[Bioperl-l] cdd-search with remoteblast?
Cook, Malcolm
MEC at stowers.org
Fri Jul 10 15:45:13 UTC 2009
Chris, I've added a test to bioperl RemoteBlast.t that demonstrates the following. Is it appropriate to submit it?
Jonas, OK, I was a little quick on the gun... but I've got it now.
You don't need to change the wrapper. Here is what you need to do:
# 1) set your database like this:
-database => 'cdsearch/cdd', # c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html for other cdd database options
# 2) add this line before submitting the job:
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
You're in - No other changes needed.
Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri
> -----Original Message-----
> From: Jonas Schaer [mailto:Brotelzwieb at gmx.de]
> Sent: Friday, July 10, 2009 4:18 AM
> To: BioPerl List; Cook, Malcolm; Chris Fields
> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
>
> Hi,
> I tried to do what Malcom proposed my ($prog = 'rpsblast';
> my $db =
> 'CDD';) but that didn't work.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Value rpsblast for PUT parameter PROGRAM does not match
> expression t?blast[ pnx]. Rejecting.
> STACK: Error::throw
> STACK: Bio::Root::Root::throw C:/Perl/site/lib/Bio/Root/Root.pm:359
> STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
> C:/Perl/site/lib/Bio/Tools
> /Run/RemoteBlast.pm:329
> STACK: Bio::Tools::Run::RemoteBlast::new
> C:/Perl/site/lib/Bio/Tools/Run/RemoteBl
> ast.pm:257
> STACK: blast_a_seq2.pm:14
> -----------------------------------------------------------
> So I should try to "change the wrapper to allow 'rpsblast'",
> right? Could You tell me how to do that, please? So sorry but
> I have no idea yet...:) If that doesn't work, is there any
> other way to run cdd-searches with perl?
> Thank you so much!
> Regards, Jonas
>
> ----- Original Message -----
> From: "Chris Fields" <cjfields1 at gmail.com>
> To: "Cook, Malcolm" <MEC at stowers.org>
> Cc: "'Jonas Schaer'" <Brotelzwieb at gmx.de>; "'BioPerl List'"
> <bioperl-l at lists.open-bio.org>; "'Smithies, Russell'"
> <Russell.Smithies at agresearch.co.nz>; <cjfields at bioperl.org>
> Sent: Thursday, July 09, 2009 9:19 PM
> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
>
>
> > I've scheduled this tentatively for the 1.6 release series (just not
> > sure when yet). It may work as is, but I haven't tried it out yet
> > (and am hazarding to guess it only retrieves the single main RID at
> > the moment).
> >
> > chris
> >
> > On Jul 9, 2009, at 10:56 AM, Cook, Malcolm wrote:
> >
> >> Jonas,
> >>
> >> If you want to continue to use the bioperl remoteblast interface,
> >> probably what you should do is simply call it twice.
> >>
> >> Once, as you already know how to do, which will return without CDD
> >> results.
> >>
> >> Secondly, to get the CDD results, call remoteblast a second time.
> >> This time, using
> >> -database => 'CDD'
> >> -program => 'rpsblast'
> >>
> >> However, the wrapper may object to the 'rpsblast' program. It is
> >> not listed in the POD -
> >>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/Tools/Run/R
> emoteBlast.pm)
> >> If so, my guess is that changing the perl wrapper to allow
> >> rpsblast will "just work" (tm). I've cc:ed
> cjfields at bioperl.org for
> >> his opinion on this.
> >>
> >> Also, you might want to perform the CDD search first, especially if
> >> you are streaming results to eyeball that might like something to
> >> look at while the second (presumably longer) search is running.
> >>
> >> Cheers,
> >>
> >> Malcolm Cook
> >> Stowers Institute for Medical Research - Kansas City, Missouri
> >>
> >>
> >>> -----Original Message-----
> >>> From: bioperl-l-bounces at lists.open-bio.org
> >>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> >>> Jonas Schaer
> >>> Sent: Thursday, July 09, 2009 5:16 AM
> >>> To: BioPerl List; Smithies, Russell
> >>> Subject: Re: [Bioperl-l] cdd-search with remoteblast?
