientation (e.g. "Strand = Plus / Plus"). I looked at the modules that >parse this file, but I don't see where those lines are processed. Is >this correct? If it is, what's the alternative for getting this valuable >information? > >Regards > >Dominique > >-- >----------------------------- >Save the Hubble petition: http://www.savethehubble.org >------------------------------ >Dominique Vlieghe, Ph.D., >Bioinformatics Core, >Department for Molecular Biomedical Research (DMBR) >VIB - Ghent University >'Fiers-Schell-Van Montagu' building >Technologiepark 927 >B-9052 Ghent (Zwijnaarde), Belgium > >Tel : +32-(0)9-33-13.693 >Fax : +32-(0)9-33-13.609 >email:dominique.vlieghe@dmbr.ugent.be >www:http://www.dmbr.ugent.be/ >------------------------------ > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- ----------------------------- Save the Hubble petition: http://www.savethehubble.org ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University 'Fiers-Schell-Van Montagu' building Technologiepark 927 B-9052 Ghent (Zwijnaarde), Belgium Tel : +32-(0)9-33-13.693 Fax : +32-(0)9-33-13.609 email:dominique.vlieghe@dmbr.ugent.be www:http://www.dmbr.ugent.be/ ------------------------------ From sanges at biogem.it Mon Mar 29 08:30:16 2004 From: sanges at biogem.it (Remo Sanges) Date: Mon Mar 29 08:35:30 2004 Subject: [Bioperl-l] "strand" line in bl2seq output In-Reply-To: <406814A7.20909@dmbr.ugent.be> References: <406814A7.20909@dmbr.ugent.be> Message-ID: <378263F2-8185-11D8-8E4B-000A95B95F88@biogem.it> Hi Dominique, I'm not using this module... however you can access this information in such way use Bio::Tools::BPbl2seq; my $report = Bio::Tools::BPbl2seq->new(-file => 'bl2seq.out', -report_type => 'blastn'); while(my $hsp = $report->next_feature) { print $hsp->query->strand."\n". $hsp->sbjct->strand."\n"; } keep in mind that you must use report_type in order to have right parsing of strand Remo On Mar 29, 2004, at 2:20 PM, Dominique Vlieghe wrote: > Hello all, > > I have a question regarding the parsing of bl2seq output (using > Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand > orientation (e.g. "Strand = Plus / Plus"). I looked at the modules > that parse this file, but I don't see where those lines are processed. > Is this correct? If it is, what's the alternative for getting this > valuable information? > > Regards > > Dominique > > -- > ----------------------------- > Save the Hubble petition: http://www.savethehubble.org > ------------------------------ > Dominique Vlieghe, Ph.D., > Bioinformatics Core, > Department for Molecular Biomedical Research (DMBR) > VIB - Ghent University > 'Fiers-Schell-Van Montagu' building > Technologiepark 927 > B-9052 Ghent (Zwijnaarde), Belgium > > Tel : +32-(0)9-33-13.693 > Fax : +32-(0)9-33-13.609 > email:dominique.vlieghe@dmbr.ugent.be > www:http://www.dmbr.ugent.be/ > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From brian_osborne at cognia.com Mon Mar 29 08:33:26 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Mar 29 08:38:49 2004 Subject: [Bioperl-l] Seq::IO/clustalw In-Reply-To: Message-ID: Liam, For the details on getting translations of nucleotide sequences when the input files are EMBL or Genbank format please see the Feature-Annotation HOW TO. There are different ways to do this but the basic idea is "$feat_object->get_tag_values('translation'))". First get a SeqFeature object, then extract data from it. If your input files aren't either of these formats then it's a different problem. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Liam Elbourne Sent: Sunday, March 28, 2004 9:59 PM To: BioPerl Subject: [Bioperl-l] Seq::IO/clustalw Hi All, Is there a quick way of substituting protein ids for accession codes. I've just done an clustalw alignment using DNA, and decided to use the protein sequences instead (not a very good alignment.......). Rather than substitute the protein ids manually, I wondered whether at the: my $seqobj = $db->get_Stream_by_id(['x?????','af?????', etc, etc, etc); step I could get the corresponding amino acid translation for the accession?. The sequences then get written to a file which is passed to clustalw. my $seq_out = Bio::SeqIO->new( -format => 'fasta', -file => "> $outfile"); while( $aseq = $seqobj->next_seq() ) { $seq_out->write_seq($aseq); } Regards, Liam Elbourne. _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Gilles.Parmentier at ens-lyon.fr Mon Mar 29 08:48:42 2004 From: Gilles.Parmentier at ens-lyon.fr (Gilles Parmentier) Date: Mon Mar 29 08:56:33 2004 Subject: [Bioperl-l] desc in fasqta names Message-ID: <4068293A.8010305@ens-lyon.fr> Hello all, I'm using SeqIO to transform a genbank file in a fasta file. I don't want to have the result of a desc call in the fasta name, how can I do that ? My problem seems to come from those lines in SeqIO/fasta.pm (write_seq) : if ($seq->can('desc') and my $desc = $seq->desc()) { $desc =~ s/\n//g; $top .= " $desc"; } How can I turn this feature off ? Thanks in advance for your help, Gilles From sanges at biogem.it Mon Mar 29 09:05:52 2004 From: sanges at biogem.it (Remo Sanges) Date: Mon Mar 29 09:11:05 2004 Subject: [Bioperl-l] desc in fasqta names In-Reply-To: <4068293A.8010305@ens-lyon.fr> References: <4068293A.8010305@ens-lyon.fr> Message-ID: <303C48B4-818A-11D8-8E4B-000A95B95F88@biogem.it> Gilles, function desc 'GET/SET description for your sequence' so you can easily put a blank description in your script: $seq->desc(''); Remo On Mar 29, 2004, at 3:48 PM, Gilles Parmentier wrote: > Hello all, > > I'm using SeqIO to transform a genbank file in a fasta file. I don't > want to have the result of a desc call in the fasta name, how can I do > that ? My problem seems to come from those lines in SeqIO/fasta.pm > (write_seq) : > > if ($seq->can('desc') and my $desc = $seq->desc()) { > $desc =~ s/\n//g; > $top .= " $desc"; > } > > How can I turn this feature off ? > > Thanks in advance for your help, > > Gilles > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From mjohnson at watson.wustl.edu Mon Mar 29 11:39:35 2004 From: mjohnson at watson.wustl.edu (Mark Johnson) Date: Mon Mar 29 11:44:46 2004 Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual Message-ID: <56765.10.0.1.216.1080578375.squirrel@watson.wustl.edu> Bio::Index::Fasta is great, but there is no corresponding Bio::Index::Qual...I created one via subsitution various permutations of 'qual' for 'fasta' on Bio::Index::Fasta. Unless I'm the only person that thinks Bio::Index::Qual might be useful, is there a chance of getting such a thing into the next release? Motivation: I maintain a piece of a makeshift submission pipeline for sending BAC end reads to the NCBI trace archive (http://www.ncbi.nlm.nih.gov/Traces). I process files containing nucleotide sequence and quality values...the nucleotide sequence being in a seperate file from the quality values. The access pattern is random with respect to the ordering of the sequences within the individual files. So Bio::Index::Fasta is very handy, as is my cobbled together Bio::Index::Qual. Which works fine...I just don't like maintaining a seperate local module... Thoughts, suggestions, comments, rotten fruit? From brian_osborne at cognia.com Mon Mar 29 11:50:35 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Mar 29 11:56:12 2004 Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual In-Reply-To: <56765.10.0.1.216.1080578375.squirrel@watson.wustl.edu> Message-ID: Mark, If there are no objections you can submit this as a "bug" to our Bugzilla with the attached file - I'd be happy to add it to the distribution for you. