From manju.rawat2 at gmail.com Sat Oct 1 03:07:48 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Sat, 1 Oct 2011 12:37:48 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.fa -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau.fa','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); pl tell me what i am doing wrong. Thanks Manju Rawat From Russell.Smithies at agresearch.co.nz Sun Oct 2 19:27:22 2011 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 3 Oct 2011 12:27:22 +1300 Subject: [Bioperl-l] how to blast a seq against multiple dbase In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF33C15FA8623@exchsth.agresearch.co.nz> Did you try this? database => 'Chr1.db,Chr2.db,Chr3.db' Blast supports comma-separated database names so thin might have made it into BioPerl. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peter Cock > Sent: Wednesday, 28 September 2011 11:02 p.m. > To: Manju Rawat > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] how to blast a seq against multiple dbase > > On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat > wrote: > > Hello, > > > > I have downloaded all the chromosome of Bos Taurus and i'd changed > > them in blast format using makeblastdb..and now i want to localy blast > > my sequence against these all chromosome.. > > now i have 29 database.Is there any method by which can i blast my > > sequence against all 29 database in my program.. > > > > > > whta should i write in database???? > > > > @params = ('database' => '????????', 'outfile' => 'blast2.out', > > ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn'); > > > > The simple answer is make a combined database. This works internally with > alias files, have a look at the NR and NT databases for example - they act like > singe databases but are actually a collection of chunks. > > Even simpler would be to combine your Bos taurus sequence files into a > single multi-entry FASTA file, and make that into a single BLAST database. > > Peter > > _______________________________________________ > 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. ======================================================================= From ross at cuhk.edu.hk Mon Oct 3 00:19:52 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 12:19:52 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> Message-ID: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And from NodeI documentation, I cannot identify a way to make a Node object to a NodeI object. By the same token, methods like is_monophyletic or is_paraphyletic are also unable to work on LCA's. Web search does not return any examples about the manipulation of the LCA. Any hints would be highly appreciated so I can continue to dig out the remaining on my own. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; #or by the following _DATA_ my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); } print "$leaf1:LCA:$lca:ACL:$leaf2"; ; #print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } #_DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 00); From David.Messina at sbc.su.se Mon Oct 3 05:17:47 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 11:17:47 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: Hi Ross, Bio::Tree::Node is a NodeI object. It inherits ? or, more accurately, implements ? all of the methods in NodeI. Admittedly, it's a little obscure. The modules ending in 'I' ? the 'I' stands for Interface ? are never meant to be called directly. Rather, they define the methods that other modules, which are called directly, like Bio::Tree::Node, must have in order to be compliant with the Bio::Tree::NodeI interface. If you look at the code for NodeI, you'll that there are only a very few methods actually coded in there; most of them are simply empty placeholders. You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? Dave On Mon, Oct 3, 2011 at 06:19, Ross KK Leung wrote: > The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And > from NodeI documentation, I cannot identify a way to make a Node object to > a > NodeI object. By the same token, methods like is_monophyletic or > is_paraphyletic are also unable to work on LCA's. Web search does not > return > any examples about the manipulation of the LCA. Any hints would be highly > appreciated so I can continue to dig out the remaining on my own. > > > > use Bio::TreeIO; > > use Bio::Tree::TreeFunctionsI; > > > > $tab = "\t"; $nl = "\n"; > > my ($testtree) = @ARGV; #or by the following _DATA_ > > my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); > > while( my $tree = $treein->next_tree ){ > > %dist_matrix = (); > > > > my @leaves = $tree->get_leaf_nodes; > > foreach my $leaf1( @leaves ){ > > my $id1 = $leaf1->id; > > foreach my $leaf2( @leaves ){ > > my $id2 = $leaf2->id; > > if ($id1 eq $id2) { > > $dist_matrix{$id1}->{$id2} = 0; > > next; > > } > > my $distance = $tree->distance( -nodes => [$leaf1, > $leaf2] ); > > if ($id1 eq "A" and $id2 eq "B") { > > my $lca = $tree->get_lca(-nodes => [$leaf1, > $leaf2] ); > > } > > print "$leaf1:LCA:$lca:ACL:$leaf2"; ; > > #print $lca->id; ; > > my $distance2 = $tree->distance( -nodes => [$lca, > $leaf2] ); > > print $distance2; ; > > > > $dist_matrix{$id1}->{$id2} = $distance; > > } > > } > > } > > > > #_DATA_ > > > ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 > > 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 > > 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( > > L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 > > .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, > > (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 > > ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 > 00); > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ross at cuhk.edu.hk Mon Oct 3 06:28:38 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 18:28:38 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Dave wrote: >You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design Thanks for this reference, it is very good for me to understand better the architecture of Bioperl. >So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? But the following codes will generate errors because lca cannot be identified. my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; my $distance = $tree->distance( -nodes => [$leaf1,$leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1,$leaf2] ); } print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca,$leaf2] ); print $distance2; ; } } } _DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.00000000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.00000000); My ultimate goal is just to conveniently derive the information that nodes M and L share the same LCA O for the following tree. +---I | +---M | | | +---H | +---O | | | | +---G | | | | +---L | | | +---F A | +---E | | | +---K | | | | | +---D | | +---N | | +---C | | +---J | +---B From David.Messina at sbc.su.se Mon Oct 3 07:28:41 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 13:28:41 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: Hi Ross, >So, if I understand your question correctly, you should be able to use all > of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit > confused, is_monophyletic is something you'd call on a Tree object, not on a > Node object, right?**** > > But the following codes will generate errors because lca cannot be > identified. > Right, but there are some compile-time errors in your code. I changed a few things so I could get it to run: http://cl.ly/AdzH In my hands, there is a Node object returned as $lca. However, it doesn't have an id so the next line where you try to print $lca->id, I get an undefined value error. When I look at $lca, it doesn't seems to be equivalent to node C, which, based on the tree you supplied, I would expect to be the LCA. SO there may in fact be something wrong in the BioPerl code here, too. However, I'm not that familiar with these modules, and I know there's been some recent work done on them, so perhaps someone else can chime in here. **** > > My ultimate goal is just to conveniently derive the information that nodes > M and L share the same LCA O for the following tree. > Ok, thanks for that clarification. I think the code should be able to do that. Incidentally, the tree you provided in Newick format does not appear to me to be the same tree you drew as ASCII art ? is that right? Dave From thomas.sharpton at gmail.com Mon Oct 3 10:35:33 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 07:35:33 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: On Mon, Oct 3, 2011 at 4:28 AM, Dave Messina wrote: In my hands, there is a Node object returned as $lca. However, it doesn't > have an id so the next line where you try to print $lca->id, I get an > undefined value error. > > When I look at $lca, it doesn't seems to be equivalent to node C, which, > based on the tree you supplied, I would expect to be the LCA. SO there may > in fact be something wrong in the BioPerl code here, too. > > However, I'm not that familiar with these modules, and I know there's been > some recent work done on them, so perhaps someone else can chime in here. > Dave is (as usual) right: $lca is a Node object. He's also right that the node $lca doesn't have an id. But I don't think this is a problem with BioPerl, but rather with how the newick tree in question is formatted. Specifically, the tree that Ross provided only has ids at the leaf nodes, which is why $lca->id() is returning an error (the internal node ids are thus undefined). Ross, you'll need to adopt the following format for your trees if you want to call internal node ids, at least as I understand how these BioPerl modules work. Instead of: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); Structure your newick trees like this: (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; ** The above trees are identical, with the exception that the internal nodes E and F have identifiers (names) associated with them. Does that make sense? You might check the wikipedia page for more information (http://en.wikipedia.org/wiki/Newick_format) and you can quickly view both of the above trees through the web-based tool PhyloWidget ( http://www.phylowidget.org) to get a better understanding of what I'm talking above. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 13:41:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 01:41:27 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Thanks Tom. This is the 2nd time you help me. Suppose I change the structure to: ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; I have identified two problems. 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? From kboggavarapu2 at uh.edu Sun Oct 2 13:40:53 2011 From: kboggavarapu2 at uh.edu (krishna mohan) Date: Sun, 2 Oct 2011 12:40:53 -0500 Subject: [Bioperl-l] extract fasta headers of genes Message-ID: hi, How to obtain FASTA headers of genes associated to particular genomen using eUtils and BIOPERL From angel at mpi-marburg.mpg.de Mon Oct 3 13:27:07 2011 From: angel at mpi-marburg.mpg.de (roey.angel) Date: Mon, 3 Oct 2011 10:27:07 -0700 (PDT) Subject: [Bioperl-l] saving amino acids sequence to file Message-ID: <32583843.post@talk.nabble.com> Hi, I'm trying to save the amino acid sequence from a sequence object I retrieved from GenBank. I can easily save the nucleotide sequence with: my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); $out_nuc -> write_seq($seq_object); And I also managed to extract the amino acid sequence with: for my $feat_object ($seq_object->get_SeqFeatures) { # obtain features from seq object if ($feat_object->primary_tag eq "CDS") { # look for CDS features if ($feat_object->has_tag('translation')) { # look for amino acids for my $val ($feat_object->get_tag_values('translation')){ } } } } But is there a way to save that sequence into a file using write_seq or a similar method? Thanks in advance, Roey -- View this message in context: http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From thomas.sharpton at gmail.com Mon Oct 3 14:24:32 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 11:24:32 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: Hi Ross, On Mon, Oct 3, 2011 at 10:41 AM, Ross KK Leung wrote: > Thanks Tom. This is the 2nd time you help me. > This list has been a vital resource for me, so I'm happy to contribute when I can. > Suppose I change the structure to:**** > > ** ** > > ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G;**** > > ** ** > > I have identified two problems.**** > > ** ** > > 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). > > Can you provide the code you are using and the result and error it produces in your next email? This will help diagnose the problem. > **** > > 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? **** > > Yes, this is unfortunate, but you can automate the labeling of internal node ids using something like the following: #$tree_in is a TreeIO object while( my $tree = $tree_in->next_tree() ){ my $id_basename = "intnode_"; my $id_count = 0; my @nodes = $tree->get_nodes(); foreach my $node( @nodes ){ next if $node->is_Leaf(); my $id = $node->id(); if( !(defined( $id ) ) ){ $id = $id_basename . $id_count; $node->id( $id ); $id_count++; } } #print the new tree or continue processing it } Now all of the nodes in the tree will have some identifier associated with it. I haven't tried the above code block so I can't verify that it works perfectly. One issue I foresee is that node ids will be added to the tree in the order in which they appear in @nodes; you will have to cross reference a tree to interpret your results. Others might have better solutions to this problem. Let me know if you have questions. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 21:53:29 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 09:53:29 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From cjfields at illinois.edu Mon Oct 3 22:23:28 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 4 Oct 2011 02:23:28 +0000 Subject: [Bioperl-l] extract fasta headers of genes In-Reply-To: References: Message-ID: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook -c On Oct 2, 2011, at 12:40 PM, krishna mohan wrote: > hi, > How to obtain FASTA headers of genes associated to > particular genomen using eUtils and BIOPERL > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jluis.lavin at unavarra.es Tue Oct 4 05:48:31 2011 From: jluis.lavin at unavarra.es (=?ISO-8859-1?Q?Jos=E9_Luis_Lav=EDn?=) Date: Tue, 4 Oct 2011 11:48:31 +0200 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: It seems that all installation atempts failed for Perl 5.10...I'll have to upgrade my Perl version unless there'd be another Graphical module in Bioperl tah any of you could recommend. 2011/9/30 Fields, Christopher J > It's available for all perl versions from 5.8.8 up. I have it running with > perl 5.14. Now, I recall there being problems with installation on Mac OS > X, though I think that was mainly due to GD.pm and libgd. > > chris > > On Sep 30, 2011, at 3:23 AM, > wrote: > > > > > Dear All, > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > windows machine. > > > > I read about the Bio-Graphics module and it'd be wonderful to install it, > > but seems like it is only available for Perl 5.8... > > Is there any other Perl and/or Bioperl module to do the same kind of > > genomic and Blast report representation currently available? > > > > Thanks in advance > > > > -- > > Dr. Jos? Luis Lav?n Trueba > > > > Dpto. de Producci?n Agraria > > Grupo de Gen?tica y Microbiolog?a > > Universidad P?blica de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -- Dr. Jos? Luis Lav?n Trueba Dpto. de Producci?n Agraria Grupo de Gen?tica y Microbiolog?a Universidad P?blica de Navarra 31006 Pamplona Navarra SPAIN From David.Messina at sbc.su.se Tue Oct 4 06:12:51 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 4 Oct 2011 12:12:51 +0200 Subject: [Bioperl-l] saving amino acids sequence to file In-Reply-To: References: <32583843.post@talk.nabble.com> Message-ID: [Sent this yesterday just to Roey by accident; reposting to the list now.] Hi Roey, >From the feature table, I think you can only get the amino acid sequence as a string. If you'd like to be able to use the SeqIO methods on it, you'll need to create a Bio::Seq object from it first. For examples, look at the 'To and From a String' section of the SeqIO HOWTO: http://www.bioperl.org/wiki/HOWTO:SeqIO But if you just want Fasta, plain ol' print statements are often sufficient. Dave On Mon, Oct 3, 2011 at 19:27, roey.angel wrote: > Hi, > >> I'm trying to save the amino acid sequence from a sequence object I > >> retrieved from GenBank. > >> I can easily save the nucleotide sequence with: > >> > my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); > >> $out_nuc -> write_seq($seq_object); > >> > And I also managed to extract the amino acid sequence with: > >> > for my $feat_object ($seq_object->get_SeqFeatures) { # obtain > >> features from seq object > >> if ($feat_object->primary_tag eq "CDS") { # look for CDS > >> features > >> if ($feat_object->has_tag('translation')) { # look for > >> amino acids > >> for my $val > >> ($feat_object->get_tag_values('translation')){ > >> } > >> } > >> } > >> } > >> > But is there a way to save that sequence into a file using write_seq or a > >> similar method? > >> > Thanks in advance, > >> Roey > -- > View this message in context: > http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lincoln.stein at gmail.com Tue Oct 4 07:51:49 2011 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 4 Oct 2011 07:51:49 -0400 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: Exactly what problems are you encountering? Are you using ActiveState Perl, and if so, at what step is the install failing? Lincoln 2011/10/4 Jos? Luis Lav?n > It seems that all installation atempts failed for Perl 5.10...I'll have to > upgrade my Perl version unless there'd be another Graphical module in > Bioperl tah any of you could recommend. > > 2011/9/30 Fields, Christopher J > > > It's available for all perl versions from 5.8.8 up. I have it running > with > > perl 5.14. Now, I recall there being problems with installation on Mac > OS > > X, though I think that was mainly due to GD.pm and libgd. > > > > chris > > > > On Sep 30, 2011, at 3:23 AM, > > wrote: > > > > > > > > Dear All, > > > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > > windows machine. > > > > > > I read about the Bio-Graphics module and it'd be wonderful to install > it, > > > but seems like it is only available for Perl 5.8... > > > Is there any other Perl and/or Bioperl module to do the same kind of > > > genomic and Blast report representation currently available? > > > > > > Thanks in advance > > > > > > -- > > > Dr. Jos? Luis Lav?n Trueba > > > > > > Dpto. de Producci?n Agraria > > > Grupo de Gen?tica y Microbiolog?a > > > Universidad P?blica de Navarra > > > 31006 Pamplona > > > Navarra > > > SPAIN > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From thomas.sharpton at gmail.com Tue Oct 4 14:05:27 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 11:05:27 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Message-ID: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > Hi, Tom. Let me formally define my problem because this would be > more effective for communication. My objective is to assign a state > for intermediate nodes. For the following example, nodes M and J can > be assigned with (Wing). After assignment (forget the unassigned > first), the pairwise distances of these intermediate nodes and any > other nodes may be compared (e.g. Nodes M and L; Nodes J and E). > > > +---I (Wing) > | > +---M > | | > | +---H (Wing) > | > +---O > | | > | | > | | > | +---L (No-Wing) > | > | > Z > | +---E (Wing) > | | > | +---K > | | | > | | +---D (No-Wing) > | | > +---N > | > | +---C (Wing) > | | > +---J > | > +---B (Wing) > > Technically, I can either use TreeFunctionsI's method add_trait to > the leaves first. Then I back trace the ancestral nodes. While nodes > K and J are pictorially displayed to be nicely at the same level, in > fact besides exhaustively testing NodeI's methods ancestor or > get_all_Descendants etc, I cannot come up with a better idea. As you > have mentioned before, when the tree is big, this curse is > amplified, not to say "Wing" is just one of several hundred > properties to test. > > That's why I'm posting this question to see whether any convenient > data structures already exist to tackle this kind of "graph- > traversing" process. From ross at cuhk.edu.hk Tue Oct 4 19:32:42 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 07:32:42 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Message-ID: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Hi Tom, I shall infer the state based on descendant's states. In my example, Nodes H and I belong to "Wing", then their ancestor M is also assigned "Wing". After assigning these states to all the nodes of the tree, I shall calculate the distances between these nodes. Switching to C is only the last option because that involves another 2 months, not to include the time if C does not have any libraries to deal with Newick Tree. Best, Ross From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] Sent: 2011??10??5?? 2:05 To: Ross KK Leung Cc: bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From R.A.Vos at reading.ac.uk Tue Oct 4 19:59:52 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 01:59:52 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 2:05 > To: Ross KK Leung > Cc: bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > > > > Hi Ross, > > > > I understand that you want to infer ancestral states on your tree, but I'm > unclear about how you want to do so. Can you clarify how you infer the state > for node K on your example tree? In particular, is your method of inference > dependent on the branch lengths? The answers to these questions will > (hopefully) help guide you to methods that can assist you. > > > > Unfortunately, Perl is not the most efficient language for tree/graph > traversal. It can certainly be done, but for very, very large trees, I tend > to roll over to C (but only if I have to as I am not proficient in C). > > > > Best, > > Tom > > > > On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > > > > > > Hi, Tom. Let me formally define my problem because this would be more > effective for communication. My objective is to assign a state for > intermediate nodes. For the following example, nodes M and J can be assigned > with (Wing). After assignment (forget the unassigned first), the pairwise > distances of these intermediate nodes and any other nodes may be compared > (e.g. Nodes M and L; Nodes J and E). > > > > > > +---I (Wing) > > | > > +---M > > | | > > | +---H (Wing) > > | > > +---O > > | | > > | | > > | | > > | +---L (No-Wing) > > | > > | > > Z > > | +---E (Wing) > > | | > > | +---K > > | | | > > | | +---D (No-Wing) > > | | > > +---N > > | > > | +---C (Wing) > > | | > > +---J > > | > > +---B (Wing) > > > > Technically, I can either use TreeFunctionsI's method add_trait to the > leaves first. Then I back trace the ancestral nodes. While nodes K and J are > pictorially displayed to be nicely at the same level, in fact besides > exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I > cannot come up with a better idea. As you have mentioned before, when the > tree is big, this curse is amplified, not to say "Wing" is just one of > several hundred properties to test. > > > > That's why I'm posting this question to see whether any convenient data > structures already exist to tackle this kind of "graph-traversing" process. > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 20:04:22 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 08:04:22 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: <002201cc82f2$565c2e40$03148ac0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:00 To: Ross KK Leung Cc: Thomas Sharpton; bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? I will assign "undetermined" and the detailed plan of assignment is too much to mention here. From R.A.Vos at reading.ac.uk Tue Oct 4 20:42:08 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 02:42:08 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002201cc82f2$565c2e40$03148ac0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. 2011/10/5 Ross KK Leung : > -----Original Message----- > From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger > Vos > Sent: 2011??10??5?? 8:00 > To: Ross KK Leung > Cc: Thomas Sharpton; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > >> I shall infer the state based on descendant's states. In my example, Nodes > H >> and I belong to "Wing", then their ancestor M is also assigned "Wing". > After >> assigning these states to all the nodes of the tree, I shall calculate the >> distances between these nodes. > > What is your approach for when internal states are equivocal? > > I will assign "undetermined" and the detailed plan of assignment is too much > to mention here. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 21:10:33 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 09:10:33 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:42 To: Ross KK Leung Cc: bioperl-l; Thomas Sharpton Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. Thanks, Rutger. While there is a convenient function to help calculate the distances between leaf nodes, I find it difficult for ancestors. After using get_lca, it seems that bioperl has no data structures to help manipulate these LCA's. From thomas.sharpton at gmail.com Tue Oct 4 21:43:38 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 18:43:38 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> Message-ID: Hi Ross, I think Rutger has given you a good idea and it is certainly simpler than the solution I just concocted (no surprise there). Regarding your most recent note: 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help calculate the > distances between leaf nodes, I find it difficult for ancestors. After > using > get_lca, it seems that bioperl has no data structures to help manipulate > these LCA's. > > >From what I understand, the get_lca does return a node object, specifically an internal node. The following is from the BioPerl documentation (note the "Returns" line): Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no common ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes You can get the distance between any two nodes, including an internal node, using the distance method. Note that the nodes you input into the distance function do not need to have ids associated with them. For example, #$nodeA and $nodeB are BioPerl node objects that correspond to any node on the tree my $lca = get_lca( $nodeA, $nodeB ); my $distance = distance( $nodeA, $lca ); $distance will now contain the total branch length between nodeA and the last common ancestor between nodes A and B. At no point are node ids used to conduct calculation; only the node objects themselves are needed. Anything that you can do to a node, you can do to $lca. This is how I understand the functions, at least. Someone please correct me if I'm wrong, as I fear I sound like a broken record at this point.... Best, Tom From thomas.sharpton at gmail.com Wed Oct 5 13:47:53 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Wed, 5 Oct 2011 10:47:53 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <004101cc836f$6a4a6250$3edf26f0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: Hi Ross, Let's keep this discussion on the listserv so that others can benefit from and contribute to it. I just executed your script using the tree you provided (for those following along, I have copied the script and tree below my signature). It produces no warnings or errors on my machine. Look below my signature to see the terminal output of this test run on my computer. Are you working with the latest version of bioperl? What version of perl are you using? I see that the warning (which is distinct from an error) that you are getting is: "MSG: At least some nodes do not have a branch length, the distance returned could be wrong" I also see in your newick tree that you have given the root node (node G) an ID, but no branch length. I'm thinking that you may have an old version of bioperl, which might bark at you when you have a root node with an id but no branch length. Note that the distances being printed in my output (which is not the distance between the node ids that precede the value printed, but instead the distance between the LCA of these node ids and the second of the two ids printed) are indeed correct. Can you provide information on the version of BioPerl and Perl that you are trying this on? Best, Tom ########## testtree.nwk ------------------ ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; ########## test.pl ----------------- use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } # next if( defined( $dist_matrix{$id1}->{$id2} ) || defined ( $dist_matrix{$id2}->{$id1} ) ); my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); #print "$leaf1 and $leaf2 distance: $distance\n"; # print "$id1 and $id2 distance: $distance\n"; #=pod print $id1; ; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); # print $lca->id; #; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; #=cut } } } ######### output --------------- [sharpton at kazushi ~]$perl test.pl test.nwk A B 0.2 A C 0.8 A D 0.9 B A 0.1 B C 0.8 B D 0.9 C A 0.4 C B 0.5 C D 0.4 D A 0.4 D B 0.5 D C 0.3 [sharpton at kazushi ~]$ On Oct 5, 2011, at 7:59 AM, Ross KK Leung wrote: > Hi Tom, > > I personally attach this program and tree files to you and see > whether you can run the program without any error (mine does, I > can't use Modern perl as I can't request the admin to install/update > anything).... > > Thanks a lot, Ross > > > > > > > > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 9:44 > To: Ross KK Leung > Cc: Rutger Vos; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other > nodes from a tree > > Hi Ross, > > I think Rutger has given you a good idea and it is certainly simpler > than the solution I just concocted (no surprise there). > > Regarding your most recent note: > > 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help > calculate the > distances between leaf nodes, I find it difficult for ancestors. > After using > get_lca, it seems that bioperl has no data structures to help > manipulate > these LCA's. > > > From what I understand, the get_lca does return a node object, > specifically an internal node. The following is from the BioPerl > documentation (note the "Returns" line): > > > > Title : get_lca > Usage : get_lca(-nodes => \@nodes ); OR > get_lca(@nodes); > Function: given two or more nodes, returns the lowest common > ancestor (aka most > recent common ancestor) > > > Returns : node object or undef if there is no common ancestor > Args : -nodes => arrayref of nodes to test, OR > just a list of nodes > > You can get the distance between any two nodes, including an > internal node, using the distance method. Note that the nodes you > input into the distance function do not need to have ids associated > with them. For example, > > #$nodeA and $nodeB are BioPerl node objects that correspond to any > node on the tree > my $lca = get_lca( $nodeA, $nodeB ); > my $distance = distance( $nodeA, $lca ); > > $distance will now contain the total branch length between nodeA and > the last common ancestor between nodes A and B. At no point are node > ids used to conduct calculation; only the node objects themselves > are needed. Anything that you can do to a node, you can do to $lca. > > This is how I understand the functions, at least. Someone please > correct me if I'm wrong, as I fear I sound like a broken record at > this point.... > > Best, > Tom > From ross at cuhk.edu.hk Thu Oct 6 03:07:11 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Thu, 6 Oct 2011 15:07:11 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: <006501cc83f6$91830ca0$b48925e0$@edu.hk> Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } From ross at cuhk.edu.hk Fri Oct 7 04:49:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 16:49:27 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <006501cc83f6$91830ca0$b48925e0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> Message-ID: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> each_Descendent documentation mentions "not a recursive fetchall" and I find out a method called "recursion" may solve my problem. the principle is to first force_binary, then start from root and go down along the tree until Is_Leaf, and then assign ancestor and continue the "recursion". -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ross KK Leung Sent: 2011??10??6?? 15:07 To: 'Thomas Sharpton' Cc: 'bioperl-l' Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From ross at cuhk.edu.hk Fri Oct 7 09:16:12 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 21:16:12 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> <00d b01cc84ce$0592d4e0$10b87ea0$@edu.hk> Message-ID: <00f601cc84f3$49406ca0$dbc145e0$@edu.hk> I use the following codes to test and find that the root node G is not assigned state "Opter". Moreover, I find that when a tree looks like this, +---I (Wing) | +---M | | | +---H (Wing) | O | | | +---L (No-Wing) L cannot match with internal node M as L is already a leaf node. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; system("cat $testtree"); my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf( @leaves ){ $leaf->add_tag_value("state", "Wing"); } $rootnode=$tree->get_root_node; Traverse($rootnode); @tmpnodes = $tree->get_nodes; foreach $prnnode (@tmpnodes) { $prnval = $prnnode->get_tag_values("state"); print $prnnode->id, "\t"; print $prnval, "\n"; } } sub Traverse { ($node) = @_; my $state = "dummy"; foreach my $desnode ( $node->each_Descendent() ) { if (!($desnode->is_Leaf)) { Traverse($desnode); } push @cmpnodes, $desnode; } #assume binary? if ($cmpnodes[0]->get_tag_values("state") eq $cmpnodes[1]->get_tag_values("state")) { # $node->add_tag_value("state", $cmpnodes[0]->get_tag_values("state")); $node->add_tag_value("state", "Opter"); } } __DATA__ ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; From maquino at knome.com Tue Oct 11 10:44:06 2011 From: maquino at knome.com (Mark Aquino) Date: Tue, 11 Oct 2011 10:44:06 -0400 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues Message-ID: Hi, I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. Code: #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -usehistory => 'y'); $esearch->get_Response || die; my @h_genes = $esearch->get_ids; print "@h_genes\n"; my $history = $esearch->next_History || die "elink failed"; my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -history => $history, -cmd => 'neighbor_history'); $elink->get_Response; my $hist1 = $elink->next_History; my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -history => $hist1, -cookie => $elink->next_cookie); $esum->get_Response || die "esum failed"; while (my $docsum = $esum->next_DocSum){ print $docsum->get_id,"\n"; print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; } [According to what I can find, the method get_Content_by_name should work but I am getting the error: Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From cjfields at illinois.edu Tue Oct 11 16:16:00 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 11 Oct 2011 20:16:00 +0000 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues In-Reply-To: References: Message-ID: <85FDDEF8-1522-4209-AA21-E51E436E6158@illinois.edu> Mark, Some odd things going on with homologen data, but I wanted to address a few points first. The code has a number of issues: * Missing email (warnings pop up). This will be required in future releases of Bio::DB::EUtilities, it's already technically required by NCBI * 'perldoc Bio::Tools::EUtilities::Summary::DocSum' indicates the method name is 'get_contents_by_name' (note lower-case and plural). As the name implies, it returns a list of raw data * Missing the elink databases. The history will capture the original queried database, but not the database linked to; the default on NCBI's end is pubmed when db is not set), which leads to... * The last EUtilities call is to 'pubmed', from the history. If you dump the docsum output (add a 'print $docsum->to_string) this is apparent. * Content key is wrong. Dumping the raw data initially is a good idea for debugging to ensure you are capturing the correct key. In this case, the key is 'TaxId' (note the case). * Calls to get_Response() are unnecessary; this just returns the HTTP::Response object from the user agent if you need the raw output. Calls to the eutilities-specific methods will lazily grab incoming data and parse as needed, so get_ids() alone will work as you would expect. Note the homologene data is hierarchical; there is more than one gene per linked ID, so the item data is nested. The tools are meant to be fairly generic, so you could just retrieve all the TaxID information, but it might be more relevant to get the GeneIDs to go along with them for more context. The following works for me. chris =================================================== #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -email => , -usehistory => 'y'); my @h_genes = $eutil->get_ids; print "@h_genes\n"; my $history = $eutil->next_History || die "esearch failed"; $eutil->reset_parameters(-eutil => 'elink', -history => $history, -email => , -db => 'homologene', -cmd => 'neighbor_history'); $history = $eutil->next_History || die "elink failed"; $eutil->reset_parameters(-eutil => 'esummary', -email => , -history => $history); while (my $docsum = $eutil->next_DocSum) { print "Homologen ID:".