> >>>
> >>> Hi guys,
> >>> Thank you all so much for your help and patience :). Of
> >>> course you were right and I finaly found the right
> >>> put-parameter to get exactly the same hits as on the homepage.
> >>> I do have an other question though :)...
> >>> I now want to include a search for conserved domains, but
> >>> when I try to use the CDD_SEARCH-parameter
> >>> (http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node16.html#
> >>> sub:CDD_SEARCH)
> >>> like the other put-parameters the way chris once told
> >>> me(works fine with the other params):
> >>>
> >>> my %put = (
> >>> WORD_SIZE => 3,
> >>> HITLIST_SIZE => 100,
> >>> THRESHOLD => 11,
> >>> FILTER => 'R',
> >>> GENETIC_CODE => 1,
> >>> CDD_SEARCH => 'on'
> >>> ###I tried it
> >>> with 'true' and '1', too.
> >>>
> >>> );
> >>>
> >>> for my $putName (keys %put) {
> >>> $factory->submit_parameter($putName,$put{$putName});
> >>> }
> >>>
> >>>
> >>> ...an exception is thrown:
> >>>
> >>> ------------- EXCEPTION: Bio::Root::Exception -------------
> >>> MSG: CDD_SEARCH is not a valid PUT parameter.
> >>> STACK: Error::throw
> >>> STACK: Bio::Root::Root::throw
> C:/Perl/site/lib/Bio/Root/Root.pm:359
> >>> STACK: Bio::Tools::Run::RemoteBlast::submit_parameter
> >>> C:/Perl/site/lib/Bio/Tools
> >>> /Run/RemoteBlast.pm:325
> >>> STACK: main::blast_a_sequence firsteval0.8.pm:383
> >>> STACK: main::blast_it firsteval0.8.pm:288
> >>> STACK: firsteval0.8.pm:35
> >>> ----------------------------------------------------------- .
> >>> I guess somehow this could be the solution to my problem:
> >>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node78.html#s
> >>> ub:RID-for-Simultaneous
> >>> , but unfortunately I don't understand what to do.
> >>> I'm so sorry to bother you with this but please help me once
> >>> more...:)
> >>>
> >>> Best regards and thanks in advance,
> >>> Jonas
> >>>
> >>> ----- Original Message -----
> >>> From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
> >>> To: "'Jonas Schaer'" <Brotelzwieb at gmx.de>
> >>> Cc: "'Chris Fields'" <cjfields at illinois.edu>; "'BioPerl List'"
> >>> <bioperl-l at lists.open-bio.org>
> >>> Sent: Monday, July 06, 2009 10:56 PM
> >>> Subject: RE: [Bioperl-l] different results with
> remote-blast skript
> >>>
> >>>
> >>> Hi Jonas,
> >>> You can't just play with the BLAST parameters and hope
> for a "better"
> >>> result.
> >>> I'd suggest that if you aren't sure what they do, you should
> >>> leave them
> >>> alone as small changes can make huge differences in the
> >>> output - it's quite
> >>> possible to miss finding what you're looking for by using
> the wrong
> >>> parameters.
> >>> If all else fails, read the blast manual:
> >>> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall
> >>> _all.html
> >>> http://www.ncbi.nlm.nih.gov/blast/tutorial/
> >>> Or Read Ian Korfs' excellent book:
> >>> http://books.google.com/books?id=xvcnhDG9fNUC&lpg=PR17&ots=WJp
> >> fuHF6Hn&dq=ian%20korf%20%20blast%20book&pg=PA3
> >>>
> >>> Don't worry about the integer overflow bug as there's nothing
> >>> you can do
> >>> about it. If you're interested, Google and Wikipedia are your
> >>> friends:
> >>> http://en.wikipedia.org/wiki/Integer_overflow
> >>>
> >>>
> >>> Russell
> >>>
> >>>> -----Original Message-----
> >>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
> >>>> Sent: Tuesday, 7 July 2009 12:14 a.m.