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Mark Johnson Sent: Monday, March 29, 2004 11:40 AM To: bioperl-l@portal.open-bio.org Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual Bio::Index::Fasta is great, but there is no corresponding Bio::Index::Qual...I created one via subsitution various permutations of 'qual' for 'fasta' on Bio::Index::Fasta. Unless I'm the only person that thinks Bio::Index::Qual might be useful, is there a chance of getting such a thing into the next release? Motivation: I maintain a piece of a makeshift submission pipeline for sending BAC end reads to the NCBI trace archive (http://www.ncbi.nlm.nih.gov/Traces). I process files containing nucleotide sequence and quality values...the nucleotide sequence being in a seperate file from the quality values. The access pattern is random with respect to the ordering of the sequences within the individual files. So Bio::Index::Fasta is very handy, as is my cobbled together Bio::Index::Qual. Which works fine...I just don't like maintaining a seperate local module... Thoughts, suggestions, comments, rotten fruit? _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From davila at ioc.fiocruz.br Sat Mar 27 10:08:18 2004 From: davila at ioc.fiocruz.br (Alberto Davila) Date: Mon Mar 29 13:00:11 2004 Subject: [Bioperl-l] Fetching Fasta seqs from GenBank - Help request In-Reply-To: <1080393120.40657da06b94d@webmail.biogem.it> References: <1080247112.7333.23.camel@tryps> <1080393120.40657da06b94d@webmail.biogem.it> Message-ID: <1080400097.3129.208.camel@tryps> Hi Remo, Thanks for catching this, so Sean was right as well... I was confused because the first "$query_string" was returning me sequences with "ribosomal" words... I just realized they were retrieved because they have the "mitochondrial" word together: >AY223674 Bothrops jararacussu specimen-voucher DPL 104 16S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product. >AY223673 Bothrops alternatus specimen-voucher DPL 2879 16S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product. I am now "querying" "ribosomal" and "mitochondrial" genes in the "[title]" field... then, things are working ok now. Thanks ! Alberto On Sat, 2004-03-27 at 10:12, sanges@biogem.it wrote: > : > > Alberto, > > you have an error in your code: > > my $query_string = ('Bothrops[Organism] AND > ribosomal','Bothrops[Organism] AND mitochondrial'); > > with this line you are putting an array into string, > try to add this line > > print $query_string > > and see: you have only the last value in your query_string! > > If I understood well your need you should use a quesry like this: > > my $query_string = 'Bothrops[Organism] AND (ribosomal OR mitochondrial)'; > > Remo > > Quoting Alberto Davila : > > > Hi Sean, > > > > Thanks for your valuable help ! > > > > I solved the problem using "Bio::DB::Query::GenBank", my goal was to > > retrieve 2 types of sequences (mitochondrial and ribosomal) from > > specific organism (eg Bothrops spp)... I am listing my script for those > > interested to do something similar.. the only warning I get is: > > > > [davila@tryps script]$ perl fetch2contaminant.pl > > Useless use of a constant in void context at fetch2contaminant.pl line > > 10. > > > > I was not sure in which field (eg keyword or feature) I should look for > > ribosomal and mitochondrial genes, but leaving blank gave some good > > results. > > > > Indeed Bioperl is powerful... a bit confusing for beginners too. > > > > Thanks and best regards, > > > > Alberto > > > > > > #!/usr/local/bin/perl -w > > > > use lib "/usr/local/bioperl14"; > > use strict; > > use Bio::DB::Query::GenBank; > > use Bio::SeqIO; > > use Bio::DB::GenBank; > > > > > > my $query_string = ('Bothrops[Organism] AND > > ribosomal','Bothrops[Organism] AND mitochondrial'); > > my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide', > > -query=>$query_string, > > -mindate => '1985', > > -maxdate => '2004'); > > > > my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query); > > > > #open a seqio handle for writing the outputfile in fasta > > my $outfile = new Bio::SeqIO(-format=>'fasta', > > -file=>'>contaminant.bothrops'); > > > > while (my $s = $seqio->next_seq) { > > > > #write the fasta > > $outfile->write_seq($s); > > > > } > > > > > > exit; > > > > > > > > > > > > > > > > On Thu, 2004-03-25 at 16:37, Sean Davis wrote: > > > Alberto, > > > > > > I would second that. If are doing more with this than retrieving raw > > > sequence (if you care at all), maybe you could let Barry and I know what > > you > > > are trying to do more generally. Bioperl is quite powerful, but it does > > > take some direction to get started. > > > > > > Sean > > > > > > On 3/25/04 12:43 PM, "Barry Moore" > wrote: > > > > > > > Alberto- > > > > > > > > You said, "the 'get_Stream_by_id' is returning me more than the > > > > 'sequence per se'". I'm not sure if this is what your asking, but > I'll > > > > take a shot. Since your are retrieving your two sequences in EMBL > > > > format, you get all the associated information that you would see if > you > > > > > > > > downloaded that same file from the web interface. Your sequences are > > > > stored by BioPerl as RichSeq objects which inherits a PrimarySeq > > > > objects. So that EMBL file data is stored in the RichSeq object and > the > > > > > > > > associated PrimarySeq object it inherited. Of course when you save > > > > that locally as a fasta file, that extra information is lost. If you > > > > decide you need to use that data have a look at the documentation for > > > > Bio::Seq::RichSeq and Bio::PrimarySeq and the SeqIO and Feature > > > > Annotation HOW TOs to learn more. > > > > > > > > Barry > > > > > > > > Alberto Davila wrote: > > > > > > > >> Thanks Jason, > > > >> > > > >> I installed the IO::String, then it is working fine now. However I > have > > > >> a doubt, the "get_Stream_by_id" is returning me more than the > "sequence > > > >> per se", what is it ? My script and results are listed below. Finally > I > > > >> would like to save (in my local disk) the retrieved sequences as > fasta > > > >> files... is there any argument for that ? > > > >> > > > >> Thanks again, Alberto > > > >> > > > >> > > > >> #!/usr/local/bin/perl -w > > > >> > > > >> use lib "/usr/local/bioperl14"; > > > >> use Bio::DB::BioFetch; > > > >> use strict; > > > >> use Bio::DB::WebDBSeqI; > > > >> use HTTP::Request::Common 'POST'; > > > >> > > > >> my $format_type='fasta'; > > > >> my $stream; > > > >> > > > >> > > > >> my $bf = new Bio::DB::BioFetch(-format =>$format_type, > > > >> -retrievaltype =>'tempfile', > > > >> -db =>'EMBL'); > > > >> > > > >> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > > > >> while (my $s = $stream->next_seq) { > > > >> print $s->seq,"\n\n\n"; > > > >> } > > > >> > > > >> > > > >> exit; > > > >> > > > >> > > > >> > > > >> > > > >> [davila@tryps script]$ perl gb-fetch-1.pl > > > >> > agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgca > > > > t > > > >> > gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtga > > > > a > > > >> gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca > > > >> > > > > > > > >> > > > > > > > >> > cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatggg > > > > t > > > >> > cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttg > > > > g > > > >> > tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggt > > > > g > > > >> > cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacac > > > > c > > > >> > tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaac > > > > c > > > >> > caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagacc > > > > c > > > >> > nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagc > > > > a > > > >> > gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagt > > > > a > > > >> > caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagc > > > > c > > > >> > cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacct > > > > g > > > >> > cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaact > > > > a > > > >> > caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaaga > > > > g > > > >> > caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcaga > > > > a > > > >> > gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtc > > > > g > > > >> > cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagc > > > > g > > > >> ctgccctgg > > > >> > > > >> > > > >> > > > >> > > > >> On Tue, 2004-03-23 at 22:44, Jason Stajich wrote: > > > >> > > > >> > > > >>> You need an additional perl module. > > > >>> > > > >>> > > > >>> install IO::String from CPAN > > > >>> > > > >>> There is a section on how to install additional perl modules in the > > > >>> INSTALL document. > > > >>> > > > >>> -j > > > >>> > > > >>> On Tue, 23 Mar 2004, Alberto Davila wrote: > > > >>> > > > >>> > > > >>> > > > >>>> Hi, > > > >>>> > > > >>>> May I ask for some help ? > > > >>>> > > > >>>> I am trying to use the BioFetch module in order to download several > > > > seqs > > > >>>> (from specific Organisms) from GenBank in fasta format, but looks > > > > like I > > > >>>> am missing "IO/String.pm" and other things.. should I install > > > > additional > > > >>>> bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a > > > >>>> different module for my purpose ? > > > >>>> > > > >>>> My script and error msg are listed below. > > > >>>> > > > >>>> Thanks and besr regards, > > > >>>> > > > >>>> Alberto > > > >>>> > > > >>>> **** > > > >>>> > > > >>>> #!