$docsum->get_id."\n"; print "Label: ".($docsum->get_contents_by_name('Caption'))[0]."\n"; while (my $item = $docsum->next_Item) { # HomoloGeneDataList while (my $sub = $item->next_subItem) { # HomoloGeneData print "\tGeneId: ".($sub->get_contents_by_name('GeneID'))[0]."\n"; print "\tTaxId: ".($sub->get_contents_by_name('TaxId'))[0]."\n"; } } } On Oct 11, 2011, at 9:44 AM, Mark Aquino wrote: > Hi, > > I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. > > Code: > > #!/usr/bin/perl > use strict; > use warnings; > use Bio::DB::EUtilities; > my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', > -db => 'homologene', > -term => 'Copg AND mouse', > -usehistory => 'y'); > $esearch->get_Response || die; > my @h_genes = $esearch->get_ids; > print "@h_genes\n"; > my $history = $esearch->next_History || die "elink failed"; > my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', > -history => $history, > -cmd => 'neighbor_history'); > > $elink->get_Response; > my $hist1 = $elink->next_History; > my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', > -history => $hist1, > -cookie => $elink->next_cookie); > $esum->get_Response || die "esum failed"; > while (my $docsum = $esum->next_DocSum){ > print $docsum->get_id,"\n"; > print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; > } > > [According to what I can find, the method get_Content_by_name should work but I am getting the error: > Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From manju.rawat2 at gmail.com Wed Oct 12 01:32:06 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Wed, 12 Oct 2011 11:02:06 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin In-Reply-To: References: Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.txt -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); it working fine in terminal with following command but showing error in programming.. agl at agl-desktop:~/BP$ blastall -p blastn -d btau -i test_query.fa -o test.out pl tell me what i am doing wrong. Thanks Manju Rawat From rajasimhah at nei.nih.gov Wed Oct 12 12:07:03 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 12:07:03 -0400 Subject: [Bioperl-l] Installation problem Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> I am trying to install Bioperl since yesterday without any luck. I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. I am attaching errors encountered during one such attempt below. Please help. root at comp1z BioPerl-1.6.1]# perl Build.PL This package requires Module::Build v0.2805 or greater to install itself. Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at (eval 2) line 1 BEGIN failed--compilation aborted at (eval 2) line 1. BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. Compilation failed in require at Build.PL line 14. BEGIN failed--compilation aborted at Build.PL line 14. I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). Please help!!! Harsha National Eye Institute, Bethesda, MD 301-402-5734 From cjfields at illinois.edu Wed Oct 12 15:37:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:37:35 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> Message-ID: Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Oct 12 15:41:05 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:41:05 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> Message-ID: <54A3917D-C212-4219-9C29-8285F3254EA5@illinois.edu> Possibly, though hard to say unless you give it a try. It does have a lot of bug fixes though. chris On Oct 12, 2011, at 2:38 PM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > No Christopher, I am trying the latest stable version 1.6.1 > Should I expect a smoother install with 1.6.901? > > Harsha > > ________________________________________ > From: Fields, Christopher J [cjfields at illinois.edu] > Sent: Wednesday, October 12, 2011 3:37 PM > To: Rajasimha, Harsha (NIH/NEI) [C] > Cc: bioperl-l at bioperl.org > Subject: Re: [Bioperl-l] Installation problem > > Have you tried the latest version from CPAN (v1.6.901)? > > chris > > On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > >> I am trying to install Bioperl since yesterday without any luck. >> I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. >> I am attaching errors encountered during one such attempt below. Please help. >> >> root at comp1z BioPerl-1.6.1]# perl Build.PL >> This package requires Module::Build v0.2805 or greater to install itself. >> Base class package "Module::Build" is empty. >> (Perhaps you need to 'use' the module which defines that package first.) >> at (eval 2) line 1 >> BEGIN failed--compilation aborted at (eval 2) line 1. >> BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. >> Compilation failed in require at Build.PL line 14. >> BEGIN failed--compilation aborted at Build.PL line 14. >> >> I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). >> >> Please help!!! >> Harsha >> National Eye Institute, Bethesda, MD >> 301-402-5734 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From rajasimhah at nei.nih.gov Wed Oct 12 15:38:43 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 15:38:43 -0400 Subject: [Bioperl-l] Installation problem In-Reply-To: References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> No Christopher, I am trying the latest stable version 1.6.1 Should I expect a smoother install with 1.6.901? Harsha ________________________________________ From: Fields, Christopher J [cjfields at illinois.edu] Sent: Wednesday, October 12, 2011 3:37 PM To: Rajasimha, Harsha (NIH/NEI) [C] Cc: bioperl-l at bioperl.org Subject: Re: [Bioperl-l] Installation problem Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 09:07:18 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 09:07:18 -0400 Subject: [Bioperl-l] Fwd: [bioperl-network] Not indexed by CPAN (#1) References: Message-ID: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> bioperl-l, It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. Brian O. Begin forwarded message: > From: "Chad A. Davis" > Date: October 13, 2011 7:40:27 AM EDT > To: bosborne > Subject: [bioperl-network] Not indexed by CPAN (#1) > > I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. > > This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi > > CPAN 1.9800 > > -- > Reply to this email directly or view it on GitHub: > https://github.com/bioperl/bioperl-network/issues/1 From cjfields at illinois.edu Thu Oct 13 11:47:33 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 15:47:33 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> Message-ID: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Brian, If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. chris On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > bioperl-l, > > It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. > > Brian O. > > Begin forwarded message: > >> From: "Chad A. Davis" >> Date: October 13, 2011 7:40:27 AM EDT >> To: bosborne >> Subject: [bioperl-network] Not indexed by CPAN (#1) >> >> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >> >> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >> >> CPAN 1.9800 >> >> -- >> Reply to this email directly or view it on GitHub: >> https://github.com/bioperl/bioperl-network/issues/1 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 11:52:55 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 11:52:55 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Message-ID: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Yes, BOSBORNE. On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > Brian, > > If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? > > It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. > > chris > > On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > >> bioperl-l, >> >> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >> >> Brian O. >> >> Begin forwarded message: >> >>> From: "Chad A. Davis" >>> Date: October 13, 2011 7:40:27 AM EDT >>> To: bosborne >>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>> >>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>> >>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>> >>> CPAN 1.9800 >>> >>> -- >>> Reply to this email directly or view it on GitHub: >>> https://github.com/bioperl/bioperl-network/issues/1 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Oct 13 13:03:49 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 17:03:49 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Message-ID: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. chris On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > Yes, BOSBORNE. > > On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > >> Brian, >> >> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >> >> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >> >> chris >> >> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >> >>> bioperl-l, >>> >>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>> >>> Brian O. >>> >>> Begin forwarded message: >>> >>>> From: "Chad A. Davis" >>>> Date: October 13, 2011 7:40:27 AM EDT >>>> To: bosborne >>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>> >>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>> >>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>> >>>> CPAN 1.9800 >>>> >>>> -- >>>> Reply to this email directly or view it on GitHub: >>>> https://github.com/bioperl/bioperl-network/issues/1 >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From bosborne11 at verizon.net Thu Oct 13 21:45:56 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 21:45:56 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> Message-ID: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Chris, OK, tell me what they say when you hear from them. BIO On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. > > chris > > On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > >> Yes, BOSBORNE. >> >> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >> >>> Brian, >>> >>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>> >>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>> >>> chris >>> >>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>> >>>> bioperl-l, >>>> >>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>> >>>> Brian O. >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Chad A. Davis" >>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>> To: bosborne >>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>> >>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>> >>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>> >>>>> CPAN 1.9800 >>>>> >>>>> -- >>>>> Reply to this email directly or view it on GitHub: >>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Fri Oct 14 08:48:19 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Fri, 14 Oct 2011 14:48:19 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: Because it may be related, I wanted to mention that I am having the same problem with Bioperl-Run. In this case, however, I can find the distribution via: i /bioperl-run/ But searching for a containing module does not return the distribution: i /clustalw/ Chad On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: > Chris, > > OK, tell me what they say when you hear from them. > > BIO > > > On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > >> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >> >> chris >> >> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >> >>> Yes, BOSBORNE. >>> >>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>> >>>> Brian, >>>> >>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>> >>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>> >>>>> bioperl-l, >>>>> >>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>> >>>>> Brian O. >>>>> >>>>> Begin forwarded message: >>>>> >>>>>> From: "Chad A. Davis" >>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>> To: bosborne >>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>> >>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>> >>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>> >>>>>> CPAN 1.9800 >>>>>> >>>>>> -- >>>>>> Reply to this email directly or view it on GitHub: >>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Fri Oct 14 09:34:22 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 14 Oct 2011 13:34:22 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). chris On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > Because it may be related, I wanted to mention that I am having the > same problem with Bioperl-Run. In this case, however, I can find the > distribution via: > > i /bioperl-run/ > > But searching for a containing module does not return the distribution: > > i /clustalw/ > > Chad > > On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >> Chris, >> >> OK, tell me what they say when you hear from them. >> >> BIO >> >> >> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >> >>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>> >>> chris >>> >>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>> >>>> Yes, BOSBORNE. >>>> >>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>> >>>>> Brian, >>>>> >>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>> >>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>> >>>>>> bioperl-l, >>>>>> >>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>> >>>>>> Brian O. >>>>>> >>>>>> Begin forwarded message: >>>>>> >>>>>>> From: "Chad A. Davis" >>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>> To: bosborne >>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>> >>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>> >>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>> >>>>>>> CPAN 1.9800 >>>>>>> >>>>>>> -- >>>>>>> Reply to this email directly or view it on GitHub: >>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Oct 16 23:12:59 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 03:12:59 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? chris On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). > > chris > > On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > >> Because it may be related, I wanted to mention that I am having the >> same problem with Bioperl-Run. In this case, however, I can find the >> distribution via: >> >> i /bioperl-run/ >> >> But searching for a containing module does not return the distribution: >> >> i /clustalw/ >> >> Chad >> >> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>> Chris, >>> >>> OK, tell me what they say when you hear from them. >>> >>> BIO >>> >>> >>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>> >>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>> >>>>> Yes, BOSBORNE. >>>>> >>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>> >>>>>> Brian, >>>>>> >>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>> >>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>> >>>>>>> bioperl-l, >>>>>>> >>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>> >>>>>>> Brian O. >>>>>>> >>>>>>> Begin forwarded message: >>>>>>> >>>>>>>> From: "Chad A. Davis" >>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>> To: bosborne >>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>> >>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>> >>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>> >>>>>>>> CPAN 1.9800 >>>>>>>> >>>>>>>> -- >>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 04:08:16 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 17 Oct 2011 10:08:16 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: The index looks good now, I'm able to get the bioperl-network distro by depending on a module within it. Would it be possible to do the same for a bioperl-run 1.6.901 release? Cheers, Chad On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J wrote: > This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. > > Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? > > chris > > On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > >> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >> >> chris >> >> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >> >>> Because it may be related, I wanted to mention that I am having the >>> same problem with Bioperl-Run. In this case, however, I can find the >>> distribution via: >>> >>> i /bioperl-run/ >>> >>> But searching for a containing module does not return the distribution: >>> >>> i /clustalw/ >>> >>> Chad >>> >>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>> Chris, >>>> >>>> OK, tell me what they say when you hear from them. >>>> >>>> BIO >>>> >>>> >>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>> >>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>> >>>>>> Yes, BOSBORNE. >>>>>> >>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>> >>>>>>> Brian, >>>>>>> >>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>> >>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> bioperl-l, >>>>>>>> >>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>> >>>>>>>> Brian O. >>>>>>>> >>>>>>>> Begin forwarded message: >>>>>>>> >>>>>>>>> From: "Chad A. Davis" >>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>> To: bosborne >>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>> >>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>> >>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>> >>>>>>>>> CPAN 1.9800 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Oct 17 14:02:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 18:02:35 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. chris On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > The index looks good now, I'm able to get the bioperl-network distro > by depending on a module within it. > Would it be possible to do the same for a bioperl-run 1.6.901 release? > > Cheers, > Chad > > > On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J > wrote: >> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >> >> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >> >> chris >> >> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >> >>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>> >>> chris >>> >>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>> >>>> Because it may be related, I wanted to mention that I am having the >>>> same problem with Bioperl-Run. In this case, however, I can find the >>>> distribution via: >>>> >>>> i /bioperl-run/ >>>> >>>> But searching for a containing module does not return the distribution: >>>> >>>> i /clustalw/ >>>> >>>> Chad >>>> >>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>> Chris, >>>>> >>>>> OK, tell me what they say when you hear from them. >>>>> >>>>> BIO >>>>> >>>>> >>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>> >>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>> >>>>>>> Yes, BOSBORNE. >>>>>>> >>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> Brian, >>>>>>>> >>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>> >>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> bioperl-l, >>>>>>>>> >>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>> >>>>>>>>> Brian O. >>>>>>>>> >>>>>>>>> Begin forwarded message: >>>>>>>>> >>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>> To: bosborne >>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>> >>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>> >>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>> >>>>>>>>>> CPAN 1.9800 >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioperl-l mailing list >>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Oct 17 15:40:26 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 19:40:26 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. chris On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. > > chris > > On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > >> The index looks good now, I'm able to get the bioperl-network distro >> by depending on a module within it. >> Would it be possible to do the same for a bioperl-run 1.6.901 release? >> >> Cheers, >> Chad >> >> >> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >> wrote: >>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>> >>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>> >>> chris >>> >>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>> >>>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>> >>>>> Because it may be related, I wanted to mention that I am having the >>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>> distribution via: >>>>> >>>>> i /bioperl-run/ >>>>> >>>>> But searching for a containing module does not return the distribution: >>>>> >>>>> i /clustalw/ >>>>> >>>>> Chad >>>>> >>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>> Chris, >>>>>> >>>>>> OK, tell me what they say when you hear from them. >>>>>> >>>>>> BIO >>>>>> >>>>>> >>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>> >>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> Yes, BOSBORNE. >>>>>>>> >>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>> >>>>>>>>> Brian, >>>>>>>>> >>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>>> >>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>>> >>>>>>>>> chris >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>> >>>>>>>>>> bioperl-l, >>>>>>>>>> >>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>> >>>>>>>>>> Brian O. >>>>>>>>>> >>>>>>>>>> Begin forwarded message: >>>>>>>>>> >>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>> To: bosborne >>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>> >>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>> >>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>> >>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioperl-l mailing list >>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 18:33:00 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Tue, 18 Oct 2011 00:33:00 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Chris, Looks good. I find Bioperl-Run by querying one of the contained modules now. Thank you for sorting that out. Chad On Mon, Oct 17, 2011 at 21:40, Fields, Christopher J wrote: > I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. ?It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. > > chris > > On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > >> Yes, I planned on that ?but wanted to make sure everything was working from your end. ? Will upload that in a bit. >> >> chris >> >> On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: >> >>> The index looks good now, I'm able to get the bioperl-network distro >>> by depending on a module within it. >>> Would it be possible to do the same for a bioperl-run 1.6.901 release? >>> >>> Cheers, >>> Chad >>> >>> >>> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >>> wrote: >>>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>>> >>>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>>> >>>>> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>>> >>>>> chris >>>>> >>>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>>> >>>>>> Because it may be related, I wanted to mention that I am having the >>>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>>> distribution via: >>>>>> >>>>>> i /bioperl-run/ >>>>>> >>>>>> But searching for a containing module does not return the distribution: >>>>>> >>>>>> i /clustalw/ >>>>>> >>>>>> Chad >>>>>> >>>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>>> Chris, >>>>>>> >>>>>>> OK, tell me what they say when you hear from them. >>>>>>> >>>>>>> BIO >>>>>>> >>>>>>> >>>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> Yes, BOSBORNE. >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>>> >>>>>>>>>> Brian, >>>>>>>>>> >>>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>>>>> >>>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>>>>> >>>>>>>>>> chris >>>>>>>>>> >>>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>>> >>>>>>>>>>> bioperl-l, >>>>>>>>>>> >>>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>>> >>>>>>>>>>> Brian O. >>>>>>>>>>> >>>>>>>>>>> Begin forwarded message: >>>>>>>>>>> >>>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>>> To: bosborne >>>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>>> >>>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>>> >>>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>>> >>>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioperl-l mailing list >>>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From saxen at lbl.gov Mon Oct 17 20:37:59 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Mon, 17 Oct 2011 17:37:59 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch Message-ID: Hello, I am having problems using the Bio::DB::EUtilities module to retrieve data from Entrez. The following script is adapted from the code at http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. The input is a file containing a very long list of GI numbers from NCBI protein. When I run the script, I receive the following error message: Can't locate object method "get_Response" via package "Bio::DB::EUtilities::efetch" at getGP.pl line 23. #!/usr/bin/perl -w use warnings; use strict; use Bio::DB::EUtilities; use Bio::SeqIO; use Data::Dumper; my $id_file = $ARGV[0]; my $temp_file = 'temp.gp'; my @ids; open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; @ids = ; close IDFILE; my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', -db => 'protein', -rettype => 'gb', -email => 'saxen at lbl.gov', -id => \@ids); # dump HTTP::Response content to a file (not retained in memory) $factory->get_Response(-file => $temp_file); my $seqin = Bio::SeqIO->new(-file => $temp_file, -format => 'genbank'); while (my $seq = $seqin->next_seq) { print Dumper($seq); } I would appreciate any insight as to why I am receiving this error. Thanks in advance for your time! Seth Axen From carandraug+dev at gmail.com Mon Oct 17 21:16:40 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Tue, 18 Oct 2011 02:16:40 +0100 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On 18 October 2011 01:37, Seth D. Axen wrote: > Hello, > ? I am having problems using the Bio::DB::EUtilities module to retrieve > data from Entrez. The following script is adapted from the code at > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. > The input is a file containing a very long list of GI numbers from NCBI > protein. When I run the script, I receive the following error message: Can't > locate object method "get_Response" via package > "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > > #!/usr/bin/perl -w > use warnings; > use strict; > use Bio::DB::EUtilities; > use Bio::SeqIO; > use Data::Dumper; > > my $id_file = $ARGV[0]; > my $temp_file = 'temp.gp'; > my @ids; > > open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > @ids = ; > close IDFILE; > > my $factory = Bio::DB::EUtilities->new(-eutil ? => 'efetch', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? ?=> 'protein', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -rettype => 'gb', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -email ? => 'saxen at lbl.gov', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ?=> \@ids); > > # dump HTTP::Response content to a file (not retained in memory) > $factory->get_Response(-file => $temp_file); > > my $seqin = Bio::SeqIO->new(-file ? => $temp_file, > ? ? ? ? ? ? ? ? ? ? ? ? ? ?-format => 'genbank'); > > while (my $seq = $seqin->next_seq) { > ? print Dumper($seq); > } > > ? I would appreciate any insight as to why I am receiving this error. > Thanks in advance for your time! > ? Seth Axen Hi your code works fine for me. Can the problem be on your IDs or its file? By the way, drop the -w from the shebang line, you are alredy using warnings. Carn? From cjfields at illinois.edu Mon Oct 17 21:33:13 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 01:33:13 +0000 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > On 18 October 2011 01:37, Seth D. Axen wrote: >> Hello, >> I am having problems using the Bio::DB::EUtilities module to retrieve >> data from Entrez. The following script is adapted from the code at >> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. >> The input is a file containing a very long list of GI numbers from NCBI >> protein. When I run the script, I receive the following error message: Can't >> locate object method "get_Response" via package >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. >> >> #!/usr/bin/perl -w >> use warnings; >> use strict; >> use Bio::DB::EUtilities; >> use Bio::SeqIO; >> use Data::Dumper; >> >> my $id_file = $ARGV[0]; >> my $temp_file = 'temp.gp'; >> my @ids; >> >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; >> @ids = ; >> close IDFILE; >> >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', >> -db => 'protein', >> -rettype => 'gb', >> -email => 'saxen at lbl.gov', >> -id => \@ids); >> >> # dump HTTP::Response content to a file (not retained in memory) >> $factory->get_Response(-file => $temp_file); >> >> my $seqin = Bio::SeqIO->new(-file => $temp_file, >> -format => 'genbank'); >> >> while (my $seq = $seqin->next_seq) { >> print Dumper($seq); >> } >> >> I would appreciate any insight as to why I am receiving this error. >> Thanks in advance for your time! >> Seth Axen > > Hi > > your code works fine for me. Can the problem be on your IDs or its > file? By the way, drop the -w from the shebang line, you are alredy > using warnings. > > Carn? Also, check the BioPerl version, there was a very large change in the API before the v1.6 release. chris From jeanmarc.frigerio at gmail.com Tue Oct 18 08:43:51 2011 From: jeanmarc.frigerio at gmail.com (jmf) Date: Tue, 18 Oct 2011 05:43:51 -0700 (PDT) Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> Message-ID: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Hi I agree that it'd be nice to see it revived. I made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', Thanks Dave for the topic ! Chris can you correct the file or should I submit the patch (I don't know where ?) On 2 sep, 17:20, Jack Tanner wrote: > I also see that someone's forked it on Github and made some packaging fixes. > > It'd be nice to see it revived. > > On 9/2/2011 9:00 AM, Fields, Christopher J wrote: > > > > > > > > > > > I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. ?Otherwise I worry about the long-term support for it/ > > > chris > > > On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: > > >> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: > >>http://toolkit.tuebingen.mpg.de/hhpred > > >> He got it working thus: > >> Hi Dave, > >> thanks a lot. i made it work. The error i got later on was: > >> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; > >> recompile with -fPIC > > >> the solution is: > >> perl Makefile.PL PREFIX= ?