> >>>> To: BioPerl List; Chris Fields
> >>>> Subject: Re: [Bioperl-l] different results with
> remote-blast skript
> >>>>
> >>>> Hi guys, thanks for your answers so far.
> >>>> @jason: integer overflow in blast.... sorry, but what do
> >>> you mean by that?
> >>>> how can I fix it...?
> >>>>
> >>>> Since I never really changed any parameters I thought them
> >>> all to be
> >>>> default.
> >>>> whatever, I tried to get "better" results with my prog
> by changing
> >>>> these:
> >>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
> >>>> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
> >>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
> >>>>
> >>> $Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATI
> >>> STICS'} =
> >>>> '1';
> >>>> with no effect...I guess these were default values anyway.
> >>>>
> >>>> So please maybe you can tell me all the other parameters I
> >>> can change with
> >>>> my
> >>>> perl-skript AND how to do that?
> >>>> Unfortunately both, perl and the blast-algorithm are pretty
> >>> much new to
> >>>> me,
> >>>> maybe thats why I just cannot find out how to do that on my
> >>> own... :/
> >>>>
> >>>> Here is the output I get with my remote-blast skript:
> >>>>
> >>> ##############################################################
> >>> ################
> >>>> ###################################
> >>>> Query Name:
> >>>>
> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSL
> >>>> L
> >>>> hit name is ref|XP_001702807.1|
> >>>> score is 442
> >>>> BLASTP 2.2.21+
> >>>> Reference: Stephen F. Altschul, 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.
> >>>>
> >>>>
> >>>> Reference for composition-based statistics: Alejandro A.
> >>>> Schaffer, L. Aravind, Thomas L. Madden, Sergei Shavirin,
> >>> John L. Spouge,
> >>>> Yuri
> >>>> I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
> >>> "Improving the
> >>>> accuracy of PSI-BLAST protein database searches with
> >>> composition-based
> >>>> statistics and other refinements", Nucleic Acids Res.
> 29:2994-3005.
> >>>>
> >>>>
> >>>> RID: 53STX5G2013
> >>>>
> >>>>
> >>>> Database: All non-redundant GenBank CDS
> >>>> translations+PDB+SwissProt+PIR+PRF excluding
> environmental samples
> >>>> from WGS projects
> >>>> 9,252,587 sequences; 3,169,972,781 total letters Query=
> >>>>
> >>>
> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLRSLL
> >>>>
> >>>
> DVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDNAFRQAHQNTAM
> >>>> ATGPDPDDEYE
> >>>> Length=150
> >>>>
> >>>>
> >>>>
> >>> Score
> >>>> E
> >>>> Sequences producing significant alignments:
> >>> (Bits)
> >>>> Value
> >>>>
> >>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> >>> reinhard... 174
> >>>> 2e-42
> >>>>
> >>>>
> >>>> ALIGNMENTS
> >>>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> reinhardtii]
> >>>> gb|EDP06586.1| ClpS-like protein [Chlamydomonas reinhardtii]
> >>>> Length=303
> >>>>
> >>>> Score = 174 bits (442), Expect = 2e-42, Method:
> >>> Composition-based
> >>>> stats.