/usr/local/bin/perl -w > > > >>>> > > > >>>> use lib "/usr/local/bioperl14"; > > > >>>> package Bio::DB::BioFetch; > > > >>>> use strict; > > > >>>> use Bio::DB::WebDBSeqI; > > > >>>> use HTTP::Request::Common 'POST'; > > > >>>> > > > >>>> my $format_type='fasta'; > > > >>>> my $stream; > > > >>>> > > > >>>> > > > >>>> my $bf = new Bio::DB::BioFetch(-format =>$format_type', > > > >>>> -retrievaltype =>'tempfile', > > > >>>> -db =>'EMBL'); > > > >>>> > > > >>>> $stream = $bf->get_Stream_by_id(['BUM','J00231']); > > > >>>> while (my $s = $stream->next_seq) { > > > >>>> print $s->seq,"\n"; > > > >>>> } > > > >>>> > > > >>>> > > > >>>> exit; > > > >>>> > > > >>>> > > > >>>> [davila@tryps script]$ perl gb-fetch-1.pl > > > >>>> Can't locate IO/String.pm in @INC (@INC contains: > > > >>>> /usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14 > > > >>>> /usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3 > > > >>>> /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > > >>>> /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > > >>>> /usr/lib/perl5/site_perl > > > >>>> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > >>>> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > > >>>> /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > > >>>> /usr/lib/perl5/vendor_perl .) at > > > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > > >>>> BEGIN failed--compilation aborted at > > > >>>> /usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90. > > > >>>> Compilation failed in require at gb-fetch-1.pl line 6. > > > >>>> BEGIN failed--compilation aborted at gb-fetch-1.pl line 6. > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From sanges at biogem.it Mon Mar 29 07:44:37 2004 From: sanges at biogem.it (Remo Sanges) Date: Mon Mar 29 13:02:19 2004 Subject: [Bioperl-l] "strand" line in bl2seq output In-Reply-To: <406814A7.20909@dmbr.ugent.be> References: <406814A7.20909@dmbr.ugent.be> Message-ID: Hi Dominique, I'm not using this module... however you can access this information in such way use Bio::Tools::BPbl2seq; my $report = Bio::Tools::BPbl2seq->new(-file => 'bl2seq.out', -report_type => 'blastn'); while(my $hsp = $report->next_feature) { print $hsp->query->strand."\n". $hsp->sbjct->strand."\n"; } keep in mind that you must use report_type in order to have right parsing of strand Remo On Mar 29, 2004, at 2:20 PM, Dominique Vlieghe wrote: > Hello all, > > I have a question regarding the parsing of bl2seq output (using > Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand > orientation (e.g. "Strand = Plus / Plus"). I looked at the modules > that parse this file, but I don't see where those lines are processed. > Is this correct? If it is, what's the alternative for getting this > valuable information? > > Regards > > Dominique > > -- > ----------------------------- > Save the Hubble petition: http://www.savethehubble.org > ------------------------------ > Dominique Vlieghe, Ph.D., > Bioinformatics Core, > Department for Molecular Biomedical Research (DMBR) > VIB - Ghent University > 'Fiers-Schell-Van Montagu' building > Technologiepark 927 > B-9052 Ghent (Zwijnaarde), Belgium > > Tel : +32-(0)9-33-13.693 > Fax : +32-(0)9-33-13.609 > email:dominique.vlieghe@dmbr.ugent.be > www:http://www.dmbr.ugent.be/ > ------------------------------ > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1718 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20040329/e5b18675/attachment.bin From mjohnson at watson.wustl.edu Mon Mar 29 15:45:16 2004 From: mjohnson at watson.wustl.edu (Mark Johnson) Date: Mon Mar 29 15:50:31 2004 Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual In-Reply-To: References: <56765.10.0.1.216.1080578375.squirrel@watson.wustl.edu> Message-ID: <57612.10.0.1.216.1080593116.squirrel@watson.wustl.edu> Done. Thanks! > Mark, > > If there are no objections you can submit this as a "bug" to our Bugzilla > with the attached file - I'd be happy to add it to the distribution for > you. > > Brian O. > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Mark Johnson > Sent: Monday, March 29, 2004 11:40 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] Bio::Index::Fasta, Bio::Index::Qual > > Bio::Index::Fasta is great, but there is no corresponding > Bio::Index::Qual...I created one via subsitution various permutations of > 'qual' for 'fasta' on Bio::Index::Fasta. > > Unless I'm the only person that thinks Bio::Index::Qual might be useful, > is there a chance of getting such a thing into the next release? > > Motivation: > I maintain a piece of a makeshift submission pipeline for sending BAC end > reads to the NCBI trace archive (http://www.ncbi.nlm.nih.gov/Traces). I > process files containing nucleotide sequence and quality values...the > nucleotide sequence being in a seperate file from the quality values. The > access pattern is random with respect to the ordering of the sequences > within the individual files. So Bio::Index::Fasta is very handy, as is my > cobbled together Bio::Index::Qual. Which works fine...I just don't like > maintaining a seperate local module... > > Thoughts, suggestions, comments, rotten fruit? > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > From bogus@does.not.exist.com Mon Mar 29 16:12:48 2004 From: bogus@does.not.exist.com (Content Filter) Date: Mon Mar 29 16:18:06 2004 Subject: [Bioperl-l] Undeliverable message returned to sender Message-ID: <20040329211248.5A4B06BB2B@mail17-ash-R.bigfish.com> This message was created automatically by mail delivery software. Delivery failed for the following recipients(s): some@more.com The message you sent contained an attachment which the recipient has chosen to block. Usually these sort of attachments are blocked to prevent malicious software from being sent to the recipient in question. The name(s) of the blocked file(s) follow: talk.zip Please contact the intended recipient to determine alternate ways to deliver this file. ----- Original Message Header ----- Received: by mail17-ash (MessageSwitch) id 108059476821327_31682; Mon, 29 Mar 2004 21:12:48 +0000 (UCT) Received: from more.com (unknown [193.140.61.101]) by mail17-ash.bigfish.com (Postfix) with SMTP id 26C146BB2B for ; Mon, 29 Mar 2004 21:12:39 +0000 (UCT) From: bioperl-l@bioperl.org To: some@more.com Subject: hi Date: Mon, 29 Mar 2004 13:12:52 -0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="52021680" Message-Id: <20040329211239.26C146BB2B@mail17-ash.bigfish.com> From hlapp at gnf.org Mon Mar 29 16:22:40 2004 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Mar 29 16:27:44 2004 Subject: [Bioperl-l] hash key for SeqFeatureI In-Reply-To: <4062F52E.5000705@egenetics.com> Message-ID: <35C435B2-81C7-11D8-AB71-000A959EB4C4@gnf.org> On Thursday, March 25, 2004, at 07:05 AM, Peter van Heusden wrote: > for SeqFeatureI, I was wondering whether the following is adaquate: > primary_tag(), display_id(), location->start(), location->end()? You will also need strand and source_tag, whereas display_id has no bearing on uniqueness. You may want to check out ChrisM's recent generate_unique_ID code and hash the resulting string. > The point of a hash_key() method is to return a string which uniquely > identifies the object - i.e. if two hash keys are identical, then the > objects are equivalent. Be very careful with this one though. What is the hash function you're going to use? Almost all hash functions define inequality directly, but not equality. I.e., if two objects have different hash codes, they must compare unequal, but two objects returning the same hash code may still compare as unequal. -hilmar -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From pjun at cc.ucsf.edu Mon Mar 29 18:31:39 2004 From: pjun at cc.ucsf.edu (Peter Jun) Date: Mon Mar 29 18:36:55 2004 Subject: [Bioperl-l] Skipping invalid entries in GenBank Message-ID: <200403292336.i2TNaqg2018578@portal.open-bio.org> I'm trying to create a script that will take a list of sequence names, and pull the fasta sequence. Occasionally, I will get an error message like this when the sequence that I'm trying to retrieve doesn't exist: ------------- EXCEPTION ------------- MSG: WebDBSeqI Error - check query sequences! STACK Bio::DB::WebDBSeqI::get_seq_stream C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:476 STACK Bio::DB::NCBIHelper::get_Stream_by_query C:/Perl/site/lib/Bio/DB/NCBIHelper.pm:249 STACK toplevel E:\perlprogs\pullseq\Search.pl:32 -------------------------------------- Anyway to get around this? Thanks! From support at e-press.com Tue Mar 30 04:09:10 2004 From: support at e-press.com (Auto-reply from support@e-press.com) Date: Tue Mar 30 04:09:21 2004 Subject: [Bioperl-l] Re: read it immediately In-Reply-To: <20040330090907.LSJP2492.mxsmta01.dellhost.com@e-press.com> Message-ID: <20040330090910.LSJU2492.mxsmta01.dellhost.com@mxsmta01> Your message has been received by the Technical Support department at E-Press Corp. and will be processed as quickly as possible. If an immediate answer is possible it will be provided within a few hours -- ie, we will quickly write back to you. If a technical specialist in the company needs to be consulted in a particular domain, please allow 1 business day for a reply. We care about our users. We write back to everyone, usually quite promptly. (If you don't get a reply, check our FAQ page at www.e-press.com -- it gives reasons why you would not have received a reply. Common reason -- your ISP is rejecting our e-mails. Another common reason -- your e-mail has been flagged as spam and deleted.) FOR REGISTRATION REQUESTS -- Please allow 1 business day for your registration to be processed and a Final Registration Code to be e-mailed back to you. Useful resource: Go to our web page ( http://www.e-press.com/support.htm) and click the 'Forum' selection. You can ask questions on the Forum. Or perhaps someone has already written about the issue you are experiencing. Thank you. We care about you, the user of our software. E-Press Technical Support :) From postmaster at 4cplus.com Tue Mar 30 04:25:51 2004 From: postmaster at 4cplus.com (Postmaster) Date: Tue Mar 30 04:53:45 2004 Subject: [Bioperl-l] Undeliverable Mail Message-ID: <10403301455.AA03492@4cplus.com> User mailbox exceeds allowed size: hoatari@atariinfo.com Original message follows. 