/fftwsingle --enable-shared --with-pic --enable-single > >> > >> make > >> make install > >>http://forums.fedoraforum.org/showthread.php?t=232607 > > >> Dave > > >> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J ?wrote: > >> Yes, it's essentially deprecated (unmaintained). ?I don't know of anyone who has packaged that up in a while, if ever. > > >> chris > > >> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: > > >>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? > > >>> Does anyone have a spec file for building an SRPM for it for RHEL 6? > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioper... at lists.open-bio.org > >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioper... at lists.open-bio.org > >>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l From sarah.tincher at gmail.com Tue Oct 18 13:00:46 2011 From: sarah.tincher at gmail.com (Sarah Tincher) Date: Tue, 18 Oct 2011 12:00:46 -0500 Subject: [Bioperl-l] Issues with CLUSTALW Message-ID: Hello, I am new to BioPerl and have no computer science background. I am taking a bioinformatics course and I have an assignment to write a BioPerl script to perform the MSA of a specific six sequences, retrieving the sequences from NCBI and using CLUSTALW. This is the script I wrote based on a lecture from my course: #!usr/bin/perl use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; $gb = new Bio::DB::GenBank(); $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); $factory = Bio::Tools::Run::Alignment::Clustalw->new; @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); print "$aln\n"; And this is the error that I receive: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level /Library/Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at HW3_2.pl line 3. BEGIN failed--compilation aborted at HW3_2.pl line 3. I would appreciate any help you can provide. Thank you, Sarah Tincher From cjfields at illinois.edu Tue Oct 18 14:35:08 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:08 +0000 Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Message-ID: <364EF42F-D067-40B5-9B92-7D36ED22B6E1@illinois.edu> A patch is fine. Also, it might be worth talking to the WUSTL group on merging those changes from their fork in (fairly easy to do). At some point, if this code looks as if it needs to exist independently of bioperl-ext we can create a new repo for it. I think it will see more use that way. chris On Oct 18, 2011, at 7:43 AM, jmf wrote: > Hi > I agree that it'd be nice to see it revived. I made a patch to the Bio/ > Ext/Align/Makefile.PL to make the compiler happy, just by changing: > > 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', > to > 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', > > Thanks Dave for the topic ! > > Chris can you correct the file or should I submit the patch (I don't > know where ?) > > On 2 sep, 17:20, Jack Tanner wrote: >> I also see that someone's forked it on Github and made some packaging fixes. >> >> It'd be nice to see it revived. >> >> On 9/2/2011 9:00 AM, Fields, Christopher J wrote: >> >> >> >> >> >> >> >> >> >>> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. Otherwise I worry about the long-term support for it/ >> >>> chris >> >>> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: >> >>>> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: >>>> http://toolkit.tuebingen.mpg.de/hhpred >> >>>> He got it working thus: >>>> Hi Dave, >>>> thanks a lot. i made it work. The error i got later on was: >>>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; >>>> recompile with -fPIC >> >>>> the solution is: >>>> perl Makefile.PL PREFIX= /fftwsingle --enable-shared --with-pic --enable-single >>>> >>>> make >>>> make install >>>> http://forums.fedoraforum.org/showthread.php?t=232607 >> >>>> Dave >> >>>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J wrote: >>>> Yes, it's essentially deprecated (unmaintained). I don't know of anyone who has packaged that up in a while, if ever. >> >>>> chris >> >>>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: >> >>>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? >> >>>>> Does anyone have a spec file for building an SRPM for it for RHEL 6? >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioper... at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioper... at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Oct 18 14:35:41 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:41 +0000 Subject: [Bioperl-l] Issues with CLUSTALW In-Reply-To: References: Message-ID: <54A57FF8-5415-4798-89B5-3E256ECDE636@illinois.edu> You need to install BioPerl-Run as well as the core BioPerl modules. chris On Oct 18, 2011, at 12:00 PM, Sarah Tincher wrote: > Hello, > > I am new to BioPerl and have no computer science background. I am taking a > bioinformatics course and I have an assignment to write a BioPerl script to > perform the MSA of a specific six sequences, retrieving the sequences from > NCBI and using CLUSTALW. > > This is the script I wrote based on a lecture from my course: > > #!usr/bin/perl > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > $gb = new Bio::DB::GenBank(); > $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); > $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); > $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); > $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); > $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); > $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); > $factory = Bio::Tools::Run::Alignment::Clustalw->new; > @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); > $seq_array_ref = \@seq_array; > $aln = $factory->align($seq_array_ref); > print "$aln\n"; > > And this is the error that I receive: > > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: > /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 > /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin > /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level > /Library/Perl/Updates/5.8.8 > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) > at HW3_2.pl line 3. > BEGIN failed--compilation aborted at HW3_2.pl line 3. > > I would appreciate any help you can provide. > > Thank you, > Sarah Tincher > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From saxen at lbl.gov Tue Oct 18 20:15:21 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Tue, 18 Oct 2011 17:15:21 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: Thanks Carne and Chris! The problem was with my BioPerl version. Once I used the latest version, the script ran perfectly. Seth 2011/10/17 Fields, Christopher J > On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > > > On 18 October 2011 01:37, Seth D. Axen wrote: > >> Hello, > >> I am having problems using the Bio::DB::EUtilities module to retrieve > >> data from Entrez. The following script is adapted from the code at > >> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO > . > >> The input is a file containing a very long list of GI numbers from NCBI > >> protein. When I run the script, I receive the following error message: > Can't > >> locate object method "get_Response" via package > >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > >> > >> #!/usr/bin/perl -w > >> use warnings; > >> use strict; > >> use Bio::DB::EUtilities; > >> use Bio::SeqIO; > >> use Data::Dumper; > >> > >> my $id_file = $ARGV[0]; > >> my $temp_file = 'temp.gp'; > >> my @ids; > >> > >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > >> @ids = ; > >> close IDFILE; > >> > >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', > >> -db => 'protein', > >> -rettype => 'gb', > >> -email => 'saxen at lbl.gov', > >> -id => \@ids); > >> > >> # dump HTTP::Response content to a file (not retained in memory) > >> $factory->get_Response(-file => $temp_file); > >> > >> my $seqin = Bio::SeqIO->new(-file => $temp_file, > >> -format => 'genbank'); > >> > >> while (my $seq = $seqin->next_seq) { > >> print Dumper($seq); > >> } > >> > >> I would appreciate any insight as to why I am receiving this error. > >> Thanks in advance for your time! > >> Seth Axen > > > > Hi > > > > your code works fine for me. Can the problem be on your IDs or its > > file? By the way, drop the -w from the shebang line, you are alredy > > using warnings. > > > > Carn? > > > Also, check the BioPerl version, there was a very large change in the API > before the v1.6 release. > > chris > > > > From shachigahoimbi at gmail.com Fri Oct 21 01:59:12 2011 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 21 Oct 2011 11:29:12 +0530 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl Message-ID: Dear all, I have fasta format sequence file and I want to extract ORF ID "PITG_14194" from fasta file and then I want to rename same file with that ORF ID "PITG_14194". I have many files and I want to do same exercise with all sequence files. Please tell me how can i do this with perl or bioperl. >tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR NGIAVDHKGVICNGKAPIEIAVDENTLSAAA -- Regards, Shachi From jason.stajich at gmail.com Fri Oct 21 05:56:11 2011 From: jason.stajich at gmail.com (Jason Stajich) Date: Fri, 21 Oct 2011 02:56:11 -0700 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl In-Reply-To: References: Message-ID: easy to do this with a simple regular expression and opening a new file. Have you read up on this concept in Perl. You can use SeqIO to parse FASTA files - did you read the HOWTO and website documentation first? We don't typically do people's work for them on this mailing list so please show some effort first. On Oct 20, 2011, at 10:59 PM, Shachi Gahoi wrote: > Dear all, > > I have fasta format sequence file and I want to extract ORF ID "PITG_14194" > from fasta file and then I want to rename same file with that ORF ID > "PITG_14194". > > I have many files and I want to do same exercise with all sequence files. > > Please tell me how can i do this with perl or bioperl. > >> tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora > infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 > MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL > ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA > RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF > HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM > YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL > TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD > RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR > NGIAVDHKGVICNGKAPIEIAVDENTLSAAA > > > -- > Regards, > Shachi > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Fri Oct 21 11:09:13 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 21 Oct 2011 11:09:13 -0400 Subject: [Bioperl-l] Deobfuscator direct link? Message-ID: Hi everybody, Does anyone object to me changing the center front-page link to the Deobfuscator to go directly to http://bioperl.org/cgi-bin/deob_interface.cgi ? That would still leave the left sidebar link that goes to the wiki page. Dave From cjfields at illinois.edu Fri Oct 21 12:31:45 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 21 Oct 2011 16:31:45 +0000 Subject: [Bioperl-l] Deobfuscator direct link? In-Reply-To: References: Message-ID: <2E2B401F-F358-48AD-880C-3FA9575D9B17@illinois.edu> Go for it. chris On Oct 21, 2011, at 10:09 AM, Dave Messina wrote: > Hi everybody, > > Does anyone object to me changing the center front-page link to the > Deobfuscator to go directly to > > http://bioperl.org/cgi-bin/deob_interface.cgi > > ? > > That would still leave the left sidebar link that goes to the wiki page. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From zheboyang at gmail.com Fri Oct 21 21:38:56 2011 From: zheboyang at gmail.com (boyang zhe) Date: Sat, 22 Oct 2011 03:38:56 +0200 Subject: [Bioperl-l] bioperl-ext installation Message-ID: I try to install bioperl-ext. But I failed. So I try the method suggested by JMF< jeanmarc.frigerio at gmail.com>. made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'' Then I run make. It seems ok for compilation. However, it generate errors when I run make test. No any of the 20 tests passed. it seems that because " Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so" I did not see any Align.so file at those directory. In fact, I can only find a blank directory of blib/arch/auto/Bio/Ext. Hope for your help. It is really hard for me. Thank you very much. boyang info as below: make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic.t .. ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.04 cusr 0.00 csys = 0.08 CPU) Result: PASS make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..20 not ok 1 - use Bio::Ext::Align; # Failed test 'use Bio::Ext::Align;' # at test.pl line 15. # Tried to use 'Bio::Ext::Align'. # Error: Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_access_name_CompMat at /usr/lib/perl/5.10/DynaLoader.pm line 193. # at (eval 4) line 2 # Compilation failed in require at (eval 4) line 2. # BEGIN failed--compilation aborted at (eval 4) line 2. The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed. Please install the bioperl-ext package # Looks like you planned 20 tests but ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test exited with 1 just after 1. make[1]: *** [test_dynamic] Error 1 make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make: *** [subdirs-test] Error 2 This is the info for make. cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h cp Bio/SeqIO/staden/CHANGES blib/lib/Bio/SeqIO/staden/CHANGES cp Bio/Ext/Align/test.pl blib/lib/Bio/Ext/Align/test.pl cp Bio/Ext/Align/libs/wiseoverlay.h blib/lib/Bio/Ext/Align/libs/wiseoverlay.h cp Bio/Ext/Align/libs/proteinsw.h blib/lib/Bio/Ext/Align/libs/proteinsw.h cp Bio/Ext/Align/libs/wisebase.h blib/lib/Bio/Ext/Align/libs/wisebase.h cp Bio/Ext/Align/libs/seqaligndisplay.h blib/lib/Bio/Ext/Align/libs/seqaligndisplay.h cp Bio/Ext/Align/libs/dyna.h blib/lib/Bio/Ext/Align/libs/dyna.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/complexsequence.c blib/lib/Bio/Ext/Align/libs/complexsequence.c cp Bio/Ext/Align/libs/wisestring.h blib/lib/Bio/Ext/Align/libs/wisestring.h cp Bio/Ext/Align/libs/codon.c blib/lib/Bio/Ext/Align/libs/codon.c cp Bio/Ext/Align/libs/linspc.c blib/lib/Bio/Ext/Align/libs/linspc.c cp Bio/Ext/Align/libs/probability.h blib/lib/Bio/Ext/Align/libs/probability.h cp Bio/Ext/Align/Align.xs blib/lib/Bio/Ext/Align/Align.xs cp Bio/SeqIO/staden/t/staden/data/readtest.exp blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.exp cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h cp Bio/Ext/Align/blosum45.mat blib/lib/Bio/Ext/Align/blosum45.mat cp Bio/Ext/Align/libs/dynlibcross.c blib/lib/Bio/Ext/Align/libs/dynlibcross.c cp Bio/Ext/Align/libs/sequencedb.c blib/lib/Bio/Ext/Align/libs/sequencedb.c cp Bio/Ext/Align/libs/sw_wrap.c blib/lib/Bio/Ext/Align/libs/sw_wrap.c cp Bio/Ext/Align/libs/complexsequence.h blib/lib/Bio/Ext/Align/libs/complexsequence.h cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h cp Bio/Ext/Align/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h cp Bio/SeqIO/staden/t/staden/data/readtestabi.fa blib/lib/Bio/SeqIO/staden/t/staden/data/readtestabi.fa cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/SeqIO/staden/t/staden/data/readtest.pln blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.pln cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.c cp Bio/Ext/Align/libs/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/alnrange.c blib/lib/Bio/Ext/Align/libs/alnrange.c cp Bio/Ext/Align/libs/dpenvelope.h blib/lib/Bio/Ext/Align/libs/dpenvelope.h cp Bio/Ext/Align/blosum62.mat blib/lib/Bio/Ext/Align/blosum62.mat cp Bio/Ext/Align/libs/sequence.h blib/lib/Bio/Ext/Align/libs/sequence.h cp Bio/Ext/Align/libs/asciibtcanvas.h blib/lib/Bio/Ext/Align/libs/asciibtcanvas.h cp Bio/Ext/Align/blosum50.mat blib/lib/Bio/Ext/Align/blosum50.mat cp Bio/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm cp Bio/SeqIO/staden/README blib/lib/Bio/SeqIO/staden/README cp Bio/SeqIO/staden/read.xs blib/lib/Bio/SeqIO/staden/read.xs cp Bio/SeqIO/staden/t/staden/data/readtest.abi blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.abi cp Bio/Ext/Align/libs/protein.h blib/lib/Bio/Ext/Align/libs/protein.h cp Bio/Ext/Align/libs/sequencedb.h blib/lib/Bio/Ext/Align/libs/sequencedb.h cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/SeqIO/staden/t/staden/data/readtestref.scf blib/lib/Bio/SeqIO/staden/t/staden/data/readtestref.scf cp Bio/SeqIO/staden/Makefile.PL blib/lib/Bio/SeqIO/staden/Makefile.PL cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c cp Bio/Ext/Align/libs/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/SeqIO/staden/META.yml blib/lib/Bio/SeqIO/staden/META.yml cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/libs/histogram.h blib/lib/Bio/Ext/Align/libs/histogram.h cp Bio/Ext/Align/libs/makefile blib/lib/Bio/Ext/Align/libs/makefile cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap cp Bio/Ext/Align/libs/proteindb.h blib/lib/Bio/Ext/Align/libs/proteindb.h cp Bio/Ext/Align/libs/btcanvas.c blib/lib/Bio/Ext/Align/libs/btcanvas.c cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/dpalign.h blib/lib/Bio/Ext/Align/libs/dpalign.h cp Bio/Ext/Align/libs/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c cp Bio/SeqIO/staden/MANIFEST blib/lib/Bio/SeqIO/staden/MANIFEST cp Bio/Ext/Align/libs/wiserandom.c blib/lib/Bio/Ext/Align/libs/wiserandom.c cp Bio/Ext/Align/libs/btcanvas.h blib/lib/Bio/Ext/Align/libs/btcanvas.h cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/SeqIO/staden/t/staden/data/readtest.ctf blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ctf cp Bio/SeqIO/staden/t/staden/data/readtest.ztr blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ztr cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h cp Bio/Ext/Align/libs/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c cp Bio/Ext/Align/libs/wisememman.c blib/lib/Bio/Ext/Align/libs/wisememman.c cp Bio/Ext/Align/libs/seqaligndisplay.c blib/lib/Bio/Ext/Align/libs/seqaligndisplay.c cp Bio/Ext/Align/libs/commandline.c blib/lib/Bio/Ext/Align/libs/commandline.c cp Bio/Ext/Align/libs/alnconvert.h blib/lib/Bio/Ext/Align/libs/alnconvert.h cp Bio/Ext/Align/libs/compmat.h blib/lib/Bio/Ext/Align/libs/compmat.h cp Bio/Ext/Align/libs/dna.h blib/lib/Bio/Ext/Align/libs/dna.h cp Bio/Ext/Align/libs/basematrix.c blib/lib/Bio/Ext/Align/libs/basematrix.c cp Bio/Ext/Align/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat cp Bio/Ext/Align/libs/aln.h blib/lib/Bio/Ext/Align/libs/aln.h cp Bio/Ext/Align/libs/sequence.c blib/lib/Bio/Ext/Align/libs/sequence.c cp Bio/Ext/Align/scores.lst blib/lib/Bio/Ext/Align/scores.lst cp Bio/Ext/Align/libs/wisememman.h blib/lib/Bio/Ext/Align/libs/wisememman.h cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c cp Bio/Ext/Align/libs/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h cp Bio/SeqIO/staden/t/staden_read.t blib/lib/Bio/SeqIO/staden/t/staden_read.t cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o aln.o aln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnconvert.o alnconvert.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnrange.o alnrange.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o asciibtcanvas.o asciibtcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o basematrix.o basematrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o btcanvas.o btcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o commandline.o commandline.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexconsensi.o complexconsensi.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexevalset.o complexevalset.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexsequence.o complexsequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o compmat.o compmat.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o codon.o codon.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dna.o dna.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dnamatrix.o dnamatrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpenvelope.o dpenvelope.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dynlibcross.o dynlibcross.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o histogram.o histogram.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o hscore.o hscore.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linesubs.o linesubs.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o packaln.o packaln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o probability.o probability.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o protein.o protein.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteindb.o proteindb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteinsw.o proteinsw.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o seqaligndisplay.o seqaligndisplay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequence.o sequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequencedb.o sequencedb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sw_wrap.o sw_wrap.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseerror.o wiseerror.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisefile.o wisefile.c wisefile.dy: In function ?bp_sw_myfclose?: wisefile.dy:66: warning: format ?%d? expects type ?int?, but argument 3 has type ?struct FILE *? cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisememman.o wisememman.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseoverlay.o wiseoverlay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiserandom.o wiserandom.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisestring.o wisestring.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisetime.o wisetime.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpalign.o dpalign.c dpalign.c: In function ?dpAlign_fatal?: dpalign.c:43: warning: format not a string literal and no format arguments cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o ar: creating libsw.a make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c cc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.6.0\" -DXS_VERSION=\"1.6.0\" -fPIC "-I/usr/lib/perl/5.10/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c cc -c -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.007000\" -DXS_VERSION=\"1.007000\" -fPIC "-I/usr/lib/perl/5.10/CORE" read.c read.xs: In function ?staden_write_trace?: read.xs:17: warning: cast to pointer from integer of different size read.xs:22: warning: cast to pointer from integer of different size read.xs: In function ?staden_read_graph?: read.xs:204: warning: passing argument 2 of ?Perl_newRV? from incompatible pointer type /usr/lib/perl/5.10/CORE/proto.h:2166: note: expected ?struct SV *? but argument is of type ?struct AV *? Running Mkbootstrap for Bio::SeqIO::staden::read () chmod 644 read.bs rm -f ../blib/arch/auto/Bio/SeqIO/staden/read/read.so LD_RUN_PATH="/usr/local/lib" cc -shared -O2 -g -L/usr/local/lib -fstack-protector read.o -o ../blib/arch/auto/Bio/SeqIO/staden/read/read.so \ -L/usr/local/lib -lz -lm -lread \ chmod 755 ../blib/arch/auto/Bio/SeqIO/staden/read/read.so cp read.bs ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs chmod 644 ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' Manifying blib/man3/Bio::SeqIO::staden::read.3pm From tzhu at mail.bnu.edu.cn Mon Oct 24 07:37:06 2011 From: tzhu at mail.bnu.edu.cn (Tao Zhu) Date: Mon, 24 Oct 2011 19:37:06 +0800 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document Message-ID: <4EA54DE2.1040706@mail.bnu.edu.cn> Here is a script copied totally from documents for module Bio::DB::GenBank, use Bio::DB::GenBank; my $gb = Bio::DB::GenBank->new(); my $seq_obj = $gb->get_Seq_by_acc('J00522'); When I try to run it, it failed. The message appear like this: > Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > Compilation failed in require at (eval 2) line 2. > ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > Compilation failed in require at perlprogram_2.pl line 5. > BEGIN failed--compilation aborted at perlprogram_2.pl line 5. I've never see such error before, how does this come? -- Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing 100875, China Email: tzhu at mail.bnu.edu.cn From cjfields at illinois.edu Mon Oct 24 09:07:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 13:07:56 +0000 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <4EA54DE2.1040706@mail.bnu.edu.cn> References: <4EA54DE2.1040706@mail.bnu.edu.cn> Message-ID: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> As might be implied by the error, you do not have URI::Escape installed, which is a dependency of Bio::DB::GenBank. chris On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > Here is a script copied totally from documents for module Bio::DB::GenBank, > > > use Bio::DB::GenBank; > my $gb = Bio::DB::GenBank->new(); > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > When I try to run it, it failed. The message appear like this: >> Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> Compilation failed in require at (eval 2) line 2. >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. >> Compilation failed in require at perlprogram_2.pl line 5. >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > I've never see such error before, how does this come? > > -- > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > 100875, China > Email: tzhu at mail.bnu.edu.cn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Mon Oct 24 11:10:39 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 16:10:39 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: > Hi, > I am having problems running Bio::Index::Fastq. ?I get the following error > when a quality line begins with '@'. > > ... > > Here is an example of a fastq record that is causing this error, The last > line which starts with an '@' ?is actually the qual line. > @5:105:15806:16092:Y > GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG > + > @9;A565:=8B? > > i see that chris has partially addressed this in the mailing list > http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html > > However as he pointed out at the time, it appears this may be a fairly large > problem. Have you double checked you have the latest BioPerl with that fix Chris mentioned? > My fastq seq and qual lines are alway only one line, so I think that adding > a line count and only checking for @ in the lines that $line_count%4 ==0 > ?would work since the header lines are always the first of 4 lines , 0,4,8, > etc. Yes, *if* you can assume that for your data, which is an assumption I wouldn't like to make a general purpose library like BioPerl (or Biopython) > BioPerl fastq parsing issues aside, is there another tool which allows you > to retrieve arbitrary sequences from a fastq file by sequence ID? > There's one called cdbfasta which looks like it might work ? does anyone > have experience with it? > > Thanks, > sofia > P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? > if so, perhaps their solution could be applied here. If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) or Bio.SeqIO.index_db (using SQLite) functions will give you random access by ID to assorted files including FASTQ, even with nasty line wrapping and quality lines starting with @ or +. The Biopython FASTQ indexer basically tracks the state: @ header, seq line(s), + line, or qual line(s). You pay a slight performance hit when building the index over assuming four lines per record, but it is robust to this kind of nasty data. Peter From cjfields at illinois.edu Mon Oct 24 12:10:38 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 16:10:38 +0000 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >> Hi, >> I am having problems running Bio::Index::Fastq. I get the following error >> when a quality line begins with '@'. >> >> ... >> >> Here is an example of a fastq record that is causing this error, The last >> line which starts with an '@' is actually the qual line. >> @5:105:15806:16092:Y >> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >> + >> @9;A565:=8B?> >> >> i see that chris has partially addressed this in the mailing list >> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >> >> However as he pointed out at the time, it appears this may be a fairly large >> problem. > > Have you double checked you have the latest BioPerl with that > fix Chris mentioned? This should be fixed in both CPAN and bioperl-live. If not let me know. >> My fastq seq and qual lines are alway only one line, so I think that adding >> a line count and only checking for @ in the lines that $line_count%4 ==0 >> would work since the header lines are always the first of 4 lines , 0,4,8, >> etc. > > Yes, *if* you can assume that for your data, which is an assumption I > wouldn't like to make a general purpose library like BioPerl (or Biopython) One could build in an optimization that takes this assumption into account when explicitly requested, something worth looking into. A lot of our short read pipelines use the 4-line format. >> BioPerl fastq parsing issues aside, is there another tool which allows you >> to retrieve arbitrary sequences from a fastq file by sequence ID? >> There's one called cdbfasta which looks like it might work ? does anyone >> have experience with it? >> >> Thanks, >> sofia >> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >> if so, perhaps their solution could be applied here. > > If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) > or Bio.SeqIO.index_db (using SQLite) functions will give you random > access by ID to assorted files including FASTQ, even with nasty line > wrapping and quality lines starting with @ or +. > > The Biopython FASTQ indexer basically tracks the state: @ header, seq > line(s), + line, or qual line(s). You pay a slight performance hit when > building the index over assuming four lines per record, but it is robust > to this kind of nasty data. > > Peter We should really look into a consistent OBDA-like indexing scheme that could work cross-Bio*. Or simply resuscitate OBDA. :) chris From p.j.a.cock at googlemail.com Mon Oct 24 12:17:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 17:17:18 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 5:10 PM, Fields, Christopher J wrote: > On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > >> On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >>> Hi, >>> I am having problems running Bio::Index::Fastq. ?I get the following error >>> when a quality line begins with '@'. >>> >>> ... >>> >>> Here is an example of a fastq record that is causing this error, The last >>> line which starts with an '@' ?is actually the qual line. >>> @5:105:15806:16092:Y >>> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >>> + >>> @9;A565:=8B?>> >>> >>> i see that chris has partially addressed this in the mailing list >>> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >>> >>> However as he pointed out at the time, it appears this may be a fairly large >>> problem. >> >> Have you double checked you have the latest BioPerl with that >> fix Chris mentioned? > > This should be fixed in both CPAN and bioperl-live. ?If not let me know. Good. >>> My fastq seq and qual lines are alway only one line, so I think that adding >>> a line count and only checking for @ in the lines that $line_count%4 ==0 >>> ?would work since the header lines are always the first of 4 lines , 0,4,8, >>> etc. >> >> Yes, *if* you can assume that for your data, which is an assumption I >> wouldn't like to make a general purpose library like BioPerl (or Biopython) > > One could build in an optimization that takes this assumption into account > when explicitly requested, something worth looking into. ?A lot of our short > read pipelines use the 4-line format. That's a sensible compromise. >>> BioPerl fastq parsing issues aside, is there another tool which allows you >>> to retrieve arbitrary sequences from a fastq file by sequence ID? >>> There's one called cdbfasta which looks like it might work ? does anyone >>> have experience with it? >>> >>> Thanks, >>> sofia >>> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >>> if so, perhaps their solution could be applied here. >> >> If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) >> or Bio.SeqIO.index_db (using SQLite) functions will give you random >> access by ID to assorted files including FASTQ, even with nasty line >> wrapping and quality lines starting with @ or +. >> >> The Biopython FASTQ indexer basically tracks the state: @ header, seq >> line(s), + line, or qual line(s). You pay a slight performance hit when >> building the index over assuming four lines per record, but it is robust >> to this kind of nasty data. >> >> Peter > > We should really look into a consistent OBDA-like indexing scheme > that could work cross-Bio*. ?Or simply resuscitate OBDA. :) > > chris +1 Our SQLite index is based on OBDA but replacing the BDB / flat file index with SQLite3. Also we're using the Biopython SeqIO format names which don't 100% align with BioPerl/EMBOSS/etc. Peter From chiragmatkarbioinfo at gmail.com Mon Oct 24 12:38:24 2011 From: chiragmatkarbioinfo at gmail.com (Chirag Matkar) Date: Mon, 24 Oct 2011 22:08:24 +0530 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> References: <4EA54DE2.1040706@mail.bnu.edu.cn> <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> Message-ID: Tao, You can install URI::Escape through CPAN. On Mon, Oct 24, 2011 at 6:37 PM, Fields, Christopher J < cjfields at illinois.edu> wrote: > As might be implied by the error, you do not have URI::Escape installed, > which is a dependency of Bio::DB::GenBank. > > chris > > On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > > > Here is a script copied totally from documents for module > Bio::DB::GenBank, > > > > > > use Bio::DB::GenBank; > > my $gb = Bio::DB::GenBank->new(); > > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > > > When I try to run it, it failed. The message appear like this: > >> Can't locate URI/Escape.pm in @INC (@INC contains: > /home/zhut/bin/PerlModule > /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux > /home/zhut/localperl/lib/site_perl/5.12.3 > /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 > .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> Compilation failed in require at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> Compilation failed in require at (eval 2) line 2. > >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > >> Compilation failed in require at perlprogram_2.pl line 5. > >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > > > I've never see such error before, how does this come? > > > > -- > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > > 100875, China > > Email: tzhu at mail.bnu.edu.cn > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Regards, Chirag From carandraug+dev at gmail.com Mon Oct 31 14:05:35 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Mon, 31 Oct 2011 18:05:35 +0000 Subject: [Bioperl-l] best way to edit sequence features In-Reply-To: References: Message-ID: Hi I've been planning on writing a free (as in freedom) tool to edit sequences and make plamids maps. The idea is to build the command line tool first and maybe later work on a GUI for it. The problem I foresee at the moment while designing it, is how to change a feature of the sequence. I'm not familiar with all sequence formats (only fasta, ensembl and genbank) but I can't see how to specify from the command line what feature to edit since I can't see any unique identifiers for them. Is there a file format that makes this easier? Any tips would be most appreciated. Thank in advance, Carn? Draug From gkuffel22 at gmail.com Thu Oct 20 18:58:07 2011 From: gkuffel22 at gmail.com (Gina) Date: Thu, 20 Oct 2011 15:58:07 -0700 (PDT) Subject: [Bioperl-l] Scripts for the Gene Ontology Database (GO) Message-ID: Is there anyway to use Bioperl to take an accession number of a gene and retrieve gene function information from the GO database? I have tried go-perl but it is not easy to use and doesn't work correctly on windows 7. Thanks for any information and ideas? From sofia2341 at gmail.com Mon Oct 24 10:58:13 2011 From: sofia2341 at gmail.com (Sofia Robb) Date: Mon, 24 Oct 2011 10:58:13 -0400 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual Message-ID: Hi, I am having problems running Bio::Index::Fastq. I get the following error when a quality line begins with '@'. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No description line parsed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368 STACK: Bio::SeqIO::fastq::next_dataset /usr/share/perl5/Bio/SeqIO/fastq.pm:71 STACK: Bio::SeqIO::fastq::next_seq /usr/share/perl5/Bio/SeqIO/fastq.pm:29 STACK: Bio::Index::AbstractSeq::fetch /usr/share/perl5/Bio/Index/AbstractSeq.pm:147 STACK: Bio::Index::AbstractSeq::get_Seq_by_id /usr/share/perl5/Bio/Index/AbstractSeq.pm:198 STACK: /home_stajichlab/robb/bin/clean_pairs_indexed.pl:68 Here is an example of a fastq record that is causing this error, The last line which starts with an '@' is actually the qual line. @5:105:15806:16092:Y GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG + @9;A565:=8B?) { if (/^@/ and $line_count % 4 == 0) { # $begin is the position of the first character after the '@' my $begin = tell($FASTQ) - length( $_ ) + 1; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); $c++; } } $line_count++; } -- BioPerl fastq parsing issues aside, is there another tool which allows you to retrieve arbitrary sequences from a fastq file by sequence ID? There's one called cdbfasta which looks like it might work ? does anyone have experience with it? Thanks, sofia P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? if so, perhaps their solution could be applied here. From rispoli at tigem.it Mon Oct 31 13:19:41 2011 From: rispoli at tigem.it (Rispoli Rossella) Date: Mon, 31 Oct 2011 18:19:41 +0100 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Message-ID: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ---------------------------------------------------------------------------- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ----------------------------------------------------------------------------- From Kevin.M.Brown at asu.edu Mon Oct 31 14:25:40 2011 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 31 Oct 2011 11:25:40 -0700 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro In-Reply-To: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> References: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Message-ID: <1A4207F8295607498283FE9E93B775B407F48285@EX02.asurite.ad.asu.edu> http://search.cpan.org/~cjfields/BioPerl/Bio/DB/TFBS/transfac_pro.pm Did you read the module documentation? -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Rispoli Rossella Sent: Monday, October 31, 2011 10:20 AM To: bioperl-l at bioperl.org Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ------------------------------------------------------------------------ ---- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ------------------------------------------------------------------------ ----- _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From manju.rawat2 at gmail.com Sat Oct 1 03:07:48 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Sat, 1 Oct 2011 12:37:48 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.fa -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau.fa','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); pl tell me what i am doing wrong. Thanks Manju Rawat From Russell.Smithies at agresearch.co.nz Sun Oct 2 19:27:22 2011 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 3 Oct 2011 12:27:22 +1300 Subject: [Bioperl-l] how to blast a seq against multiple dbase In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF33C15FA8623@exchsth.agresearch.co.nz> Did you try this? database => 'Chr1.db,Chr2.db,Chr3.db' Blast supports comma-separated database names so thin might have made it into BioPerl. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peter Cock > Sent: Wednesday, 28 September 2011 11:02 p.m. > To: Manju Rawat > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] how to blast a seq against multiple dbase > > On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat > wrote: > > Hello, > > > > I have downloaded all the chromosome of Bos Taurus and i'd changed > > them in blast format using makeblastdb..and now i want to localy blast > > my sequence against these all chromosome.. > > now i have 29 database.Is there any method by which can i blast my > > sequence against all 29 database in my program.. > > > > > > whta should i write in database???? > > > > @params = ('database' => '????????', 'outfile' => 'blast2.out', > > ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn'); > > > > The simple answer is make a combined database. This works internally with > alias files, have a look at the NR and NT databases for example - they act like > singe databases but are actually a collection of chunks. > > Even simpler would be to combine your Bos taurus sequence files into a > single multi-entry FASTA file, and make that into a single BLAST database. > > Peter > > _______________________________________________ > 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. ======================================================================= From ross at cuhk.edu.hk Mon Oct 3 00:19:52 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 12:19:52 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> Message-ID: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And from NodeI documentation, I cannot identify a way to make a Node object to a NodeI object. By the same token, methods like is_monophyletic or is_paraphyletic are also unable to work on LCA's. Web search does not return any examples about the manipulation of the LCA. Any hints would be highly appreciated so I can continue to dig out the remaining on my own. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; #or by the following _DATA_ my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); } print "$leaf1:LCA:$lca:ACL:$leaf2"; ; #print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } #_DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 00); From David.Messina at sbc.su.se Mon Oct 3 05:17:47 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 11:17:47 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: Hi Ross, Bio::Tree::Node is a NodeI object. It inherits ? or, more accurately, implements ? all of the methods in NodeI. Admittedly, it's a little obscure. The modules ending in 'I' ? the 'I' stands for Interface ? are never meant to be called directly. Rather, they define the methods that other modules, which are called directly, like Bio::Tree::Node, must have in order to be compliant with the Bio::Tree::NodeI interface. If you look at the code for NodeI, you'll that there are only a very few methods actually coded in there; most of them are simply empty placeholders. You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? Dave On Mon, Oct 3, 2011 at 06:19, Ross KK Leung wrote: > The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And > from NodeI documentation, I cannot identify a way to make a Node object to > a > NodeI object. By the same token, methods like is_monophyletic or > is_paraphyletic are also unable to work on LCA's. Web search does not > return > any examples about the manipulation of the LCA. Any hints would be highly > appreciated so I can continue to dig out the remaining on my own. > > > > use Bio::TreeIO; > > use Bio::Tree::TreeFunctionsI; > > > > $tab = "\t"; $nl = "\n"; > > my ($testtree) = @ARGV; #or by the following _DATA_ > > my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); > > while( my $tree = $treein->next_tree ){ > > %dist_matrix = (); > > > > my @leaves = $tree->get_leaf_nodes; > > foreach my $leaf1( @leaves ){ > > my $id1 = $leaf1->id; > > foreach my $leaf2( @leaves ){ > > my $id2 = $leaf2->id; > > if ($id1 eq $id2) { > > $dist_matrix{$id1}->{$id2} = 0; > > next; > > } > > my $distance = $tree->distance( -nodes => [$leaf1, > $leaf2] ); > > if ($id1 eq "A" and $id2 eq "B") { > > my $lca = $tree->get_lca(-nodes => [$leaf1, > $leaf2] ); > > } > > print "$leaf1:LCA:$lca:ACL:$leaf2"; ; > > #print $lca->id; ; > > my $distance2 = $tree->distance( -nodes => [$lca, > $leaf2] ); > > print $distance2; ; > > > > $dist_matrix{$id1}->{$id2} = $distance; > > } > > } > > } > > > > #_DATA_ > > > ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 > > 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 > > 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( > > L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 > > .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, > > (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 > > ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 > 00); > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ross at cuhk.edu.hk Mon Oct 3 06:28:38 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 18:28:38 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Dave wrote: >You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design Thanks for this reference, it is very good for me to understand better the architecture of Bioperl. >So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? But the following codes will generate errors because lca cannot be identified. my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; my $distance = $tree->distance( -nodes => [$leaf1,$leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1,$leaf2] ); } print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca,$leaf2] ); print $distance2; ; } } } _DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.00000000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.00000000); My ultimate goal is just to conveniently derive the information that nodes M and L share the same LCA O for the following tree. +---I | +---M | | | +---H | +---O | | | | +---G | | | | +---L | | | +---F A | +---E | | | +---K | | | | | +---D | | +---N | | +---C | | +---J | +---B From David.Messina at sbc.su.se Mon Oct 3 07:28:41 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 13:28:41 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: Hi Ross, >So, if I understand your question correctly, you should be able to use all > of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit > confused, is_monophyletic is something you'd call on a Tree object, not on a > Node object, right?**** > > But the following codes will generate errors because lca cannot be > identified. > Right, but there are some compile-time errors in your code. I changed a few things so I could get it to run: http://cl.ly/AdzH In my hands, there is a Node object returned as $lca. However, it doesn't have an id so the next line where you try to print $lca->id, I get an undefined value error. When I look at $lca, it doesn't seems to be equivalent to node C, which, based on the tree you supplied, I would expect to be the LCA. SO there may in fact be something wrong in the BioPerl code here, too. However, I'm not that familiar with these modules, and I know there's been some recent work done on them, so perhaps someone else can chime in here. **** > > My ultimate goal is just to conveniently derive the information that nodes > M and L share the same LCA O for the following tree. > Ok, thanks for that clarification. I think the code should be able to do that. Incidentally, the tree you provided in Newick format does not appear to me to be the same tree you drew as ASCII art ? is that right? Dave From thomas.sharpton at gmail.com Mon Oct 3 10:35:33 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 07:35:33 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: On Mon, Oct 3, 2011 at 4:28 AM, Dave Messina wrote: In my hands, there is a Node object returned as $lca. However, it doesn't > have an id so the next line where you try to print $lca->id, I get an > undefined value error. > > When I look at $lca, it doesn't seems to be equivalent to node C, which, > based on the tree you supplied, I would expect to be the LCA. SO there may > in fact be something wrong in the BioPerl code here, too. > > However, I'm not that familiar with these modules, and I know there's been > some recent work done on them, so perhaps someone else can chime in here. > Dave is (as usual) right: $lca is a Node object. He's also right that the node $lca doesn't have an id. But I don't think this is a problem with BioPerl, but rather with how the newick tree in question is formatted. Specifically, the tree that Ross provided only has ids at the leaf nodes, which is why $lca->id() is returning an error (the internal node ids are thus undefined). Ross, you'll need to adopt the following format for your trees if you want to call internal node ids, at least as I understand how these BioPerl modules work. Instead of: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); Structure your newick trees like this: (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; ** The above trees are identical, with the exception that the internal nodes E and F have identifiers (names) associated with them. Does that make sense? You might check the wikipedia page for more information (http://en.wikipedia.org/wiki/Newick_format) and you can quickly view both of the above trees through the web-based tool PhyloWidget ( http://www.phylowidget.org) to get a better understanding of what I'm talking above. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 13:41:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 01:41:27 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Thanks Tom. This is the 2nd time you help me. Suppose I change the structure to: ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; I have identified two problems. 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? From kboggavarapu2 at uh.edu Sun Oct 2 13:40:53 2011 From: kboggavarapu2 at uh.edu (krishna mohan) Date: Sun, 2 Oct 2011 12:40:53 -0500 Subject: [Bioperl-l] extract fasta headers of genes Message-ID: hi, How to obtain FASTA headers of genes associated to particular genomen using eUtils and BIOPERL From angel at mpi-marburg.mpg.de Mon Oct 3 13:27:07 2011 From: angel at mpi-marburg.mpg.de (roey.angel) Date: Mon, 3 Oct 2011 10:27:07 -0700 (PDT) Subject: [Bioperl-l] saving amino acids sequence to file Message-ID: <32583843.post@talk.nabble.com> Hi, I'm trying to save the amino acid sequence from a sequence object I retrieved from GenBank. I can easily save the nucleotide sequence with: my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); $out_nuc -> write_seq($seq_object); And I also managed to extract the amino acid sequence with: for my $feat_object ($seq_object->get_SeqFeatures) { # obtain features from seq object if ($feat_object->primary_tag eq "CDS") { # look for CDS features if ($feat_object->has_tag('translation')) { # look for amino acids for my $val ($feat_object->get_tag_values('translation')){ } } } } But is there a way to save that sequence into a file using write_seq or a similar method? Thanks in advance, Roey -- View this message in context: http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From thomas.sharpton at gmail.com Mon Oct 3 14:24:32 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 11:24:32 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: Hi Ross, On Mon, Oct 3, 2011 at 10:41 AM, Ross KK Leung wrote: > Thanks Tom. This is the 2nd time you help me. > This list has been a vital resource for me, so I'm happy to contribute when I can. > Suppose I change the structure to:**** > > ** ** > > ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G;**** > > ** ** > > I have identified two problems.**** > > ** ** > > 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). > > Can you provide the code you are using and the result and error it produces in your next email? This will help diagnose the problem. > **** > > 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? **** > > Yes, this is unfortunate, but you can automate the labeling of internal node ids using something like the following: #$tree_in is a TreeIO object while( my $tree = $tree_in->next_tree() ){ my $id_basename = "intnode_"; my $id_count = 0; my @nodes = $tree->get_nodes(); foreach my $node( @nodes ){ next if $node->is_Leaf(); my $id = $node->id(); if( !(defined( $id ) ) ){ $id = $id_basename . $id_count; $node->id( $id ); $id_count++; } } #print the new tree or continue processing it } Now all of the nodes in the tree will have some identifier associated with it. I haven't tried the above code block so I can't verify that it works perfectly. One issue I foresee is that node ids will be added to the tree in the order in which they appear in @nodes; you will have to cross reference a tree to interpret your results. Others might have better solutions to this problem. Let me know if you have questions. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 21:53:29 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 09:53:29 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From cjfields at illinois.edu Mon Oct 3 22:23:28 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 4 Oct 2011 02:23:28 +0000 Subject: [Bioperl-l] extract fasta headers of genes In-Reply-To: References: Message-ID: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook -c On Oct 2, 2011, at 12:40 PM, krishna mohan wrote: > hi, > How to obtain FASTA headers of genes associated to > particular genomen using eUtils and BIOPERL > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jluis.lavin at unavarra.es Tue Oct 4 05:48:31 2011 From: jluis.lavin at unavarra.es (=?ISO-8859-1?Q?Jos=E9_Luis_Lav=EDn?=) Date: Tue, 4 Oct 2011 11:48:31 +0200 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: It seems that all installation atempts failed for Perl 5.10...I'll have to upgrade my Perl version unless there'd be another Graphical module in Bioperl tah any of you could recommend. 2011/9/30 Fields, Christopher J > It's available for all perl versions from 5.8.8 up. I have it running with > perl 5.14. Now, I recall there being problems with installation on Mac OS > X, though I think that was mainly due to GD.pm and libgd. > > chris > > On Sep 30, 2011, at 3:23 AM, > wrote: > > > > > Dear All, > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > windows machine. > > > > I read about the Bio-Graphics module and it'd be wonderful to install it, > > but seems like it is only available for Perl 5.8... > > Is there any other Perl and/or Bioperl module to do the same kind of > > genomic and Blast report representation currently available? > > > > Thanks in advance > > > > -- > > Dr. Jos? Luis Lav?n Trueba > > > > Dpto. de Producci?n Agraria > > Grupo de Gen?tica y Microbiolog?a > > Universidad P?blica de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -- Dr. Jos? Luis Lav?n Trueba Dpto. de Producci?n Agraria Grupo de Gen?tica y Microbiolog?a Universidad P?blica de Navarra 31006 Pamplona Navarra SPAIN From David.Messina at sbc.su.se Tue Oct 4 06:12:51 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 4 Oct 2011 12:12:51 +0200 Subject: [Bioperl-l] saving amino acids sequence to file In-Reply-To: References: <32583843.post@talk.nabble.com> Message-ID: [Sent this yesterday just to Roey by accident; reposting to the list now.] Hi Roey, >From the feature table, I think you can only get the amino acid sequence as a string. If you'd like to be able to use the SeqIO methods on it, you'll need to create a Bio::Seq object from it first. For examples, look at the 'To and From a String' section of the SeqIO HOWTO: http://www.bioperl.org/wiki/HOWTO:SeqIO But if you just want Fasta, plain ol' print statements are often sufficient. Dave On Mon, Oct 3, 2011 at 19:27, roey.angel wrote: > Hi, > >> I'm trying to save the amino acid sequence from a sequence object I > >> retrieved from GenBank. > >> I can easily save the nucleotide sequence with: > >> > my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); > >> $out_nuc -> write_seq($seq_object); > >> > And I also managed to extract the amino acid sequence with: > >> > for my $feat_object ($seq_object->get_SeqFeatures) { # obtain > >> features from seq object > >> if ($feat_object->primary_tag eq "CDS") { # look for CDS > >> features > >> if ($feat_object->has_tag('translation')) { # look for > >> amino acids > >> for my $val > >> ($feat_object->get_tag_values('translation')){ > >> } > >> } > >> } > >> } > >> > But is there a way to save that sequence into a file using write_seq or a > >> similar method? > >> > Thanks in advance, > >> Roey > -- > View this message in context: > http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lincoln.stein at gmail.com Tue Oct 4 07:51:49 2011 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 4 Oct 2011 07:51:49 -0400 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: Exactly what problems are you encountering? Are you using ActiveState Perl, and if so, at what step is the install failing? Lincoln 2011/10/4 Jos? Luis Lav?n > It seems that all installation atempts failed for Perl 5.10...I'll have to > upgrade my Perl version unless there'd be another Graphical module in > Bioperl tah any of you could recommend. > > 2011/9/30 Fields, Christopher J > > > It's available for all perl versions from 5.8.8 up. I have it running > with > > perl 5.14. Now, I recall there being problems with installation on Mac > OS > > X, though I think that was mainly due to GD.pm and libgd. > > > > chris > > > > On Sep 30, 2011, at 3:23 AM, > > wrote: > > > > > > > > Dear All, > > > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > > windows machine. > > > > > > I read about the Bio-Graphics module and it'd be wonderful to install > it, > > > but seems like it is only available for Perl 5.8... > > > Is there any other Perl and/or Bioperl module to do the same kind of > > > genomic and Blast report representation currently available? > > > > > > Thanks in advance > > > > > > -- > > > Dr. Jos? Luis Lav?n Trueba > > > > > > Dpto. de Producci?n Agraria > > > Grupo de Gen?tica y Microbiolog?a > > > Universidad P?blica de Navarra > > > 31006 Pamplona > > > Navarra > > > SPAIN > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From thomas.sharpton at gmail.com Tue Oct 4 14:05:27 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 11:05:27 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Message-ID: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > Hi, Tom. Let me formally define my problem because this would be > more effective for communication. My objective is to assign a state > for intermediate nodes. For the following example, nodes M and J can > be assigned with (Wing). After assignment (forget the unassigned > first), the pairwise distances of these intermediate nodes and any > other nodes may be compared (e.g. Nodes M and L; Nodes J and E). > > > +---I (Wing) > | > +---M > | | > | +---H (Wing) > | > +---O > | | > | | > | | > | +---L (No-Wing) > | > | > Z > | +---E (Wing) > | | > | +---K > | | | > | | +---D (No-Wing) > | | > +---N > | > | +---C (Wing) > | | > +---J > | > +---B (Wing) > > Technically, I can either use TreeFunctionsI's method add_trait to > the leaves first. Then I back trace the ancestral nodes. While nodes > K and J are pictorially displayed to be nicely at the same level, in > fact besides exhaustively testing NodeI's methods ancestor or > get_all_Descendants etc, I cannot come up with a better idea. As you > have mentioned before, when the tree is big, this curse is > amplified, not to say "Wing" is just one of several hundred > properties to test. > > That's why I'm posting this question to see whether any convenient > data structures already exist to tackle this kind of "graph- > traversing" process. From ross at cuhk.edu.hk Tue Oct 4 19:32:42 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 07:32:42 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Message-ID: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Hi Tom, I shall infer the state based on descendant's states. In my example, Nodes H and I belong to "Wing", then their ancestor M is also assigned "Wing". After assigning these states to all the nodes of the tree, I shall calculate the distances between these nodes. Switching to C is only the last option because that involves another 2 months, not to include the time if C does not have any libraries to deal with Newick Tree. Best, Ross From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] Sent: 2011??10??5?? 2:05 To: Ross KK Leung Cc: bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From R.A.Vos at reading.ac.uk Tue Oct 4 19:59:52 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 01:59:52 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 2:05 > To: Ross KK Leung > Cc: bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > > > > Hi Ross, > > > > I understand that you want to infer ancestral states on your tree, but I'm > unclear about how you want to do so. Can you clarify how you infer the state > for node K on your example tree? In particular, is your method of inference > dependent on the branch lengths? The answers to these questions will > (hopefully) help guide you to methods that can assist you. > > > > Unfortunately, Perl is not the most efficient language for tree/graph > traversal. It can certainly be done, but for very, very large trees, I tend > to roll over to C (but only if I have to as I am not proficient in C). > > > > Best, > > Tom > > > > On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > > > > > > Hi, Tom. Let me formally define my problem because this would be more > effective for communication. My objective is to assign a state for > intermediate nodes. For the following example, nodes M and J can be assigned > with (Wing). After assignment (forget the unassigned first), the pairwise > distances of these intermediate nodes and any other nodes may be compared > (e.g. Nodes M and L; Nodes J and E). > > > > > > +---I (Wing) > > | > > +---M > > | | > > | +---H (Wing) > > | > > +---O > > | | > > | | > > | | > > | +---L (No-Wing) > > | > > | > > Z > > | +---E (Wing) > > | | > > | +---K > > | | | > > | | +---D (No-Wing) > > | | > > +---N > > | > > | +---C (Wing) > > | | > > +---J > > | > > +---B (Wing) > > > > Technically, I can either use TreeFunctionsI's method add_trait to the > leaves first. Then I back trace the ancestral nodes. While nodes K and J are > pictorially displayed to be nicely at the same level, in fact besides > exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I > cannot come up with a better idea. As you have mentioned before, when the > tree is big, this curse is amplified, not to say "Wing" is just one of > several hundred properties to test. > > > > That's why I'm posting this question to see whether any convenient data > structures already exist to tackle this kind of "graph-traversing" process. > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 20:04:22 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 08:04:22 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: <002201cc82f2$565c2e40$03148ac0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:00 To: Ross KK Leung Cc: Thomas Sharpton; bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? I will assign "undetermined" and the detailed plan of assignment is too much to mention here. From R.A.Vos at reading.ac.uk Tue Oct 4 20:42:08 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 02:42:08 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002201cc82f2$565c2e40$03148ac0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. 2011/10/5 Ross KK Leung : > -----Original Message----- > From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger > Vos > Sent: 2011??10??5?? 8:00 > To: Ross KK Leung > Cc: Thomas Sharpton; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > >> I shall infer the state based on descendant's states. In my example, Nodes > H >> and I belong to "Wing", then their ancestor M is also assigned "Wing". > After >> assigning these states to all the nodes of the tree, I shall calculate the >> distances between these nodes. > > What is your approach for when internal states are equivocal? > > I will assign "undetermined" and the detailed plan of assignment is too much > to mention here. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 21:10:33 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 09:10:33 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:42 To: Ross KK Leung Cc: bioperl-l; Thomas Sharpton Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. Thanks, Rutger. While there is a convenient function to help calculate the distances between leaf nodes, I find it difficult for ancestors. After using get_lca, it seems that bioperl has no data structures to help manipulate these LCA's. From thomas.sharpton at gmail.com Tue Oct 4 21:43:38 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 18:43:38 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> Message-ID: Hi Ross, I think Rutger has given you a good idea and it is certainly simpler than the solution I just concocted (no surprise there). Regarding your most recent note: 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help calculate the > distances between leaf nodes, I find it difficult for ancestors. After > using > get_lca, it seems that bioperl has no data structures to help manipulate > these LCA's. > > >From what I understand, the get_lca does return a node object, specifically an internal node. The following is from the BioPerl documentation (note the "Returns" line): Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no common ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes You can get the distance between any two nodes, including an internal node, using the distance method. Note that the nodes you input into the distance function do not need to have ids associated with them. For example, #$nodeA and $nodeB are BioPerl node objects that correspond to any node on the tree my $lca = get_lca( $nodeA, $nodeB ); my $distance = distance( $nodeA, $lca ); $distance will now contain the total branch length between nodeA and the last common ancestor between nodes A and B. At no point are node ids used to conduct calculation; only the node objects themselves are needed. Anything that you can do to a node, you can do to $lca. This is how I understand the functions, at least. Someone please correct me if I'm wrong, as I fear I sound like a broken record at this point.... Best, Tom From thomas.sharpton at gmail.com Wed Oct 5 13:47:53 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Wed, 5 Oct 2011 10:47:53 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <004101cc836f$6a4a6250$3edf26f0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: Hi Ross, Let's keep this discussion on the listserv so that others can benefit from and contribute to it. I just executed your script using the tree you provided (for those following along, I have copied the script and tree below my signature). It produces no warnings or errors on my machine. Look below my signature to see the terminal output of this test run on my computer. Are you working with the latest version of bioperl? What version of perl are you using? I see that the warning (which is distinct from an error) that you are getting is: "MSG: At least some nodes do not have a branch length, the distance returned could be wrong" I also see in your newick tree that you have given the root node (node G) an ID, but no branch length. I'm thinking that you may have an old version of bioperl, which might bark at you when you have a root node with an id but no branch length. Note that the distances being printed in my output (which is not the distance between the node ids that precede the value printed, but instead the distance between the LCA of these node ids and the second of the two ids printed) are indeed correct. Can you provide information on the version of BioPerl and Perl that you are trying this on? Best, Tom ########## testtree.nwk ------------------ ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; ########## test.pl ----------------- use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } # next if( defined( $dist_matrix{$id1}->{$id2} ) || defined ( $dist_matrix{$id2}->{$id1} ) ); my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); #print "$leaf1 and $leaf2 distance: $distance\n"; # print "$id1 and $id2 distance: $distance\n"; #=pod print $id1; ; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); # print $lca->id; #; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; #=cut } } } ######### output --------------- [sharpton at kazushi ~]$perl test.pl test.nwk A B 0.2 A C 0.8 A D 0.9 B A 0.1 B C 0.8 B D 0.9 C A 0.4 C B 0.5 C D 0.4 D A 0.4 D B 0.5 D C 0.3 [sharpton at kazushi ~]$ On Oct 5, 2011, at 7:59 AM, Ross KK Leung wrote: > Hi Tom, > > I personally attach this program and tree files to you and see > whether you can run the program without any error (mine does, I > can't use Modern perl as I can't request the admin to install/update > anything).... > > Thanks a lot, Ross > > > > > > > > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 9:44 > To: Ross KK Leung > Cc: Rutger Vos; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other > nodes from a tree > > Hi Ross, > > I think Rutger has given you a good idea and it is certainly simpler > than the solution I just concocted (no surprise there). > > Regarding your most recent note: > > 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help > calculate the > distances between leaf nodes, I find it difficult for ancestors. > After using > get_lca, it seems that bioperl has no data structures to help > manipulate > these LCA's. > > > From what I understand, the get_lca does return a node object, > specifically an internal node. The following is from the BioPerl > documentation (note the "Returns" line): > > > > Title : get_lca > Usage : get_lca(-nodes => \@nodes ); OR > get_lca(@nodes); > Function: given two or more nodes, returns the lowest common > ancestor (aka most > recent common ancestor) > > > Returns : node object or undef if there is no common ancestor > Args : -nodes => arrayref of nodes to test, OR > just a list of nodes > > You can get the distance between any two nodes, including an > internal node, using the distance method. Note that the nodes you > input into the distance function do not need to have ids associated > with them. For example, > > #$nodeA and $nodeB are BioPerl node objects that correspond to any > node on the tree > my $lca = get_lca( $nodeA, $nodeB ); > my $distance = distance( $nodeA, $lca ); > > $distance will now contain the total branch length between nodeA and > the last common ancestor between nodes A and B. At no point are node > ids used to conduct calculation; only the node objects themselves > are needed. Anything that you can do to a node, you can do to $lca. > > This is how I understand the functions, at least. Someone please > correct me if I'm wrong, as I fear I sound like a broken record at > this point.... > > Best, > Tom > From ross at cuhk.edu.hk Thu Oct 6 03:07:11 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Thu, 6 Oct 2011 15:07:11 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: <006501cc83f6$91830ca0$b48925e0$@edu.hk> Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } From ross at cuhk.edu.hk Fri Oct 7 04:49:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 16:49:27 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <006501cc83f6$91830ca0$b48925e0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> Message-ID: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> each_Descendent documentation mentions "not a recursive fetchall" and I find out a method called "recursion" may solve my problem. the principle is to first force_binary, then start from root and go down along the tree until Is_Leaf, and then assign ancestor and continue the "recursion". -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ross KK Leung Sent: 2011??10??6?? 15:07 To: 'Thomas Sharpton' Cc: 'bioperl-l' Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From ross at cuhk.edu.hk Fri Oct 7 09:16:12 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 21:16:12 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> <00d b01cc84ce$0592d4e0$10b87ea0$@edu.hk> Message-ID: <00f601cc84f3$49406ca0$dbc145e0$@edu.hk> I use the following codes to test and find that the root node G is not assigned state "Opter". Moreover, I find that when a tree looks like this, +---I (Wing) | +---M | | | +---H (Wing) | O | | | +---L (No-Wing) L cannot match with internal node M as L is already a leaf node. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; system("cat $testtree"); my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf( @leaves ){ $leaf->add_tag_value("state", "Wing"); } $rootnode=$tree->get_root_node; Traverse($rootnode); @tmpnodes = $tree->get_nodes; foreach $prnnode (@tmpnodes) { $prnval = $prnnode->get_tag_values("state"); print $prnnode->id, "\t"; print $prnval, "\n"; } } sub Traverse { ($node) = @_; my $state = "dummy"; foreach my $desnode ( $node->each_Descendent() ) { if (!($desnode->is_Leaf)) { Traverse($desnode); } push @cmpnodes, $desnode; } #assume binary? if ($cmpnodes[0]->get_tag_values("state") eq $cmpnodes[1]->get_tag_values("state")) { # $node->add_tag_value("state", $cmpnodes[0]->get_tag_values("state")); $node->add_tag_value("state", "Opter"); } } __DATA__ ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; From maquino at knome.com Tue Oct 11 10:44:06 2011 From: maquino at knome.com (Mark Aquino) Date: Tue, 11 Oct 2011 10:44:06 -0400 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues Message-ID: Hi, I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. Code: #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -usehistory => 'y'); $esearch->get_Response || die; my @h_genes = $esearch->get_ids; print "@h_genes\n"; my $history = $esearch->next_History || die "elink failed"; my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -history => $history, -cmd => 'neighbor_history'); $elink->get_Response; my $hist1 = $elink->next_History; my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -history => $hist1, -cookie => $elink->next_cookie); $esum->get_Response || die "esum failed"; while (my $docsum = $esum->next_DocSum){ print $docsum->get_id,"\n"; print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; } [According to what I can find, the method get_Content_by_name should work but I am getting the error: Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From cjfields at illinois.edu Tue Oct 11 16:16:00 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 11 Oct 2011 20:16:00 +0000 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues In-Reply-To: References: Message-ID: <85FDDEF8-1522-4209-AA21-E51E436E6158@illinois.edu> Mark, Some odd things going on with homologen data, but I wanted to address a few points first. The code has a number of issues: * Missing email (warnings pop up). This will be required in future releases of Bio::DB::EUtilities, it's already technically required by NCBI * 'perldoc Bio::Tools::EUtilities::Summary::DocSum' indicates the method name is 'get_contents_by_name' (note lower-case and plural). As the name implies, it returns a list of raw data * Missing the elink databases. The history will capture the original queried database, but not the database linked to; the default on NCBI's end is pubmed when db is not set), which leads to... * The last EUtilities call is to 'pubmed', from the history. If you dump the docsum output (add a 'print $docsum->to_string) this is apparent. * Content key is wrong. Dumping the raw data initially is a good idea for debugging to ensure you are capturing the correct key. In this case, the key is 'TaxId' (note the case). * Calls to get_Response() are unnecessary; this just returns the HTTP::Response object from the user agent if you need the raw output. Calls to the eutilities-specific methods will lazily grab incoming data and parse as needed, so get_ids() alone will work as you would expect. Note the homologene data is hierarchical; there is more than one gene per linked ID, so the item data is nested. The tools are meant to be fairly generic, so you could just retrieve all the TaxID information, but it might be more relevant to get the GeneIDs to go along with them for more context. The following works for me. chris =================================================== #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -email => , -usehistory => 'y'); my @h_genes = $eutil->get_ids; print "@h_genes\n"; my $history = $eutil->next_History || die "esearch failed"; $eutil->reset_parameters(-eutil => 'elink', -history => $history, -email => , -db => 'homologene', -cmd => 'neighbor_history'); $history = $eutil->next_History || die "elink failed"; $eutil->reset_parameters(-eutil => 'esummary', -email => , -history => $history); while (my $docsum = $eutil->next_DocSum) { print "Homologen ID:".