> >>>> Identities = 150/150 (100%), Positives = 150/150 (100%),
> >>> Gaps = 0/150
> >>>> (0%)
> >>>>
> >>>> Query 1
> >>> MGSSSVGTYHLLLVLMgaggeqqavqagaevaSTEQVDGSGMAANSRGSTSGSEQPPrds
> >>>> 60
> >>>>
> >>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
> >>>> Sbjct 154
> >>> MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDS
> >>>> 213
> >>>>
> >>>> Query 61
> >>> dlgllrslldVAGVDRTalevkllalaeagaeMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>> 120
> >>>>
> >>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>> Sbjct 214
> >>> DLGLLRSLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVAR
> >>>> 273
> >>>>
> >>>> Query 121 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 150
> >>>> AWHERDDNAFRQAHQNTAMATGPDPDDEYE
> >>>> Sbjct 274 AWHERDDNAFRQAHQNTAMATGPDPDDEYE 303
> >>>>
> >>>>
> >>>>
> >>>> Database: All non-redundant GenBank CDS
> >>>> translations+PDB+SwissProt+PIR+PRF
> >>>> excluding environmental samples from WGS projects
> >>>> Posted date: Jul 5, 2009 4:41 AM
> >>>> Number of letters in database: -1,124,994,511
> >>>> Number of sequences in database: 9,252,587
> >>>>
> >>>> Lambda K H
> >>>> 0.309 0.122 0.345
> >>>> Gapped
> >>>> Lambda K H
> >>>> 0.267 0.0410 0.140
> >>>> Matrix: BLOSUM62
> >>>> Gap Penalties: Existence: 11, Extension: 1
> >>>> Number of Sequences: 9252587
> >>>> Number of Hits to DB: 60273703
> >>>> Number of extensions: 1448367
> >>>> Number of successful extensions: 2103
> >>>> Number of sequences better than 10: 0
> >>>> Number of HSP's better than 10 without gapping: 0
> >>>> Number of HSP's gapped: 2113
> >>>> Number of HSP's successfully gapped: 0
> >>>> Length of query: 150
> >>>> Length of database: 3169972781
> >>>> Length adjustment: 113
> >>>> Effective length of query: 37
> >>>> Effective length of database: 2124430450
> >>>> Effective search space: 78603926650
> >>>> Effective search space used: 78603926650
> >>>> T: 11
> >>>> A: 40
> >>>> X1: 16 (7.1 bits)
> >>>> X2: 38 (14.6 bits)
> >>>> X3: 64 (24.7 bits)
> >>>> S1: 42 (20.8 bits)
> >>>> S2: 74 (33.1 bits)
> >>>>
> >>>>
> >>> ##############################################################
> >>> ################
> >>>> ###################################
> >>>> and here are the hits (?) of the blast-algorithm on the
> >>> ncbi-homepage with
> >>>> the same query of course:
> >>>> ref|XP_001702807.1| ClpS-like protein [Chlamydomonas
> >>> reinhard... 300
> >>>> 3e-80
> >>>> ref|XP_001942719.1| PREDICTED: similar to GA16705-PA
> >>> [Acyrtho... 36.2
> >>>> 1.1
> >>>> ref|ZP_03781446.1| hypothetical protein RUMHYD_00880
> >>> [Blautia... 35.4
> >>>> 1.8
> >>>> ref|XP_001563232.1| leucyl-tRNA synthetase [Leishmania
> >>> brazil... 34.3
> >>>> 4.2
> >>>> ref|XP_680841.1| hypothetical protein AN7572.2
> >>> [Aspergillus n... 33.5
> >>>> 6.0
> >>>> ref|YP_001768110.1| hypothetical protein M446_1150
> >>> [Methyloba... 33.5
> >>>> 7.0
> >>>>
> >>> ##############################################################
> >>> ################
> >>>> ###################################at
> >>>> least the first hit is the same, but even there there is a
> >>> different score
> >>>> and e-value.
> >>>>
> >>>> thanks so much for any help :)
> >>>> regards, jonas
> >>>>
> >>>>
> >>>> ----- Original Message -----
> >>>> From: "Chris Fields" <cjfields at illinois.edu>
> >>>> To: "Jason Stajich" <jason at bioperl.org>
> >>>> Cc: "Smithies, Russell"
> >>> <Russell.Smithies at agresearch.co.nz>; "'BioPerl
> >>>> List'" <bioperl-l at lists.open-bio.org>; "'Jonas Schaer'"
> >>>> <Jonas_Schaer at gmx.de>
> >>>> Sent: Monday, July 06, 2009 12:51 AM
> >>>> Subject: Re: [Bioperl-l] different results with
> remote-blast skript
> >>>>
> >>>>
> >>>>> That inspires confidence ;>
> >>>>>
> >>>>> chris
> >>>>>
> >>>>> On Jul 5, 2009, at 4:40 PM, Jason Stajich wrote:
> >>>>>
> >>>>>> integer overflow in blast....