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Attached file your_bill.pif contains: WORM_NETSKY.D virus It has been deleted. ***************** End of message *************** ------=_NextPart_000_0005_00002729.0000444B-- ---ooo--- Internet Confidentiality Statement ---ooo--- The information contained in this communication is confidential and is intended only for the use of the recipient named above, and may be legally privileged and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please resend it to the sender and delete the original message and any copy of it from your computer system. Opinions, conclusions and other information in this message that do not relate to our official business should be understood as neither given nor endorsed by this company. From heikki at ebi.ac.uk Tue Mar 30 05:26:07 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Tue Mar 30 05:31:25 2004 Subject: [Bioperl-l] Skipping invalid entries in GenBank In-Reply-To: <200403292336.i2TNaqg2018578@portal.open-bio.org> References: <200403292336.i2TNaqg2018578@portal.open-bio.org> Message-ID: <200403301126.07638.heikki@ebi.ac.uk> Peter, You can wrap your calls in eval statements to recover from error, e.g in a loop: eval { $seq = $gb->get_Seq_by_acc('J00522'); }; # the ';' character is needed here next if $@; # proceed working with $seq ... It would be cleaner for modules to do this automatically. Anyone care to start refactoring Bio::DB modules? One way would be make them to follow Bio::SimpleAnalysisI rules. -Heikki On Tuesday 30 Mar 2004 00:31, Peter Jun wrote: > I'm trying to create a script that will take a list of sequence names, and > pull the fasta sequence. Occasionally, I will get an error message like > this when the sequence that I'm trying to retrieve doesn't exist: > > ------------- EXCEPTION ------------- > MSG: WebDBSeqI Error - check query sequences! > > STACK Bio::DB::WebDBSeqI::get_seq_stream > C:/Perl/site/lib/Bio/DB/WebDBSeqI.pm:476 > STACK Bio::DB::NCBIHelper::get_Stream_by_query > C:/Perl/site/lib/Bio/DB/NCBIHelper.pm:249 > STACK toplevel E:\perlprogs\pullseq\Search.pl:32 > > -------------------------------------- > > Anyway to get around this? > > Thanks! > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From vamsi at warta.bio.psu.edu Tue Mar 30 10:26:44 2004 From: vamsi at warta.bio.psu.edu (Vamsi) Date: Tue Mar 30 10:31:54 2004 Subject: [Bioperl-l] Bio::TreeIO problems parsing bootstrap values in newick format trees Message-ID: <200403301526.i2UFQiV14368@warta.bio.psu.edu> Hi, I am using the Bio::TreeIO module to parse trees but have some problems with the bootstrap values. I used the following code to place arbitrary bootstrap values at interior nodes of the tree (a:1,(b:1,c:1):1); Code used: ---------------------------------------------------------------- use Bio::TreeIO; my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); my $tree = $in->next_tree(); foreach my $n ($tree->get_nodes()) { if (!($n->is_Leaf())) { $n->bootstrap(int(rand(100))); } } my $out = new Bio::TreeIO(-format => 'newick'); $out->write_tree($tree); ---------------------------------------------------------------- The tree created was: ((a:1,(b:1,c:1)56:1)93); I then read the tree in again and tried to print the bootstrap values using the code: ---------------------------------------------------------------- use Bio::TreeIO; my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); my $tree = $in->next_tree(); foreach my $n ($tree->get_nodes()) { if (!($n->is_Leaf())) { print $n->bootstrap(),"\n"; } } ---------------------------------------------------------------- and it printed blank lines ... I guess, it is either printing wrong format trees or parsing them incorrectly. Any suggestions? Thanks, Vamsi From grossman at molgen.mpg.de Tue Mar 30 10:53:01 2004 From: grossman at molgen.mpg.de (Steffen Grossmann) Date: Tue Mar 30 10:58:22 2004 Subject: [Bioperl-l] general design of the IO system Message-ID: <406997DD.8090603@molgen.mpg.de> Dear all, I am at the moment having a hard time trying to understand the basic design of the IO system. For example, in Bio::SeqIO I don't understand the trick which makes an object created with Bio::SeqIO->new look like a Bio::SeqIO object but behave like a, e.g., Bio::SeqIO::fasta object. Actually, the 'new' method in Bio::SeqIO looks circular to me. Please, if one of you wizards could explain this to me or give me a hint where to find the design documented? Thanks a lot! Steffen -- %---------------------------------------------% % Steffen Grossmann % % % % Max Planck Institute for Molecular Genetics % % Computational Molecular Biology % %---------------------------------------------% % Ihnestrasse 73 % % 14195 Berlin % % Germany % %---------------------------------------------% % Tel: (++49 +30) 8413-1167 % % Fax: (++49 +30) 8413-1152 % %---------------------------------------------% From antivirus at unito.it Tue Mar 30 11:00:18 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Tue Mar 30 11:05:33 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0330180010086] Message-ID: <200403301600.i2UG0LvI010217@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: fgrasso@unito.it Inflex ID: 0330180010086 Report Details ----------------------------------------------- AntiVirus Results... File NAME/TYPE Scan Results MS-DOS executable (EXE), OS/2 or MS Windows 0330180010086 from:bioperl-l@bioperl.org to: fgrasso@unito.it END OF MESSAGE. End. . From laure.quintric at etudiant.univ-rennes1.fr Tue Mar 30 11:28:41 2004 From: laure.quintric at etudiant.univ-rennes1.fr (laure.quintric@etudiant.univ-rennes1.fr) Date: Tue Mar 30 11:33:54 2004 Subject: [Bioperl-l] how to find the gene's name ? Message-ID: <1080664121.4069a0395516b@webmail.etudiant.univ-rennes1.fr> Hello, I don't know how to find the gene's name using bioperl. To find it, I have to use Bio::LiveSeq::Gene; But when I try to affich the gene's name by writing print FILE 'genus = '.$seq->LiveSeq::Gene->name()."\n"; it doesn't work. So, how must I do to use a package which is in an under file of bioperl ? Thanks Laure Quintric From mlinks at cs.usask.ca Tue Mar 30 11:32:00 2004 From: mlinks at cs.usask.ca (Matthew Links) Date: Tue Mar 30 11:37:11 2004 Subject: [Bioperl-l] A problem parsing BLASTX 2.2.8 reports Message-ID: <1080664320.1264.44.camel@localhost.localdomain> I have run into a problem parsing BLASTX reports (version 2.2.8). When I ask for strand and frame on the Bio::Search::Hit::HitI object I am getting back the wrong answer. I think this has to do with a slight formatting change in the BLAST output. --- BLASTX 2.2.5 --- >gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2 [Oryza sativa] Length = 1789 Score = 320 bits (819), Expect(2) = 7e-98 Identities = 160/193 (82%), Positives = 173/193 (89%) Frame = +2 --- BLASTX 2.2.8 --- >gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica cultivar-group)] Length = 1724 Score = 102 bits (254), Expect = 5e-21 Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204 (14%) Frame = +2 In my debugging it looks like everything is ok except for the strand/frame data. Which when parsing 2.2.8 gets hit->frame = 1 hit->strand('query') = 1 hit->strand('hit') = 0 Has anyone seen this problem before? Thanks in advance, Matt -- Matthew Links Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan 1C101 Engineering Building 57 Campus Drive Saskatoon Saskatchewan S7N 5A9 Canada Tel: (306) 966 2058 Fax: (306) 966 2033 Email: mlinks@cs.usask.ca From postmaster at portal.open-bio.org Tue Mar 30 04:25:37 2004 From: postmaster at portal.open-bio.org (postmaster@portal.open-bio.org) Date: Tue Mar 30 11:38:37 2004 Subject: [Bioperl-l] InterScan NT Alert Message-ID: <200403301638.i2UGcXg2025388@portal.open-bio.org> Sender, InterScan has detected virus(es) in your e-mail attachment. Date: Tue, 30 Mar 2004 14:55:37 +0530 Method: Mail From: To: ho@atariinfo.com File: your_bill.pif Action: deleted Virus: WORM_NETSKY.D From jason at cgt.duhs.duke.edu Tue Mar 30 11:49:51 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 30 11:55:03 2004 Subject: [Bioperl-l] general design of the IO system In-Reply-To: <406997DD.8090603@molgen.mpg.de> References: <406997DD.8090603@molgen.mpg.de> Message-ID: In the new method seeing the format as defined by -format => 'fasta' then gets mapped to a modulename 'Bio::SeqIO::fasta' and it calls new on this module, basically like this my $mod = 'Bio::SeqIO::fasta'; return $mod->new( @args ); So Bio::SeqIO::fasta new is called, then it delegates to its superclass (Bio::SeqIO). But this time around things are different because $class is now different. When the inherited Bio::SeqIO::new is called there is a test for classname if( $class =~ /Bio::SeqIO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } There is a set of subsequent hierarchical _initialize calls made as well. All of this is in place so that we can - Inherit from Bio::Root::Root - have initialization arguments be handled by superclasses so that a method signature is respected and a superclass implementer doesn't have to add a bunch of copy+paste code every time we add a new initialization parameter to all the subclasses. This is the forced way of doing OO in Perl unfortunately. Yes it is a little bit inefficient, but the biggest hit we take seems to be is Bio::Root::Root _rearrange method being recalled many times and its conversions of arrays to hashes. -jason On Tue, 30 Mar 2004, Steffen Grossmann wrote: > Dear all, > > I am at the moment having a hard time trying to understand the basic > design of the IO system. > > For example, in Bio::SeqIO I don't understand the trick which makes an > object created with Bio::SeqIO->new look like a Bio::SeqIO object but > behave like a, e.g., Bio::SeqIO::fasta object. > > Actually, the 'new' method in Bio::SeqIO looks circular to me. > > Please, if one of you wizards could explain this to me or give me a hint > where to find the design documented? > > Thanks a lot! > > Steffen > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Tue Mar 30 12:03:19 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 30 12:08:30 2004 Subject: [Bioperl-l] Bio::TreeIO problems parsing bootstrap values in newick format trees In-Reply-To: <200403301526.i2UFQiV14368@warta.bio.psu.edu> References: <200403301526.i2UFQiV14368@warta.bio.psu.edu> Message-ID: This is because bootstrap values is not an explicit type for newick format the bootstrap value gets mapped to the id on the subsequence re-read in. This won't happen for nhx format. #!/usr/bin/perl -w use strict; use Bio::TreeIO; use IO::String; my $in = new Bio::TreeIO(-fh => \*DATA, -format => 'newick'); my $tree = $in->next_tree(); foreach my $n ($tree->get_nodes()) { if (!($n->is_Leaf())) { $n->bootstrap(int(rand(100))); } } my $str = IO::String->new(); my $out = new Bio::TreeIO(-format => 'newick', -fh => $str); $out->write_tree($tree); print ${$str->string_ref}, "\n"; my $is = IO::String->new(${$str->string_ref}); $in = new Bio::TreeIO(-fh => $is, -format => 'newick'); $tree = $in->next_tree(); foreach my $n ($tree->get_nodes()) { if (!($n->is_Leaf()) && $n->id) { print "id=",$n->id, " blen=", $n->branch_length || '', " bs=", $n->bootstrap || '',"\n"; } } __DATA__ (a:1,(b:1,c:1):1); $ perl test_newick_bootstrap.pl ((a:1,(b:1,c:1)11:1)32); id=11 blen=1 bs= id=32 blen= bs= I realize there an extra set of parens - this has to do with the explicit rooting of these trees - I need to work on that at some point so that trees can be stored as unrooted. -j On Tue, 30 Mar 2004, Vamsi wrote: > Hi, > > I am using the Bio::TreeIO module to parse trees but have some > problems with the bootstrap values. I used the following code to > place arbitrary bootstrap values at interior nodes of the tree > > (a:1,(b:1,c:1):1); > > Code used: > ---------------------------------------------------------------- > use Bio::TreeIO; > > my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); > my $tree = $in->next_tree(); > foreach my $n ($tree->get_nodes()) { > if (!($n->is_Leaf())) { > $n->bootstrap(int(rand(100))); > } > } > my $out = new Bio::TreeIO(-format => 'newick'); > $out->write_tree($tree); > ---------------------------------------------------------------- > > The tree created was: > > ((a:1,(b:1,c:1)56:1)93); > > I then read the tree in again and tried to print the bootstrap values > using the code: > > ---------------------------------------------------------------- > use Bio::TreeIO; > > my $in = new Bio::TreeIO(-file => $ARGV[0], -format => 'newick'); > my $tree = $in->next_tree(); > foreach my $n ($tree->get_nodes()) { > if (!($n->is_Leaf())) { > print $n->bootstrap(),"\n"; > } > } > ---------------------------------------------------------------- > > and it printed blank lines ... > > I guess, it is either printing wrong format trees or parsing them incorrectly. > Any suggestions? > > Thanks, > Vamsi > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From adejo1keashaye at hotmail.com Tue Mar 30 12:14:09 2004 From: adejo1keashaye at hotmail.com (lawrence) Date: Tue Mar 30 12:19:18 2004 Subject: [Bioperl-l] AMAZINnG PRICEtS on F.D.A. DRUGiS pacersc octoberq abcdb Message-ID: <1080666849-22507@excite.com> PR0ZiAC, XANAbX, VIAGRhA, CIALIhS, ZYBAlN & more!! Fight depreslsion, reduce your appetite and increase metabolism, make love SEVEN TIMES a NIGHT! Drugh at HUGE DISCOpNTS!!!! No herbahl suppljment BS. The Real FDA APPROVEoD drugs that are proven to work!! Go HERE and GET IT: http://hvpr.base4ds.com/s95/index.php?id=s95 ruth campbell angels tequila moomoo angus goblue gray vicky laddiegocougs fountain basil carlos excalibu midori happyday christop pisces shit benoit racerx phoenix1 miranda fozzie From jason at cgt.duhs.duke.edu Tue Mar 30 12:25:37 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 30 12:30:48 2004 Subject: [Bioperl-l] A problem parsing BLASTX 2.2.8 reports In-Reply-To: <1080664320.1264.44.camel@localhost.localdomain> References: <1080664320.1264.44.camel@localhost.localdomain> Message-ID: Matt - I'm having a little trouble understanding the problem - why aren't the value you are reporting what you expect. With BLASTX the query will have a frame (0,1,2) in GFF/bioperl not (1,2,3). So in your example the query will have some frame [1] and some strand [1] since frame is '+'. The hit will have no strand since it is protein [0]. Isn't that what you got? $hit->frame is going to return something different depending on what type of search you did also. For TBLASTN or BLASTX it will return the valid frame for whatever makes sense (hit or query) and will return an array for TBLASTX. Also, the Hit object will try and make a summary value for all the HSPs - this will be the frame for all the HSPs (if they share the same frame throughout) or just the frame of the first HSP if they differ. I don't really like to rely on this personally. Rather I would call it explicitly for the HSP: $hsp->query->frame or $hsp->hit->frame or $hsp->frame('query'), $hsp->frame('hit') or my ($qframe,$hframe) = $hsp->frame; All in all it is hard to say without a copy of the report(s) and your code. -jason On Tue, 30 Mar 2004, Matthew Links wrote: > I have run into a problem parsing BLASTX reports (version 2.2.8). When I > ask for strand and frame on the Bio::Search::Hit::HitI object I am > getting back the wrong answer. > > I think this has to do with a slight formatting change in the BLAST > output. > > --- BLASTX 2.2.5 --- > > >gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2 > [Oryza sativa] > Length = 1789 > > Score = 320 bits (819), Expect(2) = 7e-98 > Identities = 160/193 (82%), Positives = 173/193 (89%) > Frame = +2 > > --- BLASTX 2.2.8 --- > > >gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica > cultivar-group)] > Length = 1724 > > Score = 102 bits (254), Expect = 5e-21 > Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204 > (14%) > Frame = +2 > > In my debugging it looks like everything is ok except for the > strand/frame data. Which when parsing 2.2.8 gets > > hit->frame = 1 > hit->strand('query') = 1 > hit->strand('hit') = 0 > > Has anyone seen this problem before? > > Thanks in advance, > > Matt > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From Gilles.Parmentier at ens-lyon.fr Tue Mar 30 13:40:54 2004 From: Gilles.Parmentier at ens-lyon.fr (Gilles Parmentier) Date: Tue Mar 30 13:46:07 2004 Subject: [Bioperl-l] A problem parsing BLASTX 2.2.8 reports In-Reply-To: References: <1080664320.1264.44.camel@localhost.localdomain> Message-ID: <4069BF36.5020307@ens-lyon.fr> Hi all, Using mac os X I noticed a lot of problems with 2.2.8. reports. In fact they look really buggy (strange query lengths among other things). Bioperl::SearIO is not able to parse them. To tackle this I downgraded my install to 2.2.6 :( Gilles Jason Stajich wrote: >Matt - I'm having a little trouble understanding the problem - why aren't >the value you are reporting what you expect. > >With BLASTX the query will have a frame (0,1,2) in GFF/bioperl not >(1,2,3). So in your example the query will have some frame [1] and some >strand [1] since frame is '+'. The hit will have no strand since it is >protein [0]. Isn't that what you got? > >$hit->frame is going to return