$docsum->get_id."\n"; print "Label: ".($docsum->get_contents_by_name('Caption'))[0]."\n"; while (my $item = $docsum->next_Item) { # HomoloGeneDataList while (my $sub = $item->next_subItem) { # HomoloGeneData print "\tGeneId: ".($sub->get_contents_by_name('GeneID'))[0]."\n"; print "\tTaxId: ".($sub->get_contents_by_name('TaxId'))[0]."\n"; } } } On Oct 11, 2011, at 9:44 AM, Mark Aquino wrote: > Hi, > > I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. > > Code: > > #!/usr/bin/perl > use strict; > use warnings; > use Bio::DB::EUtilities; > my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', > -db => 'homologene', > -term => 'Copg AND mouse', > -usehistory => 'y'); > $esearch->get_Response || die; > my @h_genes = $esearch->get_ids; > print "@h_genes\n"; > my $history = $esearch->next_History || die "elink failed"; > my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', > -history => $history, > -cmd => 'neighbor_history'); > > $elink->get_Response; > my $hist1 = $elink->next_History; > my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', > -history => $hist1, > -cookie => $elink->next_cookie); > $esum->get_Response || die "esum failed"; > while (my $docsum = $esum->next_DocSum){ > print $docsum->get_id,"\n"; > print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; > } > > [According to what I can find, the method get_Content_by_name should work but I am getting the error: > Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From manju.rawat2 at gmail.com Wed Oct 12 01:32:06 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Wed, 12 Oct 2011 11:02:06 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin In-Reply-To: References: Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.txt -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); it working fine in terminal with following command but showing error in programming.. agl at agl-desktop:~/BP$ blastall -p blastn -d btau -i test_query.fa -o test.out pl tell me what i am doing wrong. Thanks Manju Rawat From rajasimhah at nei.nih.gov Wed Oct 12 12:07:03 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 12:07:03 -0400 Subject: [Bioperl-l] Installation problem Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> I am trying to install Bioperl since yesterday without any luck. I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. I am attaching errors encountered during one such attempt below. Please help. root at comp1z BioPerl-1.6.1]# perl Build.PL This package requires Module::Build v0.2805 or greater to install itself. Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at (eval 2) line 1 BEGIN failed--compilation aborted at (eval 2) line 1. BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. Compilation failed in require at Build.PL line 14. BEGIN failed--compilation aborted at Build.PL line 14. I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). Please help!!! Harsha National Eye Institute, Bethesda, MD 301-402-5734 From cjfields at illinois.edu Wed Oct 12 15:37:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:37:35 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> Message-ID: Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Oct 12 15:41:05 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:41:05 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> Message-ID: <54A3917D-C212-4219-9C29-8285F3254EA5@illinois.edu> Possibly, though hard to say unless you give it a try. It does have a lot of bug fixes though. chris On Oct 12, 2011, at 2:38 PM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > No Christopher, I am trying the latest stable version 1.6.1 > Should I expect a smoother install with 1.6.901? > > Harsha > > ________________________________________ > From: Fields, Christopher J [cjfields at illinois.edu] > Sent: Wednesday, October 12, 2011 3:37 PM > To: Rajasimha, Harsha (NIH/NEI) [C] > Cc: bioperl-l at bioperl.org > Subject: Re: [Bioperl-l] Installation problem > > Have you tried the latest version from CPAN (v1.6.901)? > > chris > > On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > >> I am trying to install Bioperl since yesterday without any luck. >> I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. >> I am attaching errors encountered during one such attempt below. Please help. >> >> root at comp1z BioPerl-1.6.1]# perl Build.PL >> This package requires Module::Build v0.2805 or greater to install itself. >> Base class package "Module::Build" is empty. >> (Perhaps you need to 'use' the module which defines that package first.) >> at (eval 2) line 1 >> BEGIN failed--compilation aborted at (eval 2) line 1. >> BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. >> Compilation failed in require at Build.PL line 14. >> BEGIN failed--compilation aborted at Build.PL line 14. >> >> I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). >> >> Please help!!! >> Harsha >> National Eye Institute, Bethesda, MD >> 301-402-5734 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From rajasimhah at nei.nih.gov Wed Oct 12 15:38:43 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 15:38:43 -0400 Subject: [Bioperl-l] Installation problem In-Reply-To: References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> No Christopher, I am trying the latest stable version 1.6.1 Should I expect a smoother install with 1.6.901? Harsha ________________________________________ From: Fields, Christopher J [cjfields at illinois.edu] Sent: Wednesday, October 12, 2011 3:37 PM To: Rajasimha, Harsha (NIH/NEI) [C] Cc: bioperl-l at bioperl.org Subject: Re: [Bioperl-l] Installation problem Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 09:07:18 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 09:07:18 -0400 Subject: [Bioperl-l] Fwd: [bioperl-network] Not indexed by CPAN (#1) References: Message-ID: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> bioperl-l, It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. Brian O. Begin forwarded message: > From: "Chad A. Davis" > Date: October 13, 2011 7:40:27 AM EDT > To: bosborne > Subject: [bioperl-network] Not indexed by CPAN (#1) > > I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. > > This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi > > CPAN 1.9800 > > -- > Reply to this email directly or view it on GitHub: > https://github.com/bioperl/bioperl-network/issues/1 From cjfields at illinois.edu Thu Oct 13 11:47:33 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 15:47:33 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> Message-ID: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Brian, If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. chris On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > bioperl-l, > > It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. > > Brian O. > > Begin forwarded message: > >> From: "Chad A. Davis" >> Date: October 13, 2011 7:40:27 AM EDT >> To: bosborne >> Subject: [bioperl-network] Not indexed by CPAN (#1) >> >> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >> >> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >> >> CPAN 1.9800 >> >> -- >> Reply to this email directly or view it on GitHub: >> https://github.com/bioperl/bioperl-network/issues/1 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 11:52:55 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 11:52:55 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Message-ID: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Yes, BOSBORNE. On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > Brian, > > If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? > > It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. > > chris > > On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > >> bioperl-l, >> >> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >> >> Brian O. >> >> Begin forwarded message: >> >>> From: "Chad A. Davis" >>> Date: October 13, 2011 7:40:27 AM EDT >>> To: bosborne >>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>> >>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>> >>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>> >>> CPAN 1.9800 >>> >>> -- >>> Reply to this email directly or view it on GitHub: >>> https://github.com/bioperl/bioperl-network/issues/1 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Oct 13 13:03:49 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 17:03:49 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Message-ID: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. chris On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > Yes, BOSBORNE. > > On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > >> Brian, >> >> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >> >> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >> >> chris >> >> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >> >>> bioperl-l, >>> >>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>> >>> Brian O. >>> >>> Begin forwarded message: >>> >>>> From: "Chad A. Davis" >>>> Date: October 13, 2011 7:40:27 AM EDT >>>> To: bosborne >>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>> >>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>> >>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>> >>>> CPAN 1.9800 >>>> >>>> -- >>>> Reply to this email directly or view it on GitHub: >>>> https://github.com/bioperl/bioperl-network/issues/1 >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From bosborne11 at verizon.net Thu Oct 13 21:45:56 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 21:45:56 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> Message-ID: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Chris, OK, tell me what they say when you hear from them. BIO On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. > > chris > > On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > >> Yes, BOSBORNE. >> >> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >> >>> Brian, >>> >>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>> >>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>> >>> chris >>> >>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>> >>>> bioperl-l, >>>> >>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>> >>>> Brian O. >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Chad A. Davis" >>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>> To: bosborne >>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>> >>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>> >>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>> >>>>> CPAN 1.9800 >>>>> >>>>> -- >>>>> Reply to this email directly or view it on GitHub: >>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Fri Oct 14 08:48:19 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Fri, 14 Oct 2011 14:48:19 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: Because it may be related, I wanted to mention that I am having the same problem with Bioperl-Run. In this case, however, I can find the distribution via: i /bioperl-run/ But searching for a containing module does not return the distribution: i /clustalw/ Chad On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: > Chris, > > OK, tell me what they say when you hear from them. > > BIO > > > On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > >> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >> >> chris >> >> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >> >>> Yes, BOSBORNE. >>> >>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>> >>>> Brian, >>>> >>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>> >>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>> >>>>> bioperl-l, >>>>> >>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>> >>>>> Brian O. >>>>> >>>>> Begin forwarded message: >>>>> >>>>>> From: "Chad A. Davis" >>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>> To: bosborne >>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>> >>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>> >>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>> >>>>>> CPAN 1.9800 >>>>>> >>>>>> -- >>>>>> Reply to this email directly or view it on GitHub: >>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Fri Oct 14 09:34:22 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 14 Oct 2011 13:34:22 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). chris On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > Because it may be related, I wanted to mention that I am having the > same problem with Bioperl-Run. In this case, however, I can find the > distribution via: > > i /bioperl-run/ > > But searching for a containing module does not return the distribution: > > i /clustalw/ > > Chad > > On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >> Chris, >> >> OK, tell me what they say when you hear from them. >> >> BIO >> >> >> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >> >>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>> >>> chris >>> >>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>> >>>> Yes, BOSBORNE. >>>> >>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>> >>>>> Brian, >>>>> >>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>> >>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>> >>>>>> bioperl-l, >>>>>> >>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>> >>>>>> Brian O. >>>>>> >>>>>> Begin forwarded message: >>>>>> >>>>>>> From: "Chad A. Davis" >>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>> To: bosborne >>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>> >>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>> >>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>> >>>>>>> CPAN 1.9800 >>>>>>> >>>>>>> -- >>>>>>> Reply to this email directly or view it on GitHub: >>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Oct 16 23:12:59 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 03:12:59 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? chris On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). > > chris > > On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > >> Because it may be related, I wanted to mention that I am having the >> same problem with Bioperl-Run. In this case, however, I can find the >> distribution via: >> >> i /bioperl-run/ >> >> But searching for a containing module does not return the distribution: >> >> i /clustalw/ >> >> Chad >> >> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>> Chris, >>> >>> OK, tell me what they say when you hear from them. >>> >>> BIO >>> >>> >>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>> >>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>> >>>>> Yes, BOSBORNE. >>>>> >>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>> >>>>>> Brian, >>>>>> >>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>> >>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>> >>>>>>> bioperl-l, >>>>>>> >>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>> >>>>>>> Brian O. >>>>>>> >>>>>>> Begin forwarded message: >>>>>>> >>>>>>>> From: "Chad A. Davis" >>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>> To: bosborne >>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>> >>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>> >>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>> >>>>>>>> CPAN 1.9800 >>>>>>>> >>>>>>>> -- >>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 04:08:16 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 17 Oct 2011 10:08:16 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: The index looks good now, I'm able to get the bioperl-network distro by depending on a module within it. Would it be possible to do the same for a bioperl-run 1.6.901 release? Cheers, Chad On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J wrote: > This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. > > Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? > > chris > > On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > >> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >> >> chris >> >> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >> >>> Because it may be related, I wanted to mention that I am having the >>> same problem with Bioperl-Run. In this case, however, I can find the >>> distribution via: >>> >>> i /bioperl-run/ >>> >>> But searching for a containing module does not return the distribution: >>> >>> i /clustalw/ >>> >>> Chad >>> >>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>> Chris, >>>> >>>> OK, tell me what they say when you hear from them. >>>> >>>> BIO >>>> >>>> >>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>> >>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>> >>>>>> Yes, BOSBORNE. >>>>>> >>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>> >>>>>>> Brian, >>>>>>> >>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>> >>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> bioperl-l, >>>>>>>> >>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>> >>>>>>>> Brian O. >>>>>>>> >>>>>>>> Begin forwarded message: >>>>>>>> >>>>>>>>> From: "Chad A. Davis" >>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>> To: bosborne >>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>> >>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>> >>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>> >>>>>>>>> CPAN 1.9800 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Oct 17 14:02:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 18:02:35 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. chris On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > The index looks good now, I'm able to get the bioperl-network distro > by depending on a module within it. > Would it be possible to do the same for a bioperl-run 1.6.901 release? > > Cheers, > Chad > > > On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J > wrote: >> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >> >> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >> >> chris >> >> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >> >>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>> >>> chris >>> >>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>> >>>> Because it may be related, I wanted to mention that I am having the >>>> same problem with Bioperl-Run. In this case, however, I can find the >>>> distribution via: >>>> >>>> i /bioperl-run/ >>>> >>>> But searching for a containing module does not return the distribution: >>>> >>>> i /clustalw/ >>>> >>>> Chad >>>> >>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>> Chris, >>>>> >>>>> OK, tell me what they say when you hear from them. >>>>> >>>>> BIO >>>>> >>>>> >>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>> >>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>> >>>>>>> Yes, BOSBORNE. >>>>>>> >>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> Brian, >>>>>>>> >>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>> >>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> bioperl-l, >>>>>>>>> >>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>> >>>>>>>>> Brian O. >>>>>>>>> >>>>>>>>> Begin forwarded message: >>>>>>>>> >>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>> To: bosborne >>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>> >>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>> >>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>> >>>>>>>>>> CPAN 1.9800 >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioperl-l mailing list >>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Oct 17 15:40:26 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 19:40:26 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. chris On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. > > chris > > On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > >> The index looks good now, I'm able to get the bioperl-network distro >> by depending on a module within it. >> Would it be possible to do the same for a bioperl-run 1.6.901 release? >> >> Cheers, >> Chad >> >> >> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >> wrote: >>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>> >>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>> >>> chris >>> >>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>> >>>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>> >>>>> Because it may be related, I wanted to mention that I am having the >>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>> distribution via: >>>>> >>>>> i /bioperl-run/ >>>>> >>>>> But searching for a containing module does not return the distribution: >>>>> >>>>> i /clustalw/ >>>>> >>>>> Chad >>>>> >>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>> Chris, >>>>>> >>>>>> OK, tell me what they say when you hear from them. >>>>>> >>>>>> BIO >>>>>> >>>>>> >>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>> >>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> Yes, BOSBORNE. >>>>>>>> >>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>> >>>>>>>>> Brian, >>>>>>>>> >>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>>> >>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>>> >>>>>>>>> chris >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>> >>>>>>>>>> bioperl-l, >>>>>>>>>> >>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>> >>>>>>>>>> Brian O. >>>>>>>>>> >>>>>>>>>> Begin forwarded message: >>>>>>>>>> >>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>> To: bosborne >>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>> >>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>> >>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>> >>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioperl-l mailing list >>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 18:33:00 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Tue, 18 Oct 2011 00:33:00 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Chris, Looks good. I find Bioperl-Run by querying one of the contained modules now. Thank you for sorting that out. Chad On Mon, Oct 17, 2011 at 21:40, Fields, Christopher J wrote: > I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. ?It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. > > chris > > On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > >> Yes, I planned on that ?but wanted to make sure everything was working from your end. ? Will upload that in a bit. >> >> chris >> >> On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: >> >>> The index looks good now, I'm able to get the bioperl-network distro >>> by depending on a module within it. >>> Would it be possible to do the same for a bioperl-run 1.6.901 release? >>> >>> Cheers, >>> Chad >>> >>> >>> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >>> wrote: >>>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>>> >>>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>>> >>>>> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>>> >>>>> chris >>>>> >>>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>>> >>>>>> Because it may be related, I wanted to mention that I am having the >>>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>>> distribution via: >>>>>> >>>>>> i /bioperl-run/ >>>>>> >>>>>> But searching for a containing module does not return the distribution: >>>>>> >>>>>> i /clustalw/ >>>>>> >>>>>> Chad >>>>>> >>>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>>> Chris, >>>>>>> >>>>>>> OK, tell me what they say when you hear from them. >>>>>>> >>>>>>> BIO >>>>>>> >>>>>>> >>>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> Yes, BOSBORNE. >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>>> >>>>>>>>>> Brian, >>>>>>>>>> >>>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>>>>> >>>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>>>>> >>>>>>>>>> chris >>>>>>>>>> >>>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>>> >>>>>>>>>>> bioperl-l, >>>>>>>>>>> >>>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>>> >>>>>>>>>>> Brian O. >>>>>>>>>>> >>>>>>>>>>> Begin forwarded message: >>>>>>>>>>> >>>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>>> To: bosborne >>>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>>> >>>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>>> >>>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>>> >>>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioperl-l mailing list >>>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From saxen at lbl.gov Mon Oct 17 20:37:59 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Mon, 17 Oct 2011 17:37:59 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch Message-ID: Hello, I am having problems using the Bio::DB::EUtilities module to retrieve data from Entrez. The following script is adapted from the code at http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. The input is a file containing a very long list of GI numbers from NCBI protein. When I run the script, I receive the following error message: Can't locate object method "get_Response" via package "Bio::DB::EUtilities::efetch" at getGP.pl line 23. #!/usr/bin/perl -w use warnings; use strict; use Bio::DB::EUtilities; use Bio::SeqIO; use Data::Dumper; my $id_file = $ARGV[0]; my $temp_file = 'temp.gp'; my @ids; open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; @ids = ; close IDFILE; my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', -db => 'protein', -rettype => 'gb', -email => 'saxen at lbl.gov', -id => \@ids); # dump HTTP::Response content to a file (not retained in memory) $factory->get_Response(-file => $temp_file); my $seqin = Bio::SeqIO->new(-file => $temp_file, -format => 'genbank'); while (my $seq = $seqin->next_seq) { print Dumper($seq); } I would appreciate any insight as to why I am receiving this error. Thanks in advance for your time! Seth Axen From carandraug+dev at gmail.com Mon Oct 17 21:16:40 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Tue, 18 Oct 2011 02:16:40 +0100 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On 18 October 2011 01:37, Seth D. Axen wrote: > Hello, > ? I am having problems using the Bio::DB::EUtilities module to retrieve > data from Entrez. The following script is adapted from the code at > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. > The input is a file containing a very long list of GI numbers from NCBI > protein. When I run the script, I receive the following error message: Can't > locate object method "get_Response" via package > "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > > #!/usr/bin/perl -w > use warnings; > use strict; > use Bio::DB::EUtilities; > use Bio::SeqIO; > use Data::Dumper; > > my $id_file = $ARGV[0]; > my $temp_file = 'temp.gp'; > my @ids; > > open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > @ids = ; > close IDFILE; > > my $factory = Bio::DB::EUtilities->new(-eutil ? => 'efetch', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? ?=> 'protein', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -rettype => 'gb', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -email ? => 'saxen at lbl.gov', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ?=> \@ids); > > # dump HTTP::Response content to a file (not retained in memory) > $factory->get_Response(-file => $temp_file); > > my $seqin = Bio::SeqIO->new(-file ? => $temp_file, > ? ? ? ? ? ? ? ? ? ? ? ? ? ?-format => 'genbank'); > > while (my $seq = $seqin->next_seq) { > ? print Dumper($seq); > } > > ? I would appreciate any insight as to why I am receiving this error. > Thanks in advance for your time! > ? Seth Axen Hi your code works fine for me. Can the problem be on your IDs or its file? By the way, drop the -w from the shebang line, you are alredy using warnings. Carn? From cjfields at illinois.edu Mon Oct 17 21:33:13 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 01:33:13 +0000 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > On 18 October 2011 01:37, Seth D. Axen wrote: >> Hello, >> I am having problems using the Bio::DB::EUtilities module to retrieve >> data from Entrez. The following script is adapted from the code at >> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. >> The input is a file containing a very long list of GI numbers from NCBI >> protein. When I run the script, I receive the following error message: Can't >> locate object method "get_Response" via package >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. >> >> #!/usr/bin/perl -w >> use warnings; >> use strict; >> use Bio::DB::EUtilities; >> use Bio::SeqIO; >> use Data::Dumper; >> >> my $id_file = $ARGV[0]; >> my $temp_file = 'temp.gp'; >> my @ids; >> >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; >> @ids = ; >> close IDFILE; >> >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', >> -db => 'protein', >> -rettype => 'gb', >> -email => 'saxen at lbl.gov', >> -id => \@ids); >> >> # dump HTTP::Response content to a file (not retained in memory) >> $factory->get_Response(-file => $temp_file); >> >> my $seqin = Bio::SeqIO->new(-file => $temp_file, >> -format => 'genbank'); >> >> while (my $seq = $seqin->next_seq) { >> print Dumper($seq); >> } >> >> I would appreciate any insight as to why I am receiving this error. >> Thanks in advance for your time! >> Seth Axen > > Hi > > your code works fine for me. Can the problem be on your IDs or its > file? By the way, drop the -w from the shebang line, you are alredy > using warnings. > > Carn? Also, check the BioPerl version, there was a very large change in the API before the v1.6 release. chris From jeanmarc.frigerio at gmail.com Tue Oct 18 08:43:51 2011 From: jeanmarc.frigerio at gmail.com (jmf) Date: Tue, 18 Oct 2011 05:43:51 -0700 (PDT) Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> Message-ID: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Hi I agree that it'd be nice to see it revived. I made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', Thanks Dave for the topic ! Chris can you correct the file or should I submit the patch (I don't know where ?) On 2 sep, 17:20, Jack Tanner wrote: > I also see that someone's forked it on Github and made some packaging fixes. > > It'd be nice to see it revived. > > On 9/2/2011 9:00 AM, Fields, Christopher J wrote: > > > > > > > > > > > I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. ?Otherwise I worry about the long-term support for it/ > > > chris > > > On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: > > >> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: > >>http://toolkit.tuebingen.mpg.de/hhpred > > >> He got it working thus: > >> Hi Dave, > >> thanks a lot. i made it work. The error i got later on was: > >> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; > >> recompile with -fPIC > > >> the solution is: > >> perl Makefile.PL PREFIX= ?/fftwsingle --enable-shared --with-pic --enable-single > >> > >> make > >> make install > >>http://forums.fedoraforum.org/showthread.php?t=232607 > > >> Dave > > >> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J ?wrote: > >> Yes, it's essentially deprecated (unmaintained). ?I don't know of anyone who has packaged that up in a while, if ever. > > >> chris > > >> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: > > >>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? > > >>> Does anyone have a spec file for building an SRPM for it for RHEL 6? > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioper... at lists.open-bio.org > >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioper... at lists.open-bio.org > >>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l From sarah.tincher at gmail.com Tue Oct 18 13:00:46 2011 From: sarah.tincher at gmail.com (Sarah Tincher) Date: Tue, 18 Oct 2011 12:00:46 -0500 Subject: [Bioperl-l] Issues with CLUSTALW Message-ID: Hello, I am new to BioPerl and have no computer science background. I am taking a bioinformatics course and I have an assignment to write a BioPerl script to perform the MSA of a specific six sequences, retrieving the sequences from NCBI and using CLUSTALW. This is the script I wrote based on a lecture from my course: #!usr/bin/perl use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; $gb = new Bio::DB::GenBank(); $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); $factory = Bio::Tools::Run::Alignment::Clustalw->new; @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); print "$aln\n"; And this is the error that I receive: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level /Library/Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at HW3_2.pl line 3. BEGIN failed--compilation aborted at HW3_2.pl line 3. I would appreciate any help you can provide. Thank you, Sarah Tincher From cjfields at illinois.edu Tue Oct 18 14:35:08 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:08 +0000 Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Message-ID: <364EF42F-D067-40B5-9B92-7D36ED22B6E1@illinois.edu> A patch is fine. Also, it might be worth talking to the WUSTL group on merging those changes from their fork in (fairly easy to do). At some point, if this code looks as if it needs to exist independently of bioperl-ext we can create a new repo for it. I think it will see more use that way. chris On Oct 18, 2011, at 7:43 AM, jmf wrote: > Hi > I agree that it'd be nice to see it revived. I made a patch to the Bio/ > Ext/Align/Makefile.PL to make the compiler happy, just by changing: > > 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', > to > 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', > > Thanks Dave for the topic ! > > Chris can you correct the file or should I submit the patch (I don't > know where ?) > > On 2 sep, 17:20, Jack Tanner wrote: >> I also see that someone's forked it on Github and made some packaging fixes. >> >> It'd be nice to see it revived. >> >> On 9/2/2011 9:00 AM, Fields, Christopher J wrote: >> >> >> >> >> >> >> >> >> >>> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. Otherwise I worry about the long-term support for it/ >> >>> chris >> >>> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: >> >>>> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: >>>> http://toolkit.tuebingen.mpg.de/hhpred >> >>>> He got it working thus: >>>> Hi Dave, >>>> thanks a lot. i made it work. The error i got later on was: >>>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; >>>> recompile with -fPIC >> >>>> the solution is: >>>> perl Makefile.PL PREFIX= /fftwsingle --enable-shared --with-pic --enable-single >>>> >>>> make >>>> make install >>>> http://forums.fedoraforum.org/showthread.php?t=232607 >> >>>> Dave >> >>>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J wrote: >>>> Yes, it's essentially deprecated (unmaintained). I don't know of anyone who has packaged that up in a while, if ever. >> >>>> chris >> >>>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: >> >>>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? >> >>>>> Does anyone have a spec file for building an SRPM for it for RHEL 6? >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioper... at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioper... at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Oct 18 14:35:41 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:41 +0000 Subject: [Bioperl-l] Issues with CLUSTALW In-Reply-To: References: Message-ID: <54A57FF8-5415-4798-89B5-3E256ECDE636@illinois.edu> You need to install BioPerl-Run as well as the core BioPerl modules. chris On Oct 18, 2011, at 12:00 PM, Sarah Tincher wrote: > Hello, > > I am new to BioPerl and have no computer science background. I am taking a > bioinformatics course and I have an assignment to write a BioPerl script to > perform the MSA of a specific six sequences, retrieving the sequences from > NCBI and using CLUSTALW. > > This is the script I wrote based on a lecture from my course: > > #!usr/bin/perl > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > $gb = new Bio::DB::GenBank(); > $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); > $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); > $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); > $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); > $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); > $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); > $factory = Bio::Tools::Run::Alignment::Clustalw->new; > @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); > $seq_array_ref = \@seq_array; > $aln = $factory->align($seq_array_ref); > print "$aln\n"; > > And this is the error that I receive: > > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: > /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 > /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin > /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level > /Library/Perl/Updates/5.8.8 > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) > at HW3_2.pl line 3. > BEGIN failed--compilation aborted at HW3_2.pl line 3. > > I would appreciate any help you can provide. > > Thank you, > Sarah Tincher > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From saxen at lbl.gov Tue Oct 18 20:15:21 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Tue, 18 Oct 2011 17:15:21 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: Thanks Carne and Chris! The problem was with my BioPerl version. Once I used the latest version, the script ran perfectly. Seth 2011/10/17 Fields, Christopher J > On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > > > On 18 October 2011 01:37, Seth D. Axen wrote: > >> Hello, > >> I am having problems using the Bio::DB::EUtilities module to retrieve > >> data from Entrez. The following script is adapted from the code at > >> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO > . > >> The input is a file containing a very long list of GI numbers from NCBI > >> protein. When I run the script, I receive the following error message: > Can't > >> locate object method "get_Response" via package > >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > >> > >> #!