> >>>>>>
> >>>>>> On Jul 5, 2009, at 2:00 PM, Smithies, Russell wrote:
> >>>>>>
> >>>>>>> I'd guess it's a difference in the parameters used.
> >>>>>>> Interesting that both have the number of letters in the db as
> >>>>>>> "-1,125,070,205", I assume that's a bug :-)
> >>>>>>>
> >>>>>>> Stats from your remote_blast:
> >>>>>>>
> >>>>>>> 'stats' => {
> >>>>>>> 'S1' => '42',
> >>>>>>> 'S1_bits' => '20.8',
> >>>>>>> 'lambda' => '0.309',
> >>>>>>> 'entropy' => '0.345',
> >>>>>>> 'kappa_gapped' => '0.0410',
> >>>>>>> 'T' => '11',
> >>>>>>> 'kappa' => '0.122',
> >>>>>>> 'X3_bits' => '24.7',
> >>>>>>> 'X1' => '16',
> >>>>>>> 'lambda_gapped' => '0.267',
> >>>>>>> 'X2' => '38',
> >>>>>>> 'S2' => '74',
> >>>>>>> 'seqs_better_than_cutoff' => '0',
> >>>>>>> 'posted_date' => 'Jul 4, 2009 4:41 AM',
> >>>>>>> 'Hits_to_DB' => '60102303',
> >>>>>>> 'dbletters' => '-1125070205',
> >>>>>>> 'A' => '40',
> >>>>>>> 'num_successful_extensions' => '2004',
> >>>>>>> 'num_extensions' => '1436892',
> >>>>>>> 'X1_bits' => '7.1',
> >>>>>>> 'X3' => '64',
> >>>>>>> 'entropy_gapped' => '0.140',
> >>>>>>> 'dbentries' => '9252258',
> >>>>>>> 'X2_bits' => '14.6',
> >>>>>>> 'S2_bits' => '33.1'
> >>>>>>> }
> >>>>>>>
> >>>>>>>
> >>>>>>> Stats from a blast done on the NCBI webpage:
> >>>>>>>
> >>>>>>> Database: All non-redundant GenBank CDS
> >>> translations+PDB+SwissProt
> >>>>>>> +PIR+PRF
> >>>>>>> excluding environmental samples from WGS projects
> >>>>>>> Posted date: Jul 4, 2009 4:41 AM
> >>>>>>> Number of letters in database: -1,125,070,205
> >>>>>>> Number of sequences in database: 9,252,258
> >>>>>>>
> >>>>>>> Lambda K H
> >>>>>>> 0.309 0.124 0.340
> >>>>>>> Gapped
> >>>>>>> Lambda K H
> >>>>>>> 0.267 0.0410 0.140
> >>>>>>> Matrix: BLOSUM62
> >>>>>>> Gap Penalties: Existence: 11, Extension: 1
> >>>>>>> Number of Sequences: 9252258
> >>>>>>> Number of Hits to DB: 86493230
> >>>>>>> Number of extensions: 3101413
> >>>>>>> Number of successful extensions: 9001
> >>>>>>> Number of sequences better than 100: 65
> >>>>>>> Number of HSP's better than 100 without gapping: 0
> >>>>>>> Number of HSP's gapped: 9000
> >>>>>>> Number of HSP's successfully gapped: 66
> >>>>>>> Length of query: 150
> >>>>>>> Length of database: 3169897087
> >>>>>>> Length adjustment: 113
> >>>>>>> Effective length of query: 37
> >>>>>>> Effective length of database: 2124391933
> >>>>>>> Effective search space: 78602501521
> >>>>>>> Effective search space used: 78602501521
> >>>>>>> T: 11
> >>>>>>> A: 40
> >>>>>>> X1: 16 (7.1 bits)
> >>>>>>> X2: 38 (14.6 bits)
> >>>>>>> X3: 64 (24.7 bits)
> >>>>>>> S1: 42 (20.8 bits)
> >>>>>>> S2: 65 (29.6 bits)
> >>>>>>>
> >>>>>>>
> >>>>>>>> -----Original Message-----
> >>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >>>>>>>> bounces at lists.open-bio.org] On Behalf Of Jonas Schaer
> >>>>>>>> Sent: Sunday, 28 June 2009 10:15 p.m.