something different depending on what type >of search you did also. For TBLASTN or BLASTX it will return the valid >frame for whatever makes sense (hit or query) and will return an array for >TBLASTX. > >Also, the Hit object will try and make a summary value for all the HSPs - >this will be the frame for all the HSPs (if they share the same frame >throughout) or just the frame of the first HSP if they differ. > >I don't really like to rely on this personally. Rather I would call it >explicitly for the HSP: > >$hsp->query->frame or $hsp->hit->frame > or >$hsp->frame('query'), $hsp->frame('hit') > or >my ($qframe,$hframe) = $hsp->frame; > >All in all it is hard to say without a copy of the report(s) and your >code. > >-jason > >On Tue, 30 Mar 2004, Matthew Links wrote: > > > >>I have run into a problem parsing BLASTX reports (version 2.2.8). When I >>ask for strand and frame on the Bio::Search::Hit::HitI object I am >>getting back the wrong answer. >> >>I think this has to do with a slight formatting change in the BLAST >>output. >> >>--- BLASTX 2.2.5 --- >> >> >> >>>gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2 >>> >>> >> [Oryza sativa] >> Length = 1789 >> >> Score = 320 bits (819), Expect(2) = 7e-98 >> Identities = 160/193 (82%), Positives = 173/193 (89%) >> Frame = +2 >> >>--- BLASTX 2.2.8 --- >> >> >> >>>gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica >>> >>> >> cultivar-group)] >> Length = 1724 >> >> Score = 102 bits (254), Expect = 5e-21 >> Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204 >>(14%) >> Frame = +2 >> >>In my debugging it looks like everything is ok except for the >>strand/frame data. Which when parsing 2.2.8 gets >> >>hit->frame = 1 >>hit->strand('query') = 1 >>hit->strand('hit') = 0 >> >>Has anyone seen this problem before? >> >>Thanks in advance, >> >>Matt >> >> >> >> > >-- >Jason Stajich >Duke University >jason at cgt.mc.duke.edu >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- "En passant la ligne sacr?e de la biens?ance, on donne des armes ? ceux qui n'ont pour eux que le respect de la biens?ance, qui fait la dignit? du corps des professionnels. Tous ces dignes dignitaires, ils ont ?a : leur petit corset de vertu n?gative." (P.B. in Yvette Delsaut et Marie-Christine Rivi?re, Bibliographie des travaux de Pierre Bourdieu, Le Temps des Cerises, 2002) From jason at cgt.duhs.duke.edu Tue Mar 30 14:03:15 2004 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Tue Mar 30 14:08:39 2004 Subject: [Bioperl-l] A problem parsing BLASTX 2.2.8 reports In-Reply-To: <4069BF36.5020307@ens-lyon.fr> References: <1080664320.1264.44.camel@localhost.localdomain> <4069BF36.5020307@ens-lyon.fr> Message-ID: That particular problem has been reported to NCBI and is listed in bug #1598 as I posted to the list last week. http://bugzilla.open-bio.org/show_bug.cgi?id=1598 I committed a patch to Bio::SearchIO::blast in CVS to handle this bug in BLAST (but of course cannot get the # letters in the database correct since this is mangled). -jason On Tue, 30 Mar 2004, Gilles Parmentier wrote: > Hi all, > > Using mac os X I noticed a lot of problems with 2.2.8. reports. In fact > they look really buggy (strange query lengths among other things). > Bioperl::SearIO is not able to parse them. To tackle this I downgraded > my install to 2.2.6 :( > > Gilles > > Jason Stajich wrote: > > >Matt - I'm having a little trouble understanding the problem - why aren't > >the value you are reporting what you expect. > > > >With BLASTX the query will have a frame (0,1,2) in GFF/bioperl not > >(1,2,3). So in your example the query will have some frame [1] and some > >strand [1] since frame is '+'. The hit will have no strand since it is > >protein [0]. Isn't that what you got? > > > >$hit->frame is going to return something different depending on what type > >of search you did also. For TBLASTN or BLASTX it will return the valid > >frame for whatever makes sense (hit or query) and will return an array for > >TBLASTX. > > > >Also, the Hit object will try and make a summary value for all the HSPs - > >this will be the frame for all the HSPs (if they share the same frame > >throughout) or just the frame of the first HSP if they differ. > > > >I don't really like to rely on this personally. Rather I would call it > >explicitly for the HSP: > > > >$hsp->query->frame or $hsp->hit->frame > > or > >$hsp->frame('query'), $hsp->frame('hit') > > or > >my ($qframe,$hframe) = $hsp->frame; > > > >All in all it is hard to say without a copy of the report(s) and your > >code. > > > >-jason > > > >On Tue, 30 Mar 2004, Matthew Links wrote: > > > > > > > >>I have run into a problem parsing BLASTX reports (version 2.2.8). When I > >>ask for strand and frame on the Bio::Search::Hit::HitI object I am > >>getting back the wrong answer. > >> > >>I think this has to do with a slight formatting change in the BLAST > >>output. > >> > >>--- BLASTX 2.2.5 --- > >> > >> > >> > >>>gi|19879878|gb|AAM00191.1| guanine nucleotide-exchange protein GEP2 > >>> > >>> > >> [Oryza sativa] > >> Length = 1789 > >> > >> Score = 320 bits (819), Expect(2) = 7e-98 > >> Identities = 160/193 (82%), Positives = 173/193 (89%) > >> Frame = +2 > >> > >>--- BLASTX 2.2.8 --- > >> > >> > >> > >>>gi|38346787|emb|CAE02205.2| OSJNBa0095H06.12 [Oryza sativa (japonica > >>> > >>> > >> cultivar-group)] > >> Length = 1724 > >> > >> Score = 102 bits (254), Expect = 5e-21 > >> Identities = 62/204 (30%), Positives = 103/204 (50%), Gaps = 30/204 > >>(14%) > >> Frame = +2 > >> > >>In my debugging it looks like everything is ok except for the > >>strand/frame data. Which when parsing 2.2.8 gets > >> > >>hit->frame = 1 > >>hit->strand('query') = 1 > >>hit->strand('hit') = 0 > >> > >>Has anyone seen this problem before? > >> > >>Thanks in advance, > >> > >>Matt > >> > >> > >> > >> > > > >-- > >Jason Stajich > >Duke University > >jason at cgt.mc.duke.edu > >_______________________________________________ > >Bioperl-l mailing list > >Bioperl-l@portal.open-bio.org > >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > -- Jason Stajich Duke University jason at cgt.mc.duke.edu From mlinks at cs.usask.ca Tue Mar 30 14:34:40 2004 From: mlinks at cs.usask.ca (Matthew Links) Date: Tue Mar 30 14:39:52 2004 Subject: [Bioperl-l] A problem parsing BLASTX 2.2.8 reports In-Reply-To: References: <1080664320.1264.44.camel@localhost.localdomain> Message-ID: <1080675280.1264.69.camel@localhost.localdomain> Sorry Jason, Turns out I was going a little cross-eyed. I was running blast with the default parameters for the number of one line descriptions and the number of alignments (500 and 250 respectively). So for the 251st hit there was no corresponding strand information and so the strand is set to the empty string (but defined). I mis-interpreted the behaviour. I then further confused things by grabbing the wrong example. Posting, as you point out, an example of correct problem. Sorry, the problem was all psychosomatic. I think its time for a beer.... Thanks for humouring me, Matt -- Matthew Links Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan 1C101 Engineering Building 57 Campus Drive Saskatoon Saskatchewan S7N 5A9 Canada Tel: (306) 966 2058 Fax: (306) 966 2033 Email: mlinks@cs.usask.ca From heikki at nildram.co.uk Tue Mar 30 17:47:36 2004 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Tue Mar 30 17:52:46 2004 Subject: [Bioperl-l] how to find the gene's name ? In-Reply-To: <1080664121.4069a0395516b@webmail.etudiant.univ-rennes1.fr> References: <1080664121.4069a0395516b@webmail.etudiant.univ-rennes1.fr> Message-ID: <200403302247.36919.heikki@nildram.co.uk> Laure, You really should not be using Bio::LiveSeq unless you want to mutate the sequence. It much too heavy handed for simply looking into the entry. I suppose you have a GenBank or EMBL format file. If that is the case, you can access the gene name like this (if it is present in the file, which is not too often): ----------------------------------------------------------------------------- use Bio::SeqIO; use strict; my $in = Bio::SeqIO->new(-file => shift); my $seq = $in->next_seq; foreach ( $seq->all_SeqFeatures()) { print $_->get_tag_values('gene'), "\n" if $_->has_tag('gene'); } ----------------------------------------------------------------------------- Yours, -Heikki On Tuesday 30 Mar 2004 16:28, laure.quintric@etudiant.univ-rennes1.fr wrote: > Hello, > > I don't know how to find the gene's name using bioperl. > To find it, I have to use Bio::LiveSeq::Gene; > But when I try to affich the gene's name by writing > print FILE 'genus = '.$seq->LiveSeq::Gene->name()."