/usr/bin/perl -w > >> use warnings; > >> use strict; > >> use Bio::DB::EUtilities; > >> use Bio::SeqIO; > >> use Data::Dumper; > >> > >> my $id_file = $ARGV[0]; > >> my $temp_file = 'temp.gp'; > >> my @ids; > >> > >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > >> @ids = ; > >> close IDFILE; > >> > >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', > >> -db => 'protein', > >> -rettype => 'gb', > >> -email => 'saxen at lbl.gov', > >> -id => \@ids); > >> > >> # dump HTTP::Response content to a file (not retained in memory) > >> $factory->get_Response(-file => $temp_file); > >> > >> my $seqin = Bio::SeqIO->new(-file => $temp_file, > >> -format => 'genbank'); > >> > >> while (my $seq = $seqin->next_seq) { > >> print Dumper($seq); > >> } > >> > >> I would appreciate any insight as to why I am receiving this error. > >> Thanks in advance for your time! > >> Seth Axen > > > > Hi > > > > your code works fine for me. Can the problem be on your IDs or its > > file? By the way, drop the -w from the shebang line, you are alredy > > using warnings. > > > > Carn? > > > Also, check the BioPerl version, there was a very large change in the API > before the v1.6 release. > > chris > > > > From shachigahoimbi at gmail.com Fri Oct 21 01:59:12 2011 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 21 Oct 2011 11:29:12 +0530 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl Message-ID: Dear all, I have fasta format sequence file and I want to extract ORF ID "PITG_14194" from fasta file and then I want to rename same file with that ORF ID "PITG_14194". I have many files and I want to do same exercise with all sequence files. Please tell me how can i do this with perl or bioperl. >tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR NGIAVDHKGVICNGKAPIEIAVDENTLSAAA -- Regards, Shachi From jason.stajich at gmail.com Fri Oct 21 05:56:11 2011 From: jason.stajich at gmail.com (Jason Stajich) Date: Fri, 21 Oct 2011 02:56:11 -0700 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl In-Reply-To: References: Message-ID: easy to do this with a simple regular expression and opening a new file. Have you read up on this concept in Perl. You can use SeqIO to parse FASTA files - did you read the HOWTO and website documentation first? We don't typically do people's work for them on this mailing list so please show some effort first. On Oct 20, 2011, at 10:59 PM, Shachi Gahoi wrote: > Dear all, > > I have fasta format sequence file and I want to extract ORF ID "PITG_14194" > from fasta file and then I want to rename same file with that ORF ID > "PITG_14194". > > I have many files and I want to do same exercise with all sequence files. > > Please tell me how can i do this with perl or bioperl. > >> tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora > infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 > MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL > ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA > RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF > HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM > YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL > TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD > RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR > NGIAVDHKGVICNGKAPIEIAVDENTLSAAA > > > -- > Regards, > Shachi > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Fri Oct 21 11:09:13 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 21 Oct 2011 11:09:13 -0400 Subject: [Bioperl-l] Deobfuscator direct link? Message-ID: Hi everybody, Does anyone object to me changing the center front-page link to the Deobfuscator to go directly to http://bioperl.org/cgi-bin/deob_interface.cgi ? That would still leave the left sidebar link that goes to the wiki page. Dave From cjfields at illinois.edu Fri Oct 21 12:31:45 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 21 Oct 2011 16:31:45 +0000 Subject: [Bioperl-l] Deobfuscator direct link? In-Reply-To: References: Message-ID: <2E2B401F-F358-48AD-880C-3FA9575D9B17@illinois.edu> Go for it. chris On Oct 21, 2011, at 10:09 AM, Dave Messina wrote: > Hi everybody, > > Does anyone object to me changing the center front-page link to the > Deobfuscator to go directly to > > http://bioperl.org/cgi-bin/deob_interface.cgi > > ? > > That would still leave the left sidebar link that goes to the wiki page. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From zheboyang at gmail.com Fri Oct 21 21:38:56 2011 From: zheboyang at gmail.com (boyang zhe) Date: Sat, 22 Oct 2011 03:38:56 +0200 Subject: [Bioperl-l] bioperl-ext installation Message-ID: I try to install bioperl-ext. But I failed. So I try the method suggested by JMF< jeanmarc.frigerio at gmail.com>. made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'' Then I run make. It seems ok for compilation. However, it generate errors when I run make test. No any of the 20 tests passed. it seems that because " Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so" I did not see any Align.so file at those directory. In fact, I can only find a blank directory of blib/arch/auto/Bio/Ext. Hope for your help. It is really hard for me. Thank you very much. boyang info as below: make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic.t .. ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.04 cusr 0.00 csys = 0.08 CPU) Result: PASS make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..20 not ok 1 - use Bio::Ext::Align; # Failed test 'use Bio::Ext::Align;' # at test.pl line 15. # Tried to use 'Bio::Ext::Align'. # Error: Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_access_name_CompMat at /usr/lib/perl/5.10/DynaLoader.pm line 193. # at (eval 4) line 2 # Compilation failed in require at (eval 4) line 2. # BEGIN failed--compilation aborted at (eval 4) line 2. The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed. Please install the bioperl-ext package # Looks like you planned 20 tests but ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test exited with 1 just after 1. make[1]: *** [test_dynamic] Error 1 make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make: *** [subdirs-test] Error 2 This is the info for make. cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h cp Bio/SeqIO/staden/CHANGES blib/lib/Bio/SeqIO/staden/CHANGES cp Bio/Ext/Align/test.pl blib/lib/Bio/Ext/Align/test.pl cp Bio/Ext/Align/libs/wiseoverlay.h blib/lib/Bio/Ext/Align/libs/wiseoverlay.h cp Bio/Ext/Align/libs/proteinsw.h blib/lib/Bio/Ext/Align/libs/proteinsw.h cp Bio/Ext/Align/libs/wisebase.h blib/lib/Bio/Ext/Align/libs/wisebase.h cp Bio/Ext/Align/libs/seqaligndisplay.h blib/lib/Bio/Ext/Align/libs/seqaligndisplay.h cp Bio/Ext/Align/libs/dyna.h blib/lib/Bio/Ext/Align/libs/dyna.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/complexsequence.c blib/lib/Bio/Ext/Align/libs/complexsequence.c cp Bio/Ext/Align/libs/wisestring.h blib/lib/Bio/Ext/Align/libs/wisestring.h cp Bio/Ext/Align/libs/codon.c blib/lib/Bio/Ext/Align/libs/codon.c cp Bio/Ext/Align/libs/linspc.c blib/lib/Bio/Ext/Align/libs/linspc.c cp Bio/Ext/Align/libs/probability.h blib/lib/Bio/Ext/Align/libs/probability.h cp Bio/Ext/Align/Align.xs blib/lib/Bio/Ext/Align/Align.xs cp Bio/SeqIO/staden/t/staden/data/readtest.exp blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.exp cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h cp Bio/Ext/Align/blosum45.mat blib/lib/Bio/Ext/Align/blosum45.mat cp Bio/Ext/Align/libs/dynlibcross.c blib/lib/Bio/Ext/Align/libs/dynlibcross.c cp Bio/Ext/Align/libs/sequencedb.c blib/lib/Bio/Ext/Align/libs/sequencedb.c cp Bio/Ext/Align/libs/sw_wrap.c blib/lib/Bio/Ext/Align/libs/sw_wrap.c cp Bio/Ext/Align/libs/complexsequence.h blib/lib/Bio/Ext/Align/libs/complexsequence.h cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h cp Bio/Ext/Align/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h cp Bio/SeqIO/staden/t/staden/data/readtestabi.fa blib/lib/Bio/SeqIO/staden/t/staden/data/readtestabi.fa cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/SeqIO/staden/t/staden/data/readtest.pln blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.pln cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.c cp Bio/Ext/Align/libs/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/alnrange.c blib/lib/Bio/Ext/Align/libs/alnrange.c cp Bio/Ext/Align/libs/dpenvelope.h blib/lib/Bio/Ext/Align/libs/dpenvelope.h cp Bio/Ext/Align/blosum62.mat blib/lib/Bio/Ext/Align/blosum62.mat cp Bio/Ext/Align/libs/sequence.h blib/lib/Bio/Ext/Align/libs/sequence.h cp Bio/Ext/Align/libs/asciibtcanvas.h blib/lib/Bio/Ext/Align/libs/asciibtcanvas.h cp Bio/Ext/Align/blosum50.mat blib/lib/Bio/Ext/Align/blosum50.mat cp Bio/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm cp Bio/SeqIO/staden/README blib/lib/Bio/SeqIO/staden/README cp Bio/SeqIO/staden/read.xs blib/lib/Bio/SeqIO/staden/read.xs cp Bio/SeqIO/staden/t/staden/data/readtest.abi blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.abi cp Bio/Ext/Align/libs/protein.h blib/lib/Bio/Ext/Align/libs/protein.h cp Bio/Ext/Align/libs/sequencedb.h blib/lib/Bio/Ext/Align/libs/sequencedb.h cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/SeqIO/staden/t/staden/data/readtestref.scf blib/lib/Bio/SeqIO/staden/t/staden/data/readtestref.scf cp Bio/SeqIO/staden/Makefile.PL blib/lib/Bio/SeqIO/staden/Makefile.PL cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c cp Bio/Ext/Align/libs/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/SeqIO/staden/META.yml blib/lib/Bio/SeqIO/staden/META.yml cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/libs/histogram.h blib/lib/Bio/Ext/Align/libs/histogram.h cp Bio/Ext/Align/libs/makefile blib/lib/Bio/Ext/Align/libs/makefile cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap cp Bio/Ext/Align/libs/proteindb.h blib/lib/Bio/Ext/Align/libs/proteindb.h cp Bio/Ext/Align/libs/btcanvas.c blib/lib/Bio/Ext/Align/libs/btcanvas.c cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/dpalign.h blib/lib/Bio/Ext/Align/libs/dpalign.h cp Bio/Ext/Align/libs/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c cp Bio/SeqIO/staden/MANIFEST blib/lib/Bio/SeqIO/staden/MANIFEST cp Bio/Ext/Align/libs/wiserandom.c blib/lib/Bio/Ext/Align/libs/wiserandom.c cp Bio/Ext/Align/libs/btcanvas.h blib/lib/Bio/Ext/Align/libs/btcanvas.h cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/SeqIO/staden/t/staden/data/readtest.ctf blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ctf cp Bio/SeqIO/staden/t/staden/data/readtest.ztr blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ztr cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h cp Bio/Ext/Align/libs/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c cp Bio/Ext/Align/libs/wisememman.c blib/lib/Bio/Ext/Align/libs/wisememman.c cp Bio/Ext/Align/libs/seqaligndisplay.c blib/lib/Bio/Ext/Align/libs/seqaligndisplay.c cp Bio/Ext/Align/libs/commandline.c blib/lib/Bio/Ext/Align/libs/commandline.c cp Bio/Ext/Align/libs/alnconvert.h blib/lib/Bio/Ext/Align/libs/alnconvert.h cp Bio/Ext/Align/libs/compmat.h blib/lib/Bio/Ext/Align/libs/compmat.h cp Bio/Ext/Align/libs/dna.h blib/lib/Bio/Ext/Align/libs/dna.h cp Bio/Ext/Align/libs/basematrix.c blib/lib/Bio/Ext/Align/libs/basematrix.c cp Bio/Ext/Align/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat cp Bio/Ext/Align/libs/aln.h blib/lib/Bio/Ext/Align/libs/aln.h cp Bio/Ext/Align/libs/sequence.c blib/lib/Bio/Ext/Align/libs/sequence.c cp Bio/Ext/Align/scores.lst blib/lib/Bio/Ext/Align/scores.lst cp Bio/Ext/Align/libs/wisememman.h blib/lib/Bio/Ext/Align/libs/wisememman.h cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c cp Bio/Ext/Align/libs/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h cp Bio/SeqIO/staden/t/staden_read.t blib/lib/Bio/SeqIO/staden/t/staden_read.t cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o aln.o aln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnconvert.o alnconvert.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnrange.o alnrange.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o asciibtcanvas.o asciibtcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o basematrix.o basematrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o btcanvas.o btcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o commandline.o commandline.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexconsensi.o complexconsensi.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexevalset.o complexevalset.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexsequence.o complexsequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o compmat.o compmat.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o codon.o codon.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dna.o dna.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dnamatrix.o dnamatrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpenvelope.o dpenvelope.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dynlibcross.o dynlibcross.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o histogram.o histogram.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o hscore.o hscore.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linesubs.o linesubs.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o packaln.o packaln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o probability.o probability.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o protein.o protein.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteindb.o proteindb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteinsw.o proteinsw.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o seqaligndisplay.o seqaligndisplay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequence.o sequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequencedb.o sequencedb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sw_wrap.o sw_wrap.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseerror.o wiseerror.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisefile.o wisefile.c wisefile.dy: In function ?bp_sw_myfclose?: wisefile.dy:66: warning: format ?%d? expects type ?int?, but argument 3 has type ?struct FILE *? cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisememman.o wisememman.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseoverlay.o wiseoverlay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiserandom.o wiserandom.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisestring.o wisestring.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisetime.o wisetime.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpalign.o dpalign.c dpalign.c: In function ?dpAlign_fatal?: dpalign.c:43: warning: format not a string literal and no format arguments cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o ar: creating libsw.a make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c cc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.6.0\" -DXS_VERSION=\"1.6.0\" -fPIC "-I/usr/lib/perl/5.10/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c cc -c -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.007000\" -DXS_VERSION=\"1.007000\" -fPIC "-I/usr/lib/perl/5.10/CORE" read.c read.xs: In function ?staden_write_trace?: read.xs:17: warning: cast to pointer from integer of different size read.xs:22: warning: cast to pointer from integer of different size read.xs: In function ?staden_read_graph?: read.xs:204: warning: passing argument 2 of ?Perl_newRV? from incompatible pointer type /usr/lib/perl/5.10/CORE/proto.h:2166: note: expected ?struct SV *? but argument is of type ?struct AV *? Running Mkbootstrap for Bio::SeqIO::staden::read () chmod 644 read.bs rm -f ../blib/arch/auto/Bio/SeqIO/staden/read/read.so LD_RUN_PATH="/usr/local/lib" cc -shared -O2 -g -L/usr/local/lib -fstack-protector read.o -o ../blib/arch/auto/Bio/SeqIO/staden/read/read.so \ -L/usr/local/lib -lz -lm -lread \ chmod 755 ../blib/arch/auto/Bio/SeqIO/staden/read/read.so cp read.bs ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs chmod 644 ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' Manifying blib/man3/Bio::SeqIO::staden::read.3pm From tzhu at mail.bnu.edu.cn Mon Oct 24 07:37:06 2011 From: tzhu at mail.bnu.edu.cn (Tao Zhu) Date: Mon, 24 Oct 2011 19:37:06 +0800 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document Message-ID: <4EA54DE2.1040706@mail.bnu.edu.cn> Here is a script copied totally from documents for module Bio::DB::GenBank, use Bio::DB::GenBank; my $gb = Bio::DB::GenBank->new(); my $seq_obj = $gb->get_Seq_by_acc('J00522'); When I try to run it, it failed. The message appear like this: > Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > Compilation failed in require at (eval 2) line 2. > ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > Compilation failed in require at perlprogram_2.pl line 5. > BEGIN failed--compilation aborted at perlprogram_2.pl line 5. I've never see such error before, how does this come? -- Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing 100875, China Email: tzhu at mail.bnu.edu.cn From cjfields at illinois.edu Mon Oct 24 09:07:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 13:07:56 +0000 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <4EA54DE2.1040706@mail.bnu.edu.cn> References: <4EA54DE2.1040706@mail.bnu.edu.cn> Message-ID: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> As might be implied by the error, you do not have URI::Escape installed, which is a dependency of Bio::DB::GenBank. chris On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > Here is a script copied totally from documents for module Bio::DB::GenBank, > > > use Bio::DB::GenBank; > my $gb = Bio::DB::GenBank->new(); > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > When I try to run it, it failed. The message appear like this: >> Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> Compilation failed in require at (eval 2) line 2. >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. >> Compilation failed in require at perlprogram_2.pl line 5. >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > I've never see such error before, how does this come? > > -- > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > 100875, China > Email: tzhu at mail.bnu.edu.cn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Mon Oct 24 11:10:39 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 16:10:39 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: > Hi, > I am having problems running Bio::Index::Fastq. ?I get the following error > when a quality line begins with '@'. > > ... > > Here is an example of a fastq record that is causing this error, The last > line which starts with an '@' ?is actually the qual line. > @5:105:15806:16092:Y > GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG > + > @9;A565:=8B? > > i see that chris has partially addressed this in the mailing list > http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html > > However as he pointed out at the time, it appears this may be a fairly large > problem. Have you double checked you have the latest BioPerl with that fix Chris mentioned? > My fastq seq and qual lines are alway only one line, so I think that adding > a line count and only checking for @ in the lines that $line_count%4 ==0 > ?would work since the header lines are always the first of 4 lines , 0,4,8, > etc. Yes, *if* you can assume that for your data, which is an assumption I wouldn't like to make a general purpose library like BioPerl (or Biopython) > BioPerl fastq parsing issues aside, is there another tool which allows you > to retrieve arbitrary sequences from a fastq file by sequence ID? > There's one called cdbfasta which looks like it might work ? does anyone > have experience with it? > > Thanks, > sofia > P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? > if so, perhaps their solution could be applied here. If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) or Bio.SeqIO.index_db (using SQLite) functions will give you random access by ID to assorted files including FASTQ, even with nasty line wrapping and quality lines starting with @ or +. The Biopython FASTQ indexer basically tracks the state: @ header, seq line(s), + line, or qual line(s). You pay a slight performance hit when building the index over assuming four lines per record, but it is robust to this kind of nasty data. Peter From cjfields at illinois.edu Mon Oct 24 12:10:38 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 16:10:38 +0000 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >> Hi, >> I am having problems running Bio::Index::Fastq. I get the following error >> when a quality line begins with '@'. >> >> ... >> >> Here is an example of a fastq record that is causing this error, The last >> line which starts with an '@' is actually the qual line. >> @5:105:15806:16092:Y >> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >> + >> @9;A565:=8B?> >> >> i see that chris has partially addressed this in the mailing list >> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >> >> However as he pointed out at the time, it appears this may be a fairly large >> problem. > > Have you double checked you have the latest BioPerl with that > fix Chris mentioned? This should be fixed in both CPAN and bioperl-live. If not let me know. >> My fastq seq and qual lines are alway only one line, so I think that adding >> a line count and only checking for @ in the lines that $line_count%4 ==0 >> would work since the header lines are always the first of 4 lines , 0,4,8, >> etc. > > Yes, *if* you can assume that for your data, which is an assumption I > wouldn't like to make a general purpose library like BioPerl (or Biopython) One could build in an optimization that takes this assumption into account when explicitly requested, something worth looking into. A lot of our short read pipelines use the 4-line format. >> BioPerl fastq parsing issues aside, is there another tool which allows you >> to retrieve arbitrary sequences from a fastq file by sequence ID? >> There's one called cdbfasta which looks like it might work ? does anyone >> have experience with it? >> >> Thanks, >> sofia >> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >> if so, perhaps their solution could be applied here. > > If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) > or Bio.SeqIO.index_db (using SQLite) functions will give you random > access by ID to assorted files including FASTQ, even with nasty line > wrapping and quality lines starting with @ or +. > > The Biopython FASTQ indexer basically tracks the state: @ header, seq > line(s), + line, or qual line(s). You pay a slight performance hit when > building the index over assuming four lines per record, but it is robust > to this kind of nasty data. > > Peter We should really look into a consistent OBDA-like indexing scheme that could work cross-Bio*. Or simply resuscitate OBDA. :) chris From p.j.a.cock at googlemail.com Mon Oct 24 12:17:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 17:17:18 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 5:10 PM, Fields, Christopher J wrote: > On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > >> On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >>> Hi, >>> I am having problems running Bio::Index::Fastq. ?I get the following error >>> when a quality line begins with '@'. >>> >>> ... >>> >>> Here is an example of a fastq record that is causing this error, The last >>> line which starts with an '@' ?is actually the qual line. >>> @5:105:15806:16092:Y >>> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >>> + >>> @9;A565:=8B?>> >>> >>> i see that chris has partially addressed this in the mailing list >>> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >>> >>> However as he pointed out at the time, it appears this may be a fairly large >>> problem. >> >> Have you double checked you have the latest BioPerl with that >> fix Chris mentioned? > > This should be fixed in both CPAN and bioperl-live. ?If not let me know. Good. >>> My fastq seq and qual lines are alway only one line, so I think that adding >>> a line count and only checking for @ in the lines that $line_count%4 ==0 >>> ?would work since the header lines are always the first of 4 lines , 0,4,8, >>> etc. >> >> Yes, *if* you can assume that for your data, which is an assumption I >> wouldn't like to make a general purpose library like BioPerl (or Biopython) > > One could build in an optimization that takes this assumption into account > when explicitly requested, something worth looking into. ?A lot of our short > read pipelines use the 4-line format. That's a sensible compromise. >>> BioPerl fastq parsing issues aside, is there another tool which allows you >>> to retrieve arbitrary sequences from a fastq file by sequence ID? >>> There's one called cdbfasta which looks like it might work ? does anyone >>> have experience with it? >>> >>> Thanks, >>> sofia >>> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >>> if so, perhaps their solution could be applied here. >> >> If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) >> or Bio.SeqIO.index_db (using SQLite) functions will give you random >> access by ID to assorted files including FASTQ, even with nasty line >> wrapping and quality lines starting with @ or +. >> >> The Biopython FASTQ indexer basically tracks the state: @ header, seq >> line(s), + line, or qual line(s). You pay a slight performance hit when >> building the index over assuming four lines per record, but it is robust >> to this kind of nasty data. >> >> Peter > > We should really look into a consistent OBDA-like indexing scheme > that could work cross-Bio*. ?Or simply resuscitate OBDA. :) > > chris +1 Our SQLite index is based on OBDA but replacing the BDB / flat file index with SQLite3. Also we're using the Biopython SeqIO format names which don't 100% align with BioPerl/EMBOSS/etc. Peter From chiragmatkarbioinfo at gmail.com Mon Oct 24 12:38:24 2011 From: chiragmatkarbioinfo at gmail.com (Chirag Matkar) Date: Mon, 24 Oct 2011 22:08:24 +0530 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> References: <4EA54DE2.1040706@mail.bnu.edu.cn> <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> Message-ID: Tao, You can install URI::Escape through CPAN. On Mon, Oct 24, 2011 at 6:37 PM, Fields, Christopher J < cjfields at illinois.edu> wrote: > As might be implied by the error, you do not have URI::Escape installed, > which is a dependency of Bio::DB::GenBank. > > chris > > On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > > > Here is a script copied totally from documents for module > Bio::DB::GenBank, > > > > > > use Bio::DB::GenBank; > > my $gb = Bio::DB::GenBank->new(); > > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > > > When I try to run it, it failed. The message appear like this: > >> Can't locate URI/Escape.pm in @INC (@INC contains: > /home/zhut/bin/PerlModule > /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux > /home/zhut/localperl/lib/site_perl/5.12.3 > /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 > .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> Compilation failed in require at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> Compilation failed in require at (eval 2) line 2. > >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > >> Compilation failed in require at perlprogram_2.pl line 5. > >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > > > I've never see such error before, how does this come? > > > > -- > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > > 100875, China > > Email: tzhu at mail.bnu.edu.cn > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Regards, Chirag From carandraug+dev at gmail.com Mon Oct 31 14:05:35 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Mon, 31 Oct 2011 18:05:35 +0000 Subject: [Bioperl-l] best way to edit sequence features In-Reply-To: References: Message-ID: Hi I've been planning on writing a free (as in freedom) tool to edit sequences and make plamids maps. The idea is to build the command line tool first and maybe later work on a GUI for it. The problem I foresee at the moment while designing it, is how to change a feature of the sequence. I'm not familiar with all sequence formats (only fasta, ensembl and genbank) but I can't see how to specify from the command line what feature to edit since I can't see any unique identifiers for them. Is there a file format that makes this easier? Any tips would be most appreciated. Thank in advance, Carn? Draug From gkuffel22 at gmail.com Thu Oct 20 18:58:07 2011 From: gkuffel22 at gmail.com (Gina) Date: Thu, 20 Oct 2011 15:58:07 -0700 (PDT) Subject: [Bioperl-l] Scripts for the Gene Ontology Database (GO) Message-ID: Is there anyway to use Bioperl to take an accession number of a gene and retrieve gene function information from the GO database? I have tried go-perl but it is not easy to use and doesn't work correctly on windows 7. Thanks for any information and ideas? From sofia2341 at gmail.com Mon Oct 24 10:58:13 2011 From: sofia2341 at gmail.com (Sofia Robb) Date: Mon, 24 Oct 2011 10:58:13 -0400 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual Message-ID: Hi, I am having problems running Bio::Index::Fastq. I get the following error when a quality line begins with '@'. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No description line parsed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368 STACK: Bio::SeqIO::fastq::next_dataset /usr/share/perl5/Bio/SeqIO/fastq.pm:71 STACK: Bio::SeqIO::fastq::next_seq /usr/share/perl5/Bio/SeqIO/fastq.pm:29 STACK: Bio::Index::AbstractSeq::fetch /usr/share/perl5/Bio/Index/AbstractSeq.pm:147 STACK: Bio::Index::AbstractSeq::get_Seq_by_id /usr/share/perl5/Bio/Index/AbstractSeq.pm:198 STACK: /home_stajichlab/robb/bin/clean_pairs_indexed.pl:68 Here is an example of a fastq record that is causing this error, The last line which starts with an '@' is actually the qual line. @5:105:15806:16092:Y GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG + @9;A565:=8B?) { if (/^@/ and $line_count % 4 == 0) { # $begin is the position of the first character after the '@' my $begin = tell($FASTQ) - length( $_ ) + 1; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); $c++; } } $line_count++; } -- BioPerl fastq parsing issues aside, is there another tool which allows you to retrieve arbitrary sequences from a fastq file by sequence ID? There's one called cdbfasta which looks like it might work ? does anyone have experience with it? Thanks, sofia P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? if so, perhaps their solution could be applied here. From rispoli at tigem.it Mon Oct 31 13:19:41 2011 From: rispoli at tigem.it (Rispoli Rossella) Date: Mon, 31 Oct 2011 18:19:41 +0100 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Message-ID: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ---------------------------------------------------------------------------- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ----------------------------------------------------------------------------- From Kevin.M.Brown at asu.edu Mon Oct 31 14:25:40 2011 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 31 Oct 2011 11:25:40 -0700 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro In-Reply-To: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> References: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Message-ID: <1A4207F8295607498283FE9E93B775B407F48285@EX02.asurite.ad.asu.edu> http://search.cpan.org/~cjfields/BioPerl/Bio/DB/TFBS/transfac_pro.pm Did you read the module documentation? -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Rispoli Rossella Sent: Monday, October 31, 2011 10:20 AM To: bioperl-l at bioperl.org Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ------------------------------------------------------------------------ ---- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ------------------------------------------------------------------------ ----- _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From manju.rawat2 at gmail.com Sat Oct 1 03:07:48 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Sat, 1 Oct 2011 12:37:48 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.fa -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau.fa','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); pl tell me what i am doing wrong. Thanks Manju Rawat From Russell.Smithies at agresearch.co.nz Sun Oct 2 19:27:22 2011 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 3 Oct 2011 12:27:22 +1300 Subject: [Bioperl-l] how to blast a seq against multiple dbase In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF33C15FA8623@exchsth.agresearch.co.nz> Did you try this? database => 'Chr1.db,Chr2.db,Chr3.db' Blast supports comma-separated database names so thin might have made it into BioPerl. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peter Cock > Sent: Wednesday, 28 September 2011 11:02 p.m. > To: Manju Rawat > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] how to blast a seq against multiple dbase > > On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat > wrote: > > Hello, > > > > I have downloaded all the chromosome of Bos Taurus and i'd changed > > them in blast format using makeblastdb..and now i want to localy blast > > my sequence against these all chromosome.. > > now i have 29 database.Is there any method by which can i blast my > > sequence against all 29 database in my program.. > > > > > > whta should i write in database???? > > > > @params = ('database' => '????????', 'outfile' => 'blast2.out', > > ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn'); > > > > The simple answer is make a combined database. This works internally with > alias files, have a look at the NR and NT databases for example - they act like > singe databases but are actually a collection of chunks. > > Even simpler would be to combine your Bos taurus sequence files into a > single multi-entry FASTA file, and make that into a single BLAST database. > > Peter > > _______________________________________________ > 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. ======================================================================= From ross at cuhk.edu.hk Mon Oct 3 00:19:52 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 12:19:52 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> Message-ID: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And from NodeI documentation, I cannot identify a way to make a Node object to a NodeI object. By the same token, methods like is_monophyletic or is_paraphyletic are also unable to work on LCA's. Web search does not return any examples about the manipulation of the LCA. Any hints would be highly appreciated so I can continue to dig out the remaining on my own. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; #or by the following _DATA_ my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); } print "$leaf1:LCA:$lca:ACL:$leaf2"; ; #print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } #_DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 00); From David.Messina at sbc.su.se Mon Oct 3 05:17:47 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 11:17:47 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: Hi Ross, Bio::Tree::Node is a NodeI object. It inherits ? or, more accurately, implements ? all of the methods in NodeI. Admittedly, it's a little obscure. The modules ending in 'I' ? the 'I' stands for Interface ? are never meant to be called directly. Rather, they define the methods that other modules, which are called directly, like Bio::Tree::Node, must have in order to be compliant with the Bio::Tree::NodeI interface. If you look at the code for NodeI, you'll that there are only a very few methods actually coded in there; most of them are simply empty placeholders. You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? Dave On Mon, Oct 3, 2011 at 06:19, Ross KK Leung wrote: > The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And > from NodeI documentation, I cannot identify a way to make a Node object to > a > NodeI object. By the same token, methods like is_monophyletic or > is_paraphyletic are also unable to work on LCA's. Web search does not > return > any examples about the manipulation of the LCA. Any hints would be highly > appreciated so I can continue to dig out the remaining on my own. > > > > use Bio::TreeIO; > > use Bio::Tree::TreeFunctionsI; > > > > $tab = "\t"; $nl = "\n"; > > my ($testtree) = @ARGV; #or by the following _DATA_ > > my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); > > while( my $tree = $treein->next_tree ){ > > %dist_matrix = (); > > > > my @leaves = $tree->get_leaf_nodes; > > foreach my $leaf1( @leaves ){ > > my $id1 = $leaf1->id; > > foreach my $leaf2( @leaves ){ > > my $id2 = $leaf2->id; > > if ($id1 eq $id2) { > > $dist_matrix{$id1}->{$id2} = 0; > > next; > > } > > my $distance = $tree->distance( -nodes => [$leaf1, > $leaf2] ); > > if ($id1 eq "A" and $id2 eq "B") { > > my $lca = $tree->get_lca(-nodes => [$leaf1, > $leaf2] ); > > } > > print "$leaf1:LCA:$lca:ACL:$leaf2"; ; > > #print $lca->id; ; > > my $distance2 = $tree->distance( -nodes => [$lca, > $leaf2] ); > > print $distance2; ; > > > > $dist_matrix{$id1}->{$id2} = $distance; > > } > > } > > } > > > > #_DATA_ > > > ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 > > 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 > > 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( > > L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 > > .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, > > (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 > > ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 > 00); > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ross at cuhk.edu.hk Mon Oct 3 06:28:38 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 18:28:38 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Dave wrote: >You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design Thanks for this reference, it is very good for me to understand better the architecture of Bioperl. >So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? But the following codes will generate errors because lca cannot be identified. my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; my $distance = $tree->distance( -nodes => [$leaf1,$leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1,$leaf2] ); } print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca,$leaf2] ); print $distance2; ; } } } _DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.00000000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.00000000); My ultimate goal is just to conveniently derive the information that nodes M and L share the same LCA O for the following tree. +---I | +---M | | | +---H | +---O | | | | +---G | | | | +---L | | | +---F A | +---E | | | +---K | | | | | +---D | | +---N | | +---C | | +---J | +---B From David.Messina at sbc.su.se Mon Oct 3 07:28:41 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 13:28:41 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: Hi Ross, >So, if I understand your question correctly, you should be able to use all > of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit > confused, is_monophyletic is something you'd call on a Tree object, not on a > Node object, right?**** > > But the following codes will generate errors because lca cannot be > identified. > Right, but there are some compile-time errors in your code. I changed a few things so I could get it to run: http://cl.ly/AdzH In my hands, there is a Node object returned as $lca. However, it doesn't have an id so the next line where you try to print $lca->id, I get an undefined value error. When I look at $lca, it doesn't seems to be equivalent to node C, which, based on the tree you supplied, I would expect to be the LCA. SO there may in fact be something wrong in the BioPerl code here, too. However, I'm not that familiar with these modules, and I know there's been some recent work done on them, so perhaps someone else can chime in here. **** > > My ultimate goal is just to conveniently derive the information that nodes > M and L share the same LCA O for the following tree. > Ok, thanks for that clarification. I think the code should be able to do that. Incidentally, the tree you provided in Newick format does not appear to me to be the same tree you drew as ASCII art ? is that right? Dave From thomas.sharpton at gmail.com Mon Oct 3 10:35:33 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 07:35:33 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: On Mon, Oct 3, 2011 at 4:28 AM, Dave Messina wrote: In my hands, there is a Node object returned as $lca. However, it doesn't > have an id so the next line where you try to print $lca->id, I get an > undefined value error. > > When I look at $lca, it doesn't seems to be equivalent to node C, which, > based on the tree you supplied, I would expect to be the LCA. SO there may > in fact be something wrong in the BioPerl code here, too. > > However, I'm not that familiar with these modules, and I know there's been > some recent work done on them, so perhaps someone else can chime in here. > Dave is (as usual) right: $lca is a Node object. He's also right that the node $lca doesn't have an id. But I don't think this is a problem with BioPerl, but rather with how the newick tree in question is formatted. Specifically, the tree that Ross provided only has ids at the leaf nodes, which is why $lca->id() is returning an error (the internal node ids are thus undefined). Ross, you'll need to adopt the following format for your trees if you want to call internal node ids, at least as I understand how these BioPerl modules work. Instead of: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); Structure your newick trees like this: (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; ** The above trees are identical, with the exception that the internal nodes E and F have identifiers (names) associated with them. Does that make sense? You might check the wikipedia page for more information (http://en.wikipedia.org/wiki/Newick_format) and you can quickly view both of the above trees through the web-based tool PhyloWidget ( http://www.phylowidget.org) to get a better understanding of what I'm talking above. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 13:41:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 01:41:27 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Thanks Tom. This is the 2nd time you help me. Suppose I change the structure to: ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; I have identified two problems. 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? From kboggavarapu2 at uh.edu Sun Oct 2 13:40:53 2011 From: kboggavarapu2 at uh.edu (krishna mohan) Date: Sun, 2 Oct 2011 12:40:53 -0500 Subject: [Bioperl-l] extract fasta headers of genes Message-ID: hi, How to obtain FASTA headers of genes associated to particular genomen using eUtils and BIOPERL From angel at mpi-marburg.mpg.de Mon Oct 3 13:27:07 2011 From: angel at mpi-marburg.mpg.de (roey.angel) Date: Mon, 3 Oct 2011 10:27:07 -0700 (PDT) Subject: [Bioperl-l] saving amino acids sequence to file Message-ID: <32583843.post@talk.nabble.com> Hi, I'm trying to save the amino acid sequence from a sequence object I retrieved from GenBank. I can easily save the nucleotide sequence with: my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); $out_nuc -> write_seq($seq_object); And I also managed to extract the amino acid sequence with: for my $feat_object ($seq_object->get_SeqFeatures) { # obtain features from seq object if ($feat_object->primary_tag eq "CDS") { # look for CDS features if ($feat_object->has_tag('translation')) { # look for amino acids for my $val ($feat_object->get_tag_values('translation')){ } } } } But is there a way to save that sequence into a file using write_seq or a similar method? Thanks in advance, Roey -- View this message in context: http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From thomas.sharpton at gmail.com Mon Oct 3 14:24:32 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 11:24:32 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: Hi Ross, On Mon, Oct 3, 2011 at 10:41 AM, Ross KK Leung wrote: > Thanks Tom. This is the 2nd time you help me. > This list has been a vital resource for me, so I'm happy to contribute when I can. > Suppose I change the structure to:**** > > ** ** > > ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G;**** > > ** ** > > I have identified two problems.**** > > ** ** > > 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). > > Can you provide the code you are using and the result and error it produces in your next email? This will help diagnose the problem. > **** > > 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? **** > > Yes, this is unfortunate, but you can automate the labeling of internal node ids using something like the following: #$tree_in is a TreeIO object while( my $tree = $tree_in->next_tree() ){ my $id_basename = "intnode_"; my $id_count = 0; my @nodes = $tree->get_nodes(); foreach my $node( @nodes ){ next if $node->is_Leaf(); my $id = $node->id(); if( !(defined( $id ) ) ){ $id = $id_basename . $id_count; $node->id( $id ); $id_count++; } } #print the new tree or continue processing it } Now all of the nodes in the tree will have some identifier associated with it. I haven't tried the above code block so I can't verify that it works perfectly. One issue I foresee is that node ids will be added to the tree in the order in which they appear in @nodes; you will have to cross reference a tree to interpret your results. Others might have better solutions to this problem. Let me know if you have questions. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 21:53:29 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 09:53:29 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From cjfields at illinois.edu Mon Oct 3 22:23:28 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 4 Oct 2011 02:23:28 +0000 Subject: [Bioperl-l] extract fasta headers of genes In-Reply-To: References: Message-ID: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook -c On Oct 2, 2011, at 12:40 PM, krishna mohan wrote: > hi, > How to obtain FASTA headers of genes associated to > particular genomen using eUtils and BIOPERL > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jluis.lavin at unavarra.es Tue Oct 4 05:48:31 2011 From: jluis.lavin at unavarra.es (=?ISO-8859-1?Q?Jos=E9_Luis_Lav=EDn?=) Date: Tue, 4 Oct 2011 11:48:31 +0200 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: It seems that all installation atempts failed for Perl 5.10...I'll have to upgrade my Perl version unless there'd be another Graphical module in Bioperl tah any of you could recommend. 2011/9/30 Fields, Christopher J > It's available for all perl versions from 5.8.8 up. I have it running with > perl 5.14. Now, I recall there being problems with installation on Mac OS > X, though I think that was mainly due to GD.pm and libgd. > > chris > > On Sep 30, 2011, at 3:23 AM, > wrote: > > > > > Dear All, > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > windows machine. > > > > I read about the Bio-Graphics module and it'd be wonderful to install it, > > but seems like it is only available for Perl 5.8... > > Is there any other Perl and/or Bioperl module to do the same kind of > > genomic and Blast report representation currently available? > > > > Thanks in advance > > > > -- > > Dr. Jos? Luis Lav?n Trueba > > > > Dpto. de Producci?n Agraria > > Grupo de Gen?tica y Microbiolog?a > > Universidad P?blica de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -- Dr. Jos? Luis Lav?n Trueba Dpto. de Producci?n Agraria Grupo de Gen?tica y Microbiolog?a Universidad P?blica de Navarra 31006 Pamplona Navarra SPAIN From David.Messina at sbc.su.se Tue Oct 4 06:12:51 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 4 Oct 2011 12:12:51 +0200 Subject: [Bioperl-l] saving amino acids sequence to file In-Reply-To: References: <32583843.post@talk.nabble.com> Message-ID: [Sent this yesterday just to Roey by accident; reposting to the list now.] Hi Roey, >From the feature table, I think you can only get the amino acid sequence as a string. If you'd like to be able to use the SeqIO methods on it, you'll need to create a Bio::Seq object from it first. For examples, look at the 'To and From a String' section of the SeqIO HOWTO: http://www.bioperl.org/wiki/HOWTO:SeqIO But if you just want Fasta, plain ol' print statements are often sufficient. Dave On Mon, Oct 3, 2011 at 19:27, roey.angel wrote: > Hi, > >> I'm trying to save the amino acid sequence from a sequence object I > >> retrieved from GenBank. > >> I can easily save the nucleotide sequence with: > >> > my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); > >> $out_nuc -> write_seq($seq_object); > >> > And I also managed to extract the amino acid sequence with: > >> > for my $feat_object ($seq_object->get_SeqFeatures) { # obtain > >> features from seq object > >> if ($feat_object->primary_tag eq "CDS") { # look for CDS > >> features > >> if ($feat_object->has_tag('translation')) { # look for > >> amino acids > >> for my $val > >> ($feat_object->get_tag_values('translation')){ > >> } > >> } > >> } > >> } > >> > But is there a way to save that sequence into a file using write_seq or a > >> similar method? > >> > Thanks in advance, > >> Roey > -- > View this message in context: > http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lincoln.stein at gmail.com Tue Oct 4 07:51:49 2011 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 4 Oct 2011 07:51:49 -0400 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: Exactly what problems are you encountering? Are you using ActiveState Perl, and if so, at what step is the install failing? Lincoln 2011/10/4 Jos? Luis Lav?n > It seems that all installation atempts failed for Perl 5.10...I'll have to > upgrade my Perl version unless there'd be another Graphical module in > Bioperl tah any of you could recommend. > > 2011/9/30 Fields, Christopher J > > > It's available for all perl versions from 5.8.8 up. I have it running > with > > perl 5.14. Now, I recall there being problems with installation on Mac > OS > > X, though I think that was mainly due to GD.pm and libgd. > > > > chris > > > > On Sep 30, 2011, at 3:23 AM, > > wrote: > > > > > > > > Dear All, > > > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > > windows machine. > > > > > > I read about the Bio-Graphics module and it'd be wonderful to install > it, > > > but seems like it is only available for Perl 5.8... > > > Is there any other Perl and/or Bioperl module to do the same kind of > > > genomic and Blast report representation currently available? > > > > > > Thanks in advance > > > > > > -- > > > Dr. Jos? Luis Lav?n Trueba > > > > > > Dpto. de Producci?n Agraria > > > Grupo de Gen?tica y Microbiolog?a > > > Universidad P?blica de Navarra > > > 31006 Pamplona > > > Navarra > > > SPAIN > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From thomas.sharpton at gmail.com Tue Oct 4 14:05:27 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 11:05:27 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Message-ID: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > Hi, Tom. Let me formally define my problem because this would be > more effective for communication. My objective is to assign a state > for intermediate nodes. For the following example, nodes M and J can > be assigned with (Wing). After assignment (forget the unassigned > first), the pairwise distances of these intermediate nodes and any > other nodes may be compared (e.g. Nodes M and L; Nodes J and E). > > > +---I (Wing) > | > +---M > | | > | +---H (Wing) > | > +---O > | | > | | > | | > | +---L (No-Wing) > | > | > Z > | +---E (Wing) > | | > | +---K > | | | > | | +---D (No-Wing) > | | > +---N > | > | +---C (Wing) > | | > +---J > | > +---B (Wing) > > Technically, I can either use TreeFunctionsI's method add_trait to > the leaves first. Then I back trace the ancestral nodes. While nodes > K and J are pictorially displayed to be nicely at the same level, in > fact besides exhaustively testing NodeI's methods ancestor or > get_all_Descendants etc, I cannot come up with a better idea. As you > have mentioned before, when the tree is big, this curse is > amplified, not to say "Wing" is just one of several hundred > properties to test. > > That's why I'm posting this question to see whether any convenient > data structures already exist to tackle this kind of "graph- > traversing" process. From ross at cuhk.edu.hk Tue Oct 4 19:32:42 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 07:32:42 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Message-ID: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Hi Tom, I shall infer the state based on descendant's states. In my example, Nodes H and I belong to "Wing", then their ancestor M is also assigned "Wing". After assigning these states to all the nodes of the tree, I shall calculate the distances between these nodes. Switching to C is only the last option because that involves another 2 months, not to include the time if C does not have any libraries to deal with Newick Tree. Best, Ross From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] Sent: 2011??10??5?? 2:05 To: Ross KK Leung Cc: bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From R.A.Vos at reading.ac.uk Tue Oct 4 19:59:52 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 01:59:52 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 2:05 > To: Ross KK Leung > Cc: bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > > > > Hi Ross, > > > > I understand that you want to infer ancestral states on your tree, but I'm > unclear about how you want to do so. Can you clarify how you infer the state > for node K on your example tree? In particular, is your method of inference > dependent on the branch lengths? The answers to these questions will > (hopefully) help guide you to methods that can assist you. > > > > Unfortunately, Perl is not the most efficient language for tree/graph > traversal. It can certainly be done, but for very, very large trees, I tend > to roll over to C (but only if I have to as I am not proficient in C). > > > > Best, > > Tom > > > > On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > > > > > > Hi, Tom. Let me formally define my problem because this would be more > effective for communication. My objective is to assign a state for > intermediate nodes. For the following example, nodes M and J can be assigned > with (Wing). After assignment (forget the unassigned first), the pairwise > distances of these intermediate nodes and any other nodes may be compared > (e.g. Nodes M and L; Nodes J and E). > > > > > > +---I (Wing) > > | > > +---M > > | | > > | +---H (Wing) > > | > > +---O > > | | > > | | > > | | > > | +---L (No-Wing) > > | > > | > > Z > > | +---E (Wing) > > | | > > | +---K > > | | | > > | | +---D (No-Wing) > > | | > > +---N > > | > > | +---C (Wing) > > | | > > +---J > > | > > +---B (Wing) > > > > Technically, I can either use TreeFunctionsI's method add_trait to the > leaves first. Then I back trace the ancestral nodes. While nodes K and J are > pictorially displayed to be nicely at the same level, in fact besides > exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I > cannot come up with a better idea. As you have mentioned before, when the > tree is big, this curse is amplified, not to say "Wing" is just one of > several hundred properties to test. > > > > That's why I'm posting this question to see whether any convenient data > structures already exist to tackle this kind of "graph-traversing" process. > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 20:04:22 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 08:04:22 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: <002201cc82f2$565c2e40$03148ac0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:00 To: Ross KK Leung Cc: Thomas Sharpton; bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? I will assign "undetermined" and the detailed plan of assignment is too much to mention here. From R.A.Vos at reading.ac.uk Tue Oct 4 20:42:08 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 02:42:08 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002201cc82f2$565c2e40$03148ac0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. 2011/10/5 Ross KK Leung : > -----Original Message----- > From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger > Vos > Sent: 2011??10??5?? 8:00 > To: Ross KK Leung > Cc: Thomas Sharpton; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > >> I shall infer the state based on descendant's states. In my example, Nodes > H >> and I belong to "Wing", then their ancestor M is also assigned "Wing". > After >> assigning these states to all the nodes of the tree, I shall calculate the >> distances between these nodes. > > What is your approach for when internal states are equivocal? > > I will assign "undetermined" and the detailed plan of assignment is too much > to mention here. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Tue Oct 4 21:10:33 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 09:10:33 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011??10??5?? 8:42 To: Ross KK Leung Cc: bioperl-l; Thomas Sharpton Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. Thanks, Rutger. While there is a convenient function to help calculate the distances between leaf nodes, I find it difficult for ancestors. After using get_lca, it seems that bioperl has no data structures to help manipulate these LCA's. From thomas.sharpton at gmail.com Tue Oct 4 21:43:38 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 18:43:38 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> Message-ID: Hi Ross, I think Rutger has given you a good idea and it is certainly simpler than the solution I just concocted (no surprise there). Regarding your most recent note: 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help calculate the > distances between leaf nodes, I find it difficult for ancestors. After > using > get_lca, it seems that bioperl has no data structures to help manipulate > these LCA's. > > >From what I understand, the get_lca does return a node object, specifically an internal node. The following is from the BioPerl documentation (note the "Returns" line): Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no common ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes You can get the distance between any two nodes, including an internal node, using the distance method. Note that the nodes you input into the distance function do not need to have ids associated with them. For example, #$nodeA and $nodeB are BioPerl node objects that correspond to any node on the tree my $lca = get_lca( $nodeA, $nodeB ); my $distance = distance( $nodeA, $lca ); $distance will now contain the total branch length between nodeA and the last common ancestor between nodes A and B. At no point are node ids used to conduct calculation; only the node objects themselves are needed. Anything that you can do to a node, you can do to $lca. This is how I understand the functions, at least. Someone please correct me if I'm wrong, as I fear I sound like a broken record at this point.... Best, Tom From thomas.sharpton at gmail.com Wed Oct 5 13:47:53 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Wed, 5 Oct 2011 10:47:53 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <004101cc836f$6a4a6250$3edf26f0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: Hi Ross, Let's keep this discussion on the listserv so that others can benefit from and contribute to it. I just executed your script using the tree you provided (for those following along, I have copied the script and tree below my signature). It produces no warnings or errors on my machine. Look below my signature to see the terminal output of this test run on my computer. Are you working with the latest version of bioperl? What version of perl are you using? I see that the warning (which is distinct from an error) that you are getting is: "MSG: At least some nodes do not have a branch length, the distance returned could be wrong" I also see in your newick tree that you have given the root node (node G) an ID, but no branch length. I'm thinking that you may have an old version of bioperl, which might bark at you when you have a root node with an id but no branch length. Note that the distances being printed in my output (which is not the distance between the node ids that precede the value printed, but instead the distance between the LCA of these node ids and the second of the two ids printed) are indeed correct. Can you provide information on the version of BioPerl and Perl that you are trying this on? Best, Tom ########## testtree.nwk ------------------ ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; ########## test.pl ----------------- use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } # next if( defined( $dist_matrix{$id1}->{$id2} ) || defined ( $dist_matrix{$id2}->{$id1} ) ); my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); #print "$leaf1 and $leaf2 distance: $distance\n"; # print "$id1 and $id2 distance: $distance\n"; #=pod print $id1; ; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); # print $lca->id; #; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; #=cut } } } ######### output --------------- [sharpton at kazushi ~]$perl test.pl test.nwk A B 0.2 A C 0.8 A D 0.9 B A 0.1 B C 0.8 B D 0.9 C A 0.4 C B 0.5 C D 0.4 D A 0.4 D B 0.5 D C 0.3 [sharpton at kazushi ~]$ On Oct 5, 2011, at 7:59 AM, Ross KK Leung wrote: > Hi Tom, > > I personally attach this program and tree files to you and see > whether you can run the program without any error (mine does, I > can't use Modern perl as I can't request the admin to install/update > anything).... > > Thanks a lot, Ross > > > > > > > > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011??10??5?? 9:44 > To: Ross KK Leung > Cc: Rutger Vos; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other > nodes from a tree > > Hi Ross, > > I think Rutger has given you a good idea and it is certainly simpler > than the solution I just concocted (no surprise there). > > Regarding your most recent note: > > 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help > calculate the > distances between leaf nodes, I find it difficult for ancestors. > After using > get_lca, it seems that bioperl has no data structures to help > manipulate > these LCA's. > > > From what I understand, the get_lca does return a node object, > specifically an internal node. The following is from the BioPerl > documentation (note the "Returns" line): > > > > Title : get_lca > Usage : get_lca(-nodes => \@nodes ); OR > get_lca(@nodes); > Function: given two or more nodes, returns the lowest common > ancestor (aka most > recent common ancestor) > > > Returns : node object or undef if there is no common ancestor > Args : -nodes => arrayref of nodes to test, OR > just a list of nodes > > You can get the distance between any two nodes, including an > internal node, using the distance method. Note that the nodes you > input into the distance function do not need to have ids associated > with them. For example, > > #$nodeA and $nodeB are BioPerl node objects that correspond to any > node on the tree > my $lca = get_lca( $nodeA, $nodeB ); > my $distance = distance( $nodeA, $lca ); > > $distance will now contain the total branch length between nodeA and > the last common ancestor between nodes A and B. At no point are node > ids used to conduct calculation; only the node objects themselves > are needed. Anything that you can do to a node, you can do to $lca. > > This is how I understand the functions, at least. Someone please > correct me if I'm wrong, as I fear I sound like a broken record at > this point.... > > Best, > Tom > From ross at cuhk.edu.hk Thu Oct 6 03:07:11 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Thu, 6 Oct 2011 15:07:11 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: <006501cc83f6$91830ca0$b48925e0$@edu.hk> Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } From ross at cuhk.edu.hk Fri Oct 7 04:49:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 16:49:27 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <006501cc83f6$91830ca0$b48925e0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> Message-ID: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> each_Descendent documentation mentions "not a recursive fetchall" and I find out a method called "recursion" may solve my problem. the principle is to first force_binary, then start from root and go down along the tree until Is_Leaf, and then assign ancestor and continue the "recursion". -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ross KK Leung Sent: 2011??10??6?? 15:07 To: 'Thomas Sharpton' Cc: 'bioperl-l' Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From ross at cuhk.edu.hk Fri Oct 7 09:16:12 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 21:16:12 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> <00d b01cc84ce$0592d4e0$10b87ea0$@edu.hk> Message-ID: <00f601cc84f3$49406ca0$dbc145e0$@edu.hk> I use the following codes to test and find that the root node G is not assigned state "Opter". Moreover, I find that when a tree looks like this, +---I (Wing) | +---M | | | +---H (Wing) | O | | | +---L (No-Wing) L cannot match with internal node M as L is already a leaf node. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; system("cat $testtree"); my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf( @leaves ){ $leaf->add_tag_value("state", "Wing"); } $rootnode=$tree->get_root_node; Traverse($rootnode); @tmpnodes = $tree->get_nodes; foreach $prnnode (@tmpnodes) { $prnval = $prnnode->get_tag_values("state"); print $prnnode->id, "\t"; print $prnval, "\n"; } } sub Traverse { ($node) = @_; my $state = "dummy"; foreach my $desnode ( $node->each_Descendent() ) { if (!($desnode->is_Leaf)) { Traverse($desnode); } push @cmpnodes, $desnode; } #assume binary? if ($cmpnodes[0]->get_tag_values("state") eq $cmpnodes[1]->get_tag_values("state")) { # $node->add_tag_value("state", $cmpnodes[0]->get_tag_values("state")); $node->add_tag_value("state", "Opter"); } } __DATA__ ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; From maquino at knome.com Tue Oct 11 10:44:06 2011 From: maquino at knome.com (Mark Aquino) Date: Tue, 11 Oct 2011 10:44:06 -0400 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues Message-ID: Hi, I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. Code: #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -usehistory => 'y'); $esearch->get_Response || die; my @h_genes = $esearch->get_ids; print "@h_genes\n"; my $history = $esearch->next_History || die "elink failed"; my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -history => $history, -cmd => 'neighbor_history'); $elink->get_Response; my $hist1 = $elink->next_History; my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -history => $hist1, -cookie => $elink->next_cookie); $esum->get_Response || die "esum failed"; while (my $docsum = $esum->next_DocSum){ print $docsum->get_id,"\n"; print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; } [According to what I can find, the method get_Content_by_name should work but I am getting the error: Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From cjfields at illinois.edu Tue Oct 11 16:16:00 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 11 Oct 2011 20:16:00 +0000 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues In-Reply-To: References: Message-ID: <85FDDEF8-1522-4209-AA21-E51E436E6158@illinois.edu> Mark, Some odd things going on with homologen data, but I wanted to address a few points first. The code has a number of issues: * Missing email (warnings pop up). This will be required in future releases of Bio::DB::EUtilities, it's already technically required by NCBI * 'perldoc Bio::Tools::EUtilities::Summary::DocSum' indicates the method name is 'get_contents_by_name' (note lower-case and plural). As the name implies, it returns a list of raw data * Missing the elink databases. The history will capture the original queried database, but not the database linked to; the default on NCBI's end is pubmed when db is not set), which leads to... * The last EUtilities call is to 'pubmed', from the history. If you dump the docsum output (add a 'print $docsum->to_string) this is apparent. * Content key is wrong. Dumping the raw data initially is a good idea for debugging to ensure you are capturing the correct key. In this case, the key is 'TaxId' (note the case). * Calls to get_Response() are unnecessary; this just returns the HTTP::Response object from the user agent if you need the raw output. Calls to the eutilities-specific methods will lazily grab incoming data and parse as needed, so get_ids() alone will work as you would expect. Note the homologene data is hierarchical; there is more than one gene per linked ID, so the item data is nested. The tools are meant to be fairly generic, so you could just retrieve all the TaxID information, but it might be more relevant to get the GeneIDs to go along with them for more context. The following works for me. chris =================================================== #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -email => , -usehistory => 'y'); my @h_genes = $eutil->get_ids; print "@h_genes\n"; my $history = $eutil->next_History || die "esearch failed"; $eutil->reset_parameters(-eutil => 'elink', -history => $history, -email => , -db => 'homologene', -cmd => 'neighbor_history'); $history = $eutil->next_History || die "elink failed"; $eutil->reset_parameters(-eutil => 'esummary', -email => , -history => $history); while (my $docsum = $eutil->next_DocSum) { print "Homologen ID:".