> >>>>>>>> To: BioPerl List
> >>>>>>>> Subject: [Bioperl-l] different results with
> remote-blast skript
> >>>>>>>>
> >>>>>>>> Hi again :)
> >>>>>>>> please, I only have this little question:
> >>>>>>>> why do I get different results with my remote::blast
> >>> perl skript
> >>>>>>>> then on the
> >>>>>>>> ncbi blast homepage?
> >>>>>>>> I am using blastp, the query is an amino-sequence (different
> >>>>>>>> results with any
> >>>>>>>> sequence, differences not only in number of hits but
> even in e-
> >>>>>>>> values, scores
> >>>>>>>> etc...), the database is 'nr'.
> >>>>>>>> PLEASE help me,
> >>>>>>>> thank you in advance,
> >>>>>>>> Jonas
> >>>>>>>>
> >>>>>>>> ps: my skript:
> >>>>>>>>
> >>>>
> >>> ##############################################################
> >>> ################
> >>>>>>>> ##
> >>>>>>>> use Bio::Seq::SeqFactory;
> >>>>>>>> use Bio::Tools::Run::RemoteBlast;
> >>>>>>>> use strict;
> >>>>>>>> my @blast_report;
> >>>>>>>> my $prog = 'blastp';
> >>>>>>>> my $db = 'nr';
> >>>>>>>> my $e_val= '1e-10';
> >>>>>>>> #my $e_val= '10';
> >>>>>>>> my @params = ( '-prog' => $prog,
> >>>>>>>> '-data' => $db,
> >>>>>>>> '-expect' => $e_val,
> >>>>>>>> '-readmethod' => 'SearchIO' );
> >>>>>>>> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
> >>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
> >>>>>>>> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
> >>>>>>>> $
> >>>>>>>> Bio
> >>>>>>>>
> >>> ::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'}
> >>>>>>>> = '1';
> >>>>>>>>
> >>>>>>>> my
> >>>>>>>> $
> >>>>>>>> blast_seq
> >>>>>>>>
> >>>
> ='MGSSSVGTYHLLLVLMGAGGEQQAVQAGAEVASTEQVDGSGMAANSRGSTSGSEQPPRDSDLGLLR
> >>>>>>>>
> >>>>
> >>> SLLDVAGVDRTALEVKLLALAEAGAEMPPAQDSQATAAGVVATLTSVYRQQVARAWHERDDN
> >>> AFRQAHQNTAMATGPD
> >>>>>>>> PDDEYE';
> >>>>>>>> #$v is just to turn on and off the messages
> >>>>>>>> my $v = 1;
> >>>>>>>> my $seqbuilder = Bio::Seq::SeqFactory->new('-type' =>
> >>>>>>>> 'Bio::PrimarySeq');
> >>>>>>>> my $seq = $seqbuilder->create(-seq =>$blast_seq,
> -display_id =>
> >>>>>>>> "$blast_seq");
> >>>>>>>> my $filename='temp2.out';
> >>>>>>>> my $r = $factory->submit_blast($seq);
> >>>>>>>> print STDERR "waiting..." if( $v > 0 );
> >>>>>>>> while ( my @rids = $factory->each_rid )
> >>>>>>>> {
> >>>>>>>> foreach my $rid ( @rids )
> >>>>>>>> {
> >>>>>>>> my $rc = $factory->retrieve_blast($rid);
> >>>>>>>> if( !ref($rc) )
> >>>>>>>> {
> >>>>>>>> if( $rc < 0 )
> >>>>>>>> {
> >>>>>>>> $factory->remove_rid($rid);
> >>>>>>>> }
> >>>>>>>> print STDERR "." if ( $v > 0 );
> >>>>>>>> }
> >>>>>>>> else
> >>>>>>>> {
> >>>>>>>> my $result = $rc->next_result();
> >>>>>>>> $factory->save_output($filename);
> >>>>>>>> $factory->remove_rid($rid);
> >>>>>>>> print "\nQuery Name: ",
> >>> $result->query_name(),
> >>>>>>>> "\n";
> >>>>>>>> while ( my $hit = $result->next_hit )
> >>>>>>>> {
> >>>>>>>> next unless ( $v > 0);