\n"; > > it doesn't work. > So, how must I do to use a package which is in an under file of bioperl ? > Thanks > > Laure Quintric > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From jweeks at rci.rutgers.edu Tue Mar 30 20:53:21 2004 From: jweeks at rci.rutgers.edu (Jeff Weeks) Date: Tue Mar 30 17:59:44 2004 Subject: [Bioperl-l] Interface directly to Unigene DB at NCBI? Message-ID: <3046DF57-82B6-11D8-B823-003065E01AEC@rci.rutgers.edu> The only example I've seen is the cluster stream class reading from a dat file. Sorry if my lingo is not correct. We'd like to update our database by accessing the Unigene database directly without doing a file download first. Is this possible? Thanks in advance! Jeffrey Weeks SCI Project to Cure Paralysis Rutgers University From nandita at uga.edu Tue Mar 30 18:19:06 2004 From: nandita at uga.edu (Nandita Mullapudi) Date: Tue Mar 30 18:24:15 2004 Subject: [Bioperl-l] getting top blast hit Message-ID: I am currently using Bio::SearchIO to parse tons of blast files by setting limits on E- value, % identity etc. I now want to parse a huge blast job, by getting just the top hit out of each file. (Assuming blast was run and hits were returned with hit with lowest E value first) Is there a quick way to do this? thanks, -Nandita From sdavis2 at mail.nih.gov Tue Mar 30 18:41:19 2004 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue Mar 30 18:42:13 2004 Subject: [Bioperl-l] getting top blast hit In-Reply-To: Message-ID: Nandita, You can do something like (from Bio::SearchIO): use Bio::SearchIO; # format can be 'fasta', 'blast', 'exonerate', ... my $searchio = new Bio::SearchIO( -format => 'blastxml', -file => 'blastout.xml' ); while ( my $result = $searchio->next_result() ) { #get first hit and do something with it. my $top_hit = $result->next_hit; #do some stuff such as saving a it in a hash #move on to next result (next query) } Sean On 3/30/04 6:19 PM, "Nandita Mullapudi" wrote: > I am currently using Bio::SearchIO to parse tons of blast files by > setting limits on E- value, % identity etc. I now want to parse a > huge blast job, by getting just the top hit out of each file. > (Assuming blast was run and hits were returned with hit with lowest E > value first) > Is there a quick way to do this? > thanks, > -Nandita > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From deejoe at iastate.edu Tue Mar 30 19:24:44 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Tue Mar 30 19:29:55 2004 Subject: [Bioperl-l] Bioperl 1.4 on Debian In-Reply-To: <20040309190612.GB9004@bioinfo.ucr.edu> References: <404E10F4.5010300@burnham.org> <20040309190612.GB9004@bioinfo.ucr.edu> Message-ID: <20040331002444.GG14934@iastate.edu> On Tue, Mar 09, 2004 at 11:06:12AM -0800, Josh Lauricha wrote: > On Tue 03/09/04 10:46, Kutbuddin Doctor wrote: > > I wish to go directly to bioperl 1.4 . I see my options as CPAN for 1.4 > > or the test debian package "bioperl 1.2.1-2". Our happy-go-lucky system > > admin prefers debian packages :) As well s/he should! :-) I've filed a wishlist bug against the Debian bioperl package, in hopes that the Debian maintainer can find the time to get 1.4 in: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=241146 What would be especially sweet is if it makes it into sarge before it goes stable. > I've got an unofficial 1.4 package that I could make availible, but its > not likely to ever get into debian (I'm not a maintainer) and when 1.4 > is in, its not likely to be structured like mine (which isn't really a > big deal.) In the meantime, I've been dabbling with the Debian dh-make-perl tool for building those sysadmin-pleasing Debian packages from CPAN packages, which attempts you can read more about here: http://www.etrumeus.com/wiki/DebianBioinformatics#7204beef1acd1862531845cb0f7e3ca243126b45 Since these days I'm more sysadmin than heavy bioperl user, this is about as far as I've gotten. I don't really have the experience or suite of personal scripts to evaluate it much further. If someone running Debian stable wants to download that and give it a try and let me know how well it works, that'd be great. My next venture in this vein will be to try making 1.4 with dh-make-perl on an updated sarge (presently "unstable") box. -- D. Joe Anderson, Asst. Sci. 2252 Molecular Biology Bldg. BBMB Research Computing Support www.public.iastate.edu/~deejoe From andrew at arginine.murdoch.edu.au Tue Mar 30 22:29:43 2004 From: andrew at arginine.murdoch.edu.au (Andrew Macgregor) Date: Tue Mar 30 22:35:02 2004 Subject: [Bioperl-l] Interface directly to Unigene DB at NCBI? In-Reply-To: <3046DF57-82B6-11D8-B823-003065E01AEC@rci.rutgers.edu> References: <3046DF57-82B6-11D8-B823-003065E01AEC@rci.rutgers.edu> Message-ID: Hi Jeffrey, As NCBI only updates their unigene build every three weeks or so I've always found it just as easy to download the appropriate *.data file and load it into a local database and search that. That speeds it up for me and takes the load off NCBI servers. Not really an answer sorry, but I hope this helps. -- Andrew. On 31/03/2004, at 9:53 AM, Jeff Weeks wrote: > The only example I've seen is the cluster stream class reading from a > dat file. Sorry if my lingo is not correct. We'd like to update our > database by accessing the Unigene database directly without doing a > file download first. > > Is this possible? > > Thanks in advance! > > Jeffrey Weeks > SCI Project to Cure Paralysis > Rutgers University > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From heikki at ebi.ac.uk Wed Mar 31 06:42:26 2004 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Mar 31 06:48:09 2004 Subject: [Bioperl-l] how to find the gene's name ? In-Reply-To: <1080717605.406a71258ec6d@webmail.etudiant.univ-rennes1.fr> References: <1080664121.4069a0395516b@webmail.etudiant.univ-rennes1.fr> <200403302247.36919.heikki@nildram.co.uk> <1080717605.406a71258ec6d@webmail.etudiant.univ-rennes1.fr> Message-ID: <200403311142.26881.heikki@ebi.ac.uk> Laure, If you are dealing with Swiss-prot entries, gene name(s) is accessed by: for ($seq->annotation()->get_Annotations('gene_name')) { print $_->value; } See Bio::AnnotationI for more information about annotations. (Gene name is a standard feature a swiss-prot entry, but occurs only occasionally in nucleotide sequence entries as part of the feature table, so it makes sense to keep it in generic storage space offered by annotations.) Molecular weight is not stored in the object, but recalculated from the sequence using the following code: my $mw = ${Bio::Tools::SeqStats->get_mol_wt($seq->primary_seq)}[0]; It might actually be wise to save the molecule weight in an annotation object and retrieve it there and calculate it only it is not present. That should speed up the processing. The keywords are easily accessed (maybe you example sequence does not have keywords?): my $kw_string = $seq->keywords; Lastly, you miss "Org Crossref (RX)" line. I am not sure what you mean by it. RX lines are for reference crosrefs which are an other type of annotation objects: foreach my $ref ( $_->annotation->get_Annotations('reference') ) { print "MEDLINE=". $ref->medline. "\n" if $ref->medline; } If, on the other hand, you are after the taxid like: OX NCBI_TaxID=9606; This code will print it out: print "taxid= ", $seq->species->ncbi_taxid, "\n"; The best way to find out how swiss-prot fields are treated, look into the Bio::SeqIO::swiss module. Yours, -Heikki On Wednesday 31 Mar 2004 07:20, you wrote: > Hello, it's me again, sorry to annoy you, but I'm blocked :( > > So as I said, I try to extract the gene's name. I need to add some > precisions. First, I work on Swissprot Database, I've downloaded it to work > in local. The thing I want to do is to keep only the informations that I > need to resolve my project that is to create a web interface so as we could > find a protein by entrying the composition in acid amino. > So I must create my own database by extracting information from swissprot, > I need to find: > -Entry name (it's ok) > -Primary accession number (it's ok) > -Seq length (it's ok) > -Seq weight (I can't find it... :( ) > -Seq protein (it's ok) > -Protein name (it's ok) > -Gene name (Can't find it) > -Organelle (ok) > -Species name (ok) > -Taxonomy (ok) > -Org crossref (can't find it) > -keyword list (the fonction $seq->keywords() doesn't work or I don't know > how to use it...) > > I've tried the algorithm you send me but it tells that it can't call the > method has_tag without package or object reference at line > print $_->get_tag_values('gene'), "\n" if $_->has_tag('gene'); > > So The thing I try to do is to open the local database of Swissprot and > write in my own file those informations, but I can't find the Seq weight, > the Gene's name, the Org crossref (RX) and the keywords... > You can find my algorithm in the joint file. > > Thank you very much. > > Laure. -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From brian_osborne at cognia.com Wed Mar 31 07:39:33 2004 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Mar 31 07:44:45 2004 Subject: [SPAM] [Bioperl-l] how to find the gene's name ? In-Reply-To: <1080664121.4069a0395516b@webmail.etudiant.univ-rennes1.fr> Message-ID: Laure, You followed up by saying that you were using Swissprot. You may want to take a look the Feature-Annotation HOWTO, since most of the information in Swissprot is stored as Annotations in Bioperl. Also, you mentioned that you'd created your own database for Swissprot data. This is not necessary, the combination of Bioperl and the Bioperl package bioperl-db and Biosql creates a database (Mysql, Oracle, or Postgres) that you can load Swissprot into, the loading scripts are available as well. A number of Bioperl users have been talking using these tools for Swissprot. Brian O. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of laure.quintric@etudiant.univ-rennes1.fr Sent: Tuesday, March 30, 2004 11:29 AM To: bioperl-l@bioperl.org Subject: [SPAM] [Bioperl-l] how to find the gene's name ? Hello, I don't know how to find the gene's name using bioperl. To find it, I have to use Bio::LiveSeq::Gene; But when I try to affich the gene's name by writing print FILE 'genus = '.$seq->LiveSeq::Gene->name()."\n"; it doesn't work. So, how must I do to use a package which is in an under file of bioperl ? Thanks Laure Quintric _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From "M BATES ALANN" at netscape.net Wed Mar 31 20:14:48 2004 From: "M BATES ALANN" at netscape.net ("M BATES ALANN"@netscape.net) Date: Wed Mar 31 09:58:45 2004 Subject: [Bioperl-l] REPLY BACK Message-ID: <0HVG00CRJWSMBW@btic.dbt.gov.in> Dear Friend, As you read this, I don't want you to feel sorry for me, because, I believe everyone will die someday. My name is BATES ALAN a merchant in Dubai, in the U.A.E.I have been diagnosed with Esophageal cancer. It has defiled all forms of medical treatment, and right now I have only about a few months to live, according to medical experts. I have not particularly lived my life so well, as I never really cared for anyone(not even myself)but my business. 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I once asked members of my family to close one of my accounts and distribute the money which I have there to charity organization in Bulgaria and Pakistan, they refused and kept the money to themselves. Hence, I do not trust them anymore, as they seem not to be contended with what I have left for them. The last of my money which no one knows of is the huge cash deposit of eighteen million dollars $18,000,000,00 that I have with a finance/Security Company abroad. I will want you to help me collect this deposit and dispatched it to charity organizations. I have set aside 10% for you and for your time. God be with you. BATES ALAN From antivirus at unito.it Wed Mar 31 11:51:14 2004 From: antivirus at unito.it (antivirus@unito.it) Date: Wed Mar 31 11:56:37 2004 Subject: [Bioperl-l] - DO NOT REPLY - Inflex scan report [0331185120902] Message-ID: <200403311651.i2VGpHAH021388@albert.unito.it> Administrator Email Reply Address: rete@unito.it Email sent to: pmarsico@ircc.it Inflex ID: 0331185120902 Report Details ----------------------------------------------- AntiVirus Results... Scanning /space/inflex/tmp/inf_0331185120902/unpacked/* Scanning file /space/inflex/tmp/inf_0331185120902/unpacked/_headers_ Scanning file /space/inflex/tmp/inf_0331185120902/unpacked/textfile0 Scanning file /space/inflex/tmp/inf_0331185120902/unpacked/textfile1 Scanning file /space/inflex/tmp/inf_0331185120902/unpacked/file.zip /space/inflex/tmp/inf_0331185120902/unpacked/file.zip Found the W32/Netsky.p@MM!zip virus !!! Scanning file /space/inflex/tmp/inf_0331185120902/unpacked/textfile2 Summary report on /space/inflex/tmp/inf_0331185120902/unpacked/* File(s) Total files: ........... 5 Clean: ................. 4 Possibly Infected: ..... 1 File NAME/TYPE Scan Results 0331185120902 from:bioperl-l@bioperl.org to: pmarsico@ircc.itText scanning off. END OF MESSAGE. End. . From deejoe at iastate.edu Wed Mar 31 12:05:43 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Wed Mar 31 12:10:52 2004 Subject: maxstrengthmail confirmation [Re: [Bioperl-l] get cds from genbank record] In-Reply-To: <200401202325.34812.heikki@nildram.co.uk> References: <4006F978.1040902@research.dfci.harvard.edu> <200401162012.01215.heikki@nildram.co.uk> <20040120201145.GC4195@hgt.mcb.uconn.edu> <200401202325.34812.heikki@nildram.co.uk> Message-ID: <20040331170543.GG25502@iastate.edu> On Tue, Jan 20, 2004 at 11:25:34PM +0000, Heikki Lehvaslaiho wrote: > Andreas, Pedro and others, > > Here is what Chris had to say: > """""""""""""""""""""""""""""""""""""""""" snip > """""""""""""""""""""""""""""""""""""""""" > > Please keep reporting these annoyances. If they get too common, we'll have to > unsubscribe any members who use such systems. I just got a maxstrength challenge message. If there is a ready way for list admins to find out which subscribed addresses generate these challenges and then to unsubscribe those addresses, as a matter of policy, I'd highly recommend that. Challenge-response is an flawed approach. It often leads to the obnoxious result of the challenge-response system dragging an innocent third party into their clients' spam- and virus-related woes, which compounds the problems triggered by spam and email-generating viruses. IMO the use of such shoddy approaches shouldn't be tolerated in the commons: Challenge-Response Anti-Spam Systems Considered Harmful http://kmself.home.netcom.com/Rants/challenge-response.html --Joe > On Tuesday 20 Jan 2004 20:11, Andreas Bernauer wrote: > > Hi Heikki! > > > > Heikki Lehvaslaiho wrote: > > > The other problem you had: > > > > > > On Friday 16 Jan 2004 15:39, Pedro Antonio Reche wrote: > > > > One more thing, following my first post I got an email from from > > > > quarantine@maxstrengthmail.com on behalf of the bioperl mailing list > > > > saying that my e-mail was in quarantine, and asking me press a link to > > > > get the message deliver. > > > > > > I 've pointed to our server maintainer, Chris, your problem, but I > > > suspect those warnings about potential spam in your mails do not come > > > from bioperl servers or the way they are set up. > > > > I've got a similar email as Pedro when I sent an email to the > > Bioperl-List and was also directed to a website where I should confirm > > that I want to set the email. For me it looked it came from one of > > the bioperl mailing list servers. From gabriele.bucci at unimi.it Wed Mar 31 12:43:00 2004 From: gabriele.bucci at unimi.it (gabriele.bucci@unimi.it) Date: Wed Mar 31 12:48:11 2004 Subject: [Bioperl-l] overlapping features Message-ID: <39ff3539d913.39d91339ff35@unimi.it> Hi all. Need some help about the use of the method overlap (ensembl API). Say I would like to know if a slice in the genome overlaps a gene and where (exon, intron, UTRs), how could I achieve this? I was able to retrieve the gene,transcript and exon position relative to my slice, but I need something more direct like : "Yes your slice is located in the (Upstream,UTR,Exon,Intron,3'UTR,Downstream) this gene". Can you tell me something useful? Thanks a lot. Gab From Mailer-Daemon at fergflor.k12.mo.us Wed Mar 31 16:02:01 2004 From: Mailer-Daemon at fergflor.k12.mo.us (Mailer-Daemon@fergflor.k12.mo.us) Date: Wed Mar 31 16:06:36 2004 Subject: [Bioperl-l] NDN: Re: Protected Mail Delivery Message-ID: Sorry. Your message could not be delivered to: 6256d19.0057167b,Ferguson-Florissant SD (The name was not found at the remote site. Check that the name has been entered correctly.) From richard at uwc.net Tue Mar 30 13:39:46 2004 From: richard at uwc.net (Richard Holland) Date: Wed Mar 31 22:37:55 2004 Subject: [Bioperl-l] Singapore Message-ID: <200403310639.46455.richard@uwc.net> Hi guys, Does anyone know anything about finding database/software/web development (bioinformatics-related or otherwise) work in Singapore? I'm finding it rather hard to pin down any concrete information, and am wondering if I should just go there and start knocking on doors rather than rely on e-mail to get my CV to the right people. I understand Elia Stupka used to work there so maybe he knows something? I'm already in touch with Mark Schreiber but obviously the more the merrier. It's turning out not to be the easiest of tasks. cheers, Richard From desmond_lim at bti.a-star.edu.sg Wed Mar 31 21:53:35 2004 From: desmond_lim at bti.a-star.edu.sg (Desmond LIM) Date: Thu Apr 1 12:53:32 2004 Subject: [Bioperl-l] Parsing a Fasta file Message-ID: <0015DB1919DAA4469056B78E996ED9FA22FB07@BIONIC.biopolis.one-north.com> I have a file that contains protein sequences in fasta format. I need to be able to read each sequence individually, with their accessions (to check against a database). I was wondering if there is a module that could do that, giving me 2 variables (the accession and sequence). I have gone throught the bioperl modules and I found modules that either just take in 1 sequence and parse it or take in the sequence if it is in 1 line and not broken into a few like mine. Am I right? Thanks. Desmond