> >>>>>>>> print "\thit name is ",
> $hit->name, "\n";
> >>>>>>>> while( my $hsp = $hit->next_hsp )
> >>>>>>>> {
> >>>>>>>> print "\t\tscore is ",
> >>> $hsp->score, "\n";
> >>>>>>>> }
> >>>>>>>> }
> >>>>>>>> }
> >>>>>>>> }
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> }
> >>>>>>>> @blast_report = get_file_data ($filename);
> >>>>>>>> return @blast_report;
> >>>>>>>>
> >>>>
> >>> ##############################################################
> >>> ################
> >>>>>>>> ####
> >>>>>>>> _______________________________________________
> >>>>>>>> Bioperl-l mailing list
> >>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>> =
> >>>>>>> =
> >>>>>>>
> >>>
> =====================================================================
> >>>>>>> Attention: The information contained in this message and/or
> >>>>>>> attachments
> >>>>>>> from AgResearch Limited is intended only for the
> >>> persons or entities
> >>>>>>> to which it is addressed and may contain confidential and/or
> >>>>>>> privileged
> >>>>>>> material. Any review, retransmission, dissemination
> or other use
> >>>>>>> of, or
> >>>>>>> taking of any action in reliance upon, this information
> >>> by persons or
> >>>>>>> entities other than the intended recipients is prohibited by
> >>>>>>> AgResearch
> >>>>>>> Limited. If you have received this message in error,
> >>> please notify
> >>>>>>> the
> >>>>>>> sender immediately.
> >>>>>>> =
> >>>>>>> =
> >>>>>>>
> >>>
> =====================================================================
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> Bioperl-l mailing list
> >>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>>>> --
> >>>>>> Jason Stajich
> >>>>>> jason at bioperl.org
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Bioperl-l mailing list
> >>>>>> Bioperl-l at lists.open-bio.org
> >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>> --------------------------------------------------------------
> >>> ----------------
> >>>> --
> >>>>
> >>>>
> >>>>
> >>>> No virus found in this incoming message.
> >>>> Checked by AVG - www.avg.com
> >>>> Version: 8.5.375 / Virus Database: 270.13.5/2219 - Release
> >>> Date: 07/05/09
> >>>> 05:53:00
> >>>
> >>>
> >>> --------------------------------------------------------------
> >>> ------------------
> >>>
> >>>
> >>>
> >>> No virus found in this incoming message.
> >>> Checked by AVG - www.avg.com
> >>> Version: 8.5.375 / Virus Database: 270.13.5/2220 - Release
> >>> Date: 07/05/09
> >>> 17:54:00
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
>
>
> --------------------------------------------------------------
> ------------------
>
>
>
> No virus found in this incoming message.
> Checked by AVG - www.avg.com
> Version: 8.5.375 / Virus Database: 270.13.8/2227 - Release
> Date: 07/09/09
> 05:55:00
>
>
More information about the Bioperl-l
mailing list