$docsum->get_id."\n"; print "Label: ".($docsum->get_contents_by_name('Caption'))[0]."\n"; while (my $item = $docsum->next_Item) { # HomoloGeneDataList while (my $sub = $item->next_subItem) { # HomoloGeneData print "\tGeneId: ".($sub->get_contents_by_name('GeneID'))[0]."\n"; print "\tTaxId: ".($sub->get_contents_by_name('TaxId'))[0]."\n"; } } } On Oct 11, 2011, at 9:44 AM, Mark Aquino wrote: > Hi, > > I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. > > Code: > > #!/usr/bin/perl > use strict; > use warnings; > use Bio::DB::EUtilities; > my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', > -db => 'homologene', > -term => 'Copg AND mouse', > -usehistory => 'y'); > $esearch->get_Response || die; > my @h_genes = $esearch->get_ids; > print "@h_genes\n"; > my $history = $esearch->next_History || die "elink failed"; > my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', > -history => $history, > -cmd => 'neighbor_history'); > > $elink->get_Response; > my $hist1 = $elink->next_History; > my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', > -history => $hist1, > -cookie => $elink->next_cookie); > $esum->get_Response || die "esum failed"; > while (my $docsum = $esum->next_DocSum){ > print $docsum->get_id,"\n"; > print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; > } > > [According to what I can find, the method get_Content_by_name should work but I am getting the error: > Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From manju.rawat2 at gmail.com Wed Oct 12 01:32:06 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Wed, 12 Oct 2011 11:02:06 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin In-Reply-To: References: Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.txt -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); it working fine in terminal with following command but showing error in programming.. agl at agl-desktop:~/BP$ blastall -p blastn -d btau -i test_query.fa -o test.out pl tell me what i am doing wrong. Thanks Manju Rawat From rajasimhah at nei.nih.gov Wed Oct 12 12:07:03 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 12:07:03 -0400 Subject: [Bioperl-l] Installation problem Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> I am trying to install Bioperl since yesterday without any luck. I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. I am attaching errors encountered during one such attempt below. Please help. root at comp1z BioPerl-1.6.1]# perl Build.PL This package requires Module::Build v0.2805 or greater to install itself. Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at (eval 2) line 1 BEGIN failed--compilation aborted at (eval 2) line 1. BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. Compilation failed in require at Build.PL line 14. BEGIN failed--compilation aborted at Build.PL line 14. I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). Please help!!! Harsha National Eye Institute, Bethesda, MD 301-402-5734 From cjfields at illinois.edu Wed Oct 12 15:37:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:37:35 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> Message-ID: Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Oct 12 15:41:05 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:41:05 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> Message-ID: <54A3917D-C212-4219-9C29-8285F3254EA5@illinois.edu> Possibly, though hard to say unless you give it a try. It does have a lot of bug fixes though. chris On Oct 12, 2011, at 2:38 PM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > No Christopher, I am trying the latest stable version 1.6.1 > Should I expect a smoother install with 1.6.901? > > Harsha > > ________________________________________ > From: Fields, Christopher J [cjfields at illinois.edu] > Sent: Wednesday, October 12, 2011 3:37 PM > To: Rajasimha, Harsha (NIH/NEI) [C] > Cc: bioperl-l at bioperl.org > Subject: Re: [Bioperl-l] Installation problem > > Have you tried the latest version from CPAN (v1.6.901)? > > chris > > On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > >> I am trying to install Bioperl since yesterday without any luck. >> I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. >> I am attaching errors encountered during one such attempt below. Please help. >> >> root at comp1z BioPerl-1.6.1]# perl Build.PL >> This package requires Module::Build v0.2805 or greater to install itself. >> Base class package "Module::Build" is empty. >> (Perhaps you need to 'use' the module which defines that package first.) >> at (eval 2) line 1 >> BEGIN failed--compilation aborted at (eval 2) line 1. >> BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. >> Compilation failed in require at Build.PL line 14. >> BEGIN failed--compilation aborted at Build.PL line 14. >> >> I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). >> >> Please help!!! >> Harsha >> National Eye Institute, Bethesda, MD >> 301-402-5734 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From rajasimhah at nei.nih.gov Wed Oct 12 15:38:43 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 15:38:43 -0400 Subject: [Bioperl-l] Installation problem In-Reply-To: References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> No Christopher, I am trying the latest stable version 1.6.1 Should I expect a smoother install with 1.6.901? Harsha ________________________________________ From: Fields, Christopher J [cjfields at illinois.edu] Sent: Wednesday, October 12, 2011 3:37 PM To: Rajasimha, Harsha (NIH/NEI) [C] Cc: bioperl-l at bioperl.org Subject: Re: [Bioperl-l] Installation problem Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 09:07:18 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 09:07:18 -0400 Subject: [Bioperl-l] Fwd: [bioperl-network] Not indexed by CPAN (#1) References: Message-ID: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> bioperl-l, It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. Brian O. Begin forwarded message: > From: "Chad A. Davis" > Date: October 13, 2011 7:40:27 AM EDT > To: bosborne > Subject: [bioperl-network] Not indexed by CPAN (#1) > > I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. > > This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi > > CPAN 1.9800 > > -- > Reply to this email directly or view it on GitHub: > https://github.com/bioperl/bioperl-network/issues/1 From cjfields at illinois.edu Thu Oct 13 11:47:33 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 15:47:33 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> Message-ID: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Brian, If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. chris On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > bioperl-l, > > It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. > > Brian O. > > Begin forwarded message: > >> From: "Chad A. Davis" >> Date: October 13, 2011 7:40:27 AM EDT >> To: bosborne >> Subject: [bioperl-network] Not indexed by CPAN (#1) >> >> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >> >> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >> >> CPAN 1.9800 >> >> -- >> Reply to this email directly or view it on GitHub: >> https://github.com/bioperl/bioperl-network/issues/1 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 11:52:55 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 11:52:55 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Message-ID: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Yes, BOSBORNE. On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > Brian, > > If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? > > It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. > > chris > > On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > >> bioperl-l, >> >> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >> >> Brian O. >> >> Begin forwarded message: >> >>> From: "Chad A. Davis" >>> Date: October 13, 2011 7:40:27 AM EDT >>> To: bosborne >>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>> >>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>> >>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>> >>> CPAN 1.9800 >>> >>> -- >>> Reply to this email directly or view it on GitHub: >>> https://github.com/bioperl/bioperl-network/issues/1 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Oct 13 13:03:49 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 17:03:49 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Message-ID: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. chris On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > Yes, BOSBORNE. > > On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > >> Brian, >> >> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >> >> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >> >> chris >> >> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >> >>> bioperl-l, >>> >>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>> >>> Brian O. >>> >>> Begin forwarded message: >>> >>>> From: "Chad A. Davis" >>>> Date: October 13, 2011 7:40:27 AM EDT >>>> To: bosborne >>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>> >>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>> >>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>> >>>> CPAN 1.9800 >>>> >>>> -- >>>> Reply to this email directly or view it on GitHub: >>>> https://github.com/bioperl/bioperl-network/issues/1 >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From bosborne11 at verizon.net Thu Oct 13 21:45:56 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 21:45:56 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> Message-ID: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Chris, OK, tell me what they say when you hear from them. BIO On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. > > chris > > On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > >> Yes, BOSBORNE. >> >> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >> >>> Brian, >>> >>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>> >>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>> >>> chris >>> >>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>> >>>> bioperl-l, >>>> >>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>> >>>> Brian O. >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Chad A. Davis" >>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>> To: bosborne >>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>> >>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>> >>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>> >>>>> CPAN 1.9800 >>>>> >>>>> -- >>>>> Reply to this email directly or view it on GitHub: >>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Fri Oct 14 08:48:19 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Fri, 14 Oct 2011 14:48:19 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: Because it may be related, I wanted to mention that I am having the same problem with Bioperl-Run. In this case, however, I can find the distribution via: i /bioperl-run/ But searching for a containing module does not return the distribution: i /clustalw/ Chad On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: > Chris, > > OK, tell me what they say when you hear from them. > > BIO > > > On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > >> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >> >> chris >> >> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >> >>> Yes, BOSBORNE. >>> >>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>> >>>> Brian, >>>> >>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>> >>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>> >>>>> bioperl-l, >>>>> >>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>> >>>>> Brian O. >>>>> >>>>> Begin forwarded message: >>>>> >>>>>> From: "Chad A. Davis" >>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>> To: bosborne >>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>> >>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>> >>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>> >>>>>> CPAN 1.9800 >>>>>> >>>>>> -- >>>>>> Reply to this email directly or view it on GitHub: >>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Fri Oct 14 09:34:22 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 14 Oct 2011 13:34:22 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). chris On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > Because it may be related, I wanted to mention that I am having the > same problem with Bioperl-Run. In this case, however, I can find the > distribution via: > > i /bioperl-run/ > > But searching for a containing module does not return the distribution: > > i /clustalw/ > > Chad > > On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >> Chris, >> >> OK, tell me what they say when you hear from them. >> >> BIO >> >> >> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >> >>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>> >>> chris >>> >>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>> >>>> Yes, BOSBORNE. >>>> >>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>> >>>>> Brian, >>>>> >>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>> >>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>> >>>>>> bioperl-l, >>>>>> >>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>> >>>>>> Brian O. >>>>>> >>>>>> Begin forwarded message: >>>>>> >>>>>>> From: "Chad A. Davis" >>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>> To: bosborne >>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>> >>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>> >>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>> >>>>>>> CPAN 1.9800 >>>>>>> >>>>>>> -- >>>>>>> Reply to this email directly or view it on GitHub: >>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Sun Oct 16 23:12:59 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 03:12:59 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? chris On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). > > chris > > On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > >> Because it may be related, I wanted to mention that I am having the >> same problem with Bioperl-Run. In this case, however, I can find the >> distribution via: >> >> i /bioperl-run/ >> >> But searching for a containing module does not return the distribution: >> >> i /clustalw/ >> >> Chad >> >> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>> Chris, >>> >>> OK, tell me what they say when you hear from them. >>> >>> BIO >>> >>> >>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>> >>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>> >>>>> Yes, BOSBORNE. >>>>> >>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>> >>>>>> Brian, >>>>>> >>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>> >>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>> >>>>>>> bioperl-l, >>>>>>> >>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>> >>>>>>> Brian O. >>>>>>> >>>>>>> Begin forwarded message: >>>>>>> >>>>>>>> From: "Chad A. Davis" >>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>> To: bosborne >>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>> >>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>> >>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>> >>>>>>>> CPAN 1.9800 >>>>>>>> >>>>>>>> -- >>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 04:08:16 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 17 Oct 2011 10:08:16 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: The index looks good now, I'm able to get the bioperl-network distro by depending on a module within it. Would it be possible to do the same for a bioperl-run 1.6.901 release? Cheers, Chad On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J wrote: > This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. > > Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? > > chris > > On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > >> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >> >> chris >> >> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >> >>> Because it may be related, I wanted to mention that I am having the >>> same problem with Bioperl-Run. In this case, however, I can find the >>> distribution via: >>> >>> i /bioperl-run/ >>> >>> But searching for a containing module does not return the distribution: >>> >>> i /clustalw/ >>> >>> Chad >>> >>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>> Chris, >>>> >>>> OK, tell me what they say when you hear from them. >>>> >>>> BIO >>>> >>>> >>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>> >>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>> >>>>>> Yes, BOSBORNE. >>>>>> >>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>> >>>>>>> Brian, >>>>>>> >>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>> >>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> bioperl-l, >>>>>>>> >>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>> >>>>>>>> Brian O. >>>>>>>> >>>>>>>> Begin forwarded message: >>>>>>>> >>>>>>>>> From: "Chad A. Davis" >>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>> To: bosborne >>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>> >>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>> >>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>> >>>>>>>>> CPAN 1.9800 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Oct 17 14:02:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 18:02:35 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. chris On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > The index looks good now, I'm able to get the bioperl-network distro > by depending on a module within it. > Would it be possible to do the same for a bioperl-run 1.6.901 release? > > Cheers, > Chad > > > On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J > wrote: >> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >> >> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >> >> chris >> >> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >> >>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>> >>> chris >>> >>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>> >>>> Because it may be related, I wanted to mention that I am having the >>>> same problem with Bioperl-Run. In this case, however, I can find the >>>> distribution via: >>>> >>>> i /bioperl-run/ >>>> >>>> But searching for a containing module does not return the distribution: >>>> >>>> i /clustalw/ >>>> >>>> Chad >>>> >>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>> Chris, >>>>> >>>>> OK, tell me what they say when you hear from them. >>>>> >>>>> BIO >>>>> >>>>> >>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>> >>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>> >>>>>>> Yes, BOSBORNE. >>>>>>> >>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> Brian, >>>>>>>> >>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>> >>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> bioperl-l, >>>>>>>>> >>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>> >>>>>>>>> Brian O. >>>>>>>>> >>>>>>>>> Begin forwarded message: >>>>>>>>> >>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>> To: bosborne >>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>> >>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>> >>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>> >>>>>>>>>> CPAN 1.9800 >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioperl-l mailing list >>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Oct 17 15:40:26 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 19:40:26 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. chris On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. > > chris > > On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > >> The index looks good now, I'm able to get the bioperl-network distro >> by depending on a module within it. >> Would it be possible to do the same for a bioperl-run 1.6.901 release? >> >> Cheers, >> Chad >> >> >> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >> wrote: >>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>> >>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>> >>> chris >>> >>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>> >>>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>> >>>>> Because it may be related, I wanted to mention that I am having the >>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>> distribution via: >>>>> >>>>> i /bioperl-run/ >>>>> >>>>> But searching for a containing module does not return the distribution: >>>>> >>>>> i /clustalw/ >>>>> >>>>> Chad >>>>> >>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>> Chris, >>>>>> >>>>>> OK, tell me what they say when you hear from them. >>>>>> >>>>>> BIO >>>>>> >>>>>> >>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>> >>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> Yes, BOSBORNE. >>>>>>>> >>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>> >>>>>>>>> Brian, >>>>>>>>> >>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>>> >>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>>> >>>>>>>>> chris >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>> >>>>>>>>>> bioperl-l, >>>>>>>>>> >>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>> >>>>>>>>>> Brian O. >>>>>>>>>> >>>>>>>>>> Begin forwarded message: >>>>>>>>>> >>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>> To: bosborne >>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>> >>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>> >>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>> >>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioperl-l mailing list >>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 18:33:00 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Tue, 18 Oct 2011 00:33:00 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Chris, Looks good. I find Bioperl-Run by querying one of the contained modules now. Thank you for sorting that out. Chad On Mon, Oct 17, 2011 at 21:40, Fields, Christopher J wrote: > I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. ?It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. > > chris > > On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > >> Yes, I planned on that ?but wanted to make sure everything was working from your end. ? Will upload that in a bit. >> >> chris >> >> On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: >> >>> The index looks good now, I'm able to get the bioperl-network distro >>> by depending on a module within it. >>> Would it be possible to do the same for a bioperl-run 1.6.901 release? >>> >>> Cheers, >>> Chad >>> >>> >>> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >>> wrote: >>>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>>> >>>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>>> >>>>> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>>> >>>>> chris >>>>> >>>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>>> >>>>>> Because it may be related, I wanted to mention that I am having the >>>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>>> distribution via: >>>>>> >>>>>> i /bioperl-run/ >>>>>> >>>>>> But searching for a containing module does not return the distribution: >>>>>> >>>>>> i /clustalw/ >>>>>> >>>>>> Chad >>>>>> >>>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>>> Chris, >>>>>>> >>>>>>> OK, tell me what they say when you hear from them. >>>>>>> >>>>>>> BIO >>>>>>> >>>>>>> >>>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> Yes, BOSBORNE. >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>>> >>>>>>>>>> Brian, >>>>>>>>>> >>>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>>>>> >>>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>>>>> >>>>>>>>>> chris >>>>>>>>>> >>>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>>> >>>>>>>>>>> bioperl-l, >>>>>>>>>>> >>>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>>> >>>>>>>>>>> Brian O. >>>>>>>>>>> >>>>>>>>>>> Begin forwarded message: >>>>>>>>>>> >>>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>>> To: bosborne >>>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>>> >>>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>>> >>>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>>> >>>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioperl-l mailing list >>>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From saxen at lbl.gov Mon Oct 17 20:37:59 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Mon, 17 Oct 2011 17:37:59 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch Message-ID: Hello, I am having problems using the Bio::DB::EUtilities module to retrieve data from Entrez. The following script is adapted from the code at http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. The input is a file containing a very long list of GI numbers from NCBI protein. When I run the script, I receive the following error message: Can't locate object method "get_Response" via package "Bio::DB::EUtilities::efetch" at getGP.pl line 23. #!/usr/bin/perl -w use warnings; use strict; use Bio::DB::EUtilities; use Bio::SeqIO; use Data::Dumper; my $id_file = $ARGV[0]; my $temp_file = 'temp.gp'; my @ids; open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; @ids = ; close IDFILE; my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', -db => 'protein', -rettype => 'gb', -email => 'saxen at lbl.gov', -id => \@ids); # dump HTTP::Response content to a file (not retained in memory) $factory->get_Response(-file => $temp_file); my $seqin = Bio::SeqIO->new(-file => $temp_file, -format => 'genbank'); while (my $seq = $seqin->next_seq) { print Dumper($seq); } I would appreciate any insight as to why I am receiving this error. Thanks in advance for your time! Seth Axen From carandraug+dev at gmail.com Mon Oct 17 21:16:40 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Tue, 18 Oct 2011 02:16:40 +0100 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On 18 October 2011 01:37, Seth D. Axen wrote: > Hello, > ? I am having problems using the Bio::DB::EUtilities module to retrieve > data from Entrez. The following script is adapted from the code at > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. > The input is a file containing a very long list of GI numbers from NCBI > protein. When I run the script, I receive the following error message: Can't > locate object method "get_Response" via package > "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > > #!/usr/bin/perl -w > use warnings; > use strict; > use Bio::DB::EUtilities; > use Bio::SeqIO; > use Data::Dumper; > > my $id_file = $ARGV[0]; > my $temp_file = 'temp.gp'; > my @ids; > > open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > @ids = ; > close IDFILE; > > my $factory = Bio::DB::EUtilities->new(-eutil ? => 'efetch', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? ?=> 'protein', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -rettype => 'gb', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -email ? => 'saxen at lbl.gov', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ?=> \@ids); > > # dump HTTP::Response content to a file (not retained in memory) > $factory->get_Response(-file => $temp_file); > > my $seqin = Bio::SeqIO->new(-file ? => $temp_file, > ? ? ? ? ? ? ? ? ? ? ? ? ? ?-format => 'genbank'); > > while (my $seq = $seqin->next_seq) { > ? print Dumper($seq); > } > > ? I would appreciate any insight as to why I am receiving this error. > Thanks in advance for your time! > ? Seth Axen Hi your code works fine for me. Can the problem be on your IDs or its file? By the way, drop the -w from the shebang line, you are alredy using warnings. Carn? From cjfields at illinois.edu Mon Oct 17 21:33:13 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 01:33:13 +0000 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > On 18 October 2011 01:37, Seth D. Axen wrote: >> Hello, >> I am having problems using the Bio::DB::EUtilities module to retrieve >> data from Entrez. The following script is adapted from the code at >> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. >> The input is a file containing a very long list of GI numbers from NCBI >> protein. When I run the script, I receive the following error message: Can't >> locate object method "get_Response" via package >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. >> >> #!/usr/bin/perl -w >> use warnings; >> use strict; >> use Bio::DB::EUtilities; >> use Bio::SeqIO; >> use Data::Dumper; >> >> my $id_file = $ARGV[0]; >> my $temp_file = 'temp.gp'; >> my @ids; >> >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; >> @ids = ; >> close IDFILE; >> >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', >> -db => 'protein', >> -rettype => 'gb', >> -email => 'saxen at lbl.gov', >> -id => \@ids); >> >> # dump HTTP::Response content to a file (not retained in memory) >> $factory->get_Response(-file => $temp_file); >> >> my $seqin = Bio::SeqIO->new(-file => $temp_file, >> -format => 'genbank'); >> >> while (my $seq = $seqin->next_seq) { >> print Dumper($seq); >> } >> >> I would appreciate any insight as to why I am receiving this error. >> Thanks in advance for your time! >> Seth Axen > > Hi > > your code works fine for me. Can the problem be on your IDs or its > file? By the way, drop the -w from the shebang line, you are alredy > using warnings. > > Carn? Also, check the BioPerl version, there was a very large change in the API before the v1.6 release. chris From jeanmarc.frigerio at gmail.com Tue Oct 18 08:43:51 2011 From: jeanmarc.frigerio at gmail.com (jmf) Date: Tue, 18 Oct 2011 05:43:51 -0700 (PDT) Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> Message-ID: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Hi I agree that it'd be nice to see it revived. I made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', Thanks Dave for the topic ! Chris can you correct the file or should I submit the patch (I don't know where ?) On 2 sep, 17:20, Jack Tanner wrote: > I also see that someone's forked it on Github and made some packaging fixes. > > It'd be nice to see it revived. > > On 9/2/2011 9:00 AM, Fields, Christopher J wrote: > > > > > > > > > > > I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. ?Otherwise I worry about the long-term support for it/ > > > chris > > > On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: > > >> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: > >>http://toolkit.tuebingen.mpg.de/hhpred > > >> He got it working thus: > >> Hi Dave, > >> thanks a lot. i made it work. The error i got later on was: > >> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; > >> recompile with -fPIC > > >> the solution is: > >> perl Makefile.PL PREFIX= ?/fftwsingle --enable-shared --with-pic --enable-single > >> > >> make > >> make install > >>http://forums.fedoraforum.org/showthread.php?t=232607 > > >> Dave > > >> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J ?wrote: > >> Yes, it's essentially deprecated (unmaintained). ?I don't know of anyone who has packaged that up in a while, if ever. > > >> chris > > >> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: > > >>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? > > >>> Does anyone have a spec file for building an SRPM for it for RHEL 6? > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioper... at lists.open-bio.org > >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioper... at lists.open-bio.org > >>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l From sarah.tincher at gmail.com Tue Oct 18 13:00:46 2011 From: sarah.tincher at gmail.com (Sarah Tincher) Date: Tue, 18 Oct 2011 12:00:46 -0500 Subject: [Bioperl-l] Issues with CLUSTALW Message-ID: Hello, I am new to BioPerl and have no computer science background. I am taking a bioinformatics course and I have an assignment to write a BioPerl script to perform the MSA of a specific six sequences, retrieving the sequences from NCBI and using CLUSTALW. This is the script I wrote based on a lecture from my course: #!usr/bin/perl use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; $gb = new Bio::DB::GenBank(); $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); $factory = Bio::Tools::Run::Alignment::Clustalw->new; @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); print "$aln\n"; And this is the error that I receive: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level /Library/Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at HW3_2.pl line 3. BEGIN failed--compilation aborted at HW3_2.pl line 3. I would appreciate any help you can provide. Thank you, Sarah Tincher From cjfields at illinois.edu Tue Oct 18 14:35:08 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:08 +0000 Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Message-ID: <364EF42F-D067-40B5-9B92-7D36ED22B6E1@illinois.edu> A patch is fine. Also, it might be worth talking to the WUSTL group on merging those changes from their fork in (fairly easy to do). At some point, if this code looks as if it needs to exist independently of bioperl-ext we can create a new repo for it. I think it will see more use that way. chris On Oct 18, 2011, at 7:43 AM, jmf wrote: > Hi > I agree that it'd be nice to see it revived. I made a patch to the Bio/ > Ext/Align/Makefile.PL to make the compiler happy, just by changing: > > 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', > to > 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', > > Thanks Dave for the topic ! > > Chris can you correct the file or should I submit the patch (I don't > know where ?) > > On 2 sep, 17:20, Jack Tanner wrote: >> I also see that someone's forked it on Github and made some packaging fixes. >> >> It'd be nice to see it revived. >> >> On 9/2/2011 9:00 AM, Fields, Christopher J wrote: >> >> >> >> >> >> >> >> >> >>> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. Otherwise I worry about the long-term support for it/ >> >>> chris >> >>> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: >> >>>> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: >>>> http://toolkit.tuebingen.mpg.de/hhpred >> >>>> He got it working thus: >>>> Hi Dave, >>>> thanks a lot. i made it work. The error i got later on was: >>>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; >>>> recompile with -fPIC >> >>>> the solution is: >>>> perl Makefile.PL PREFIX= /fftwsingle --enable-shared --with-pic --enable-single >>>> >>>> make >>>> make install >>>> http://forums.fedoraforum.org/showthread.php?t=232607 >> >>>> Dave >> >>>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J wrote: >>>> Yes, it's essentially deprecated (unmaintained). I don't know of anyone who has packaged that up in a while, if ever. >> >>>> chris >> >>>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: >> >>>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? >> >>>>> Does anyone have a spec file for building an SRPM for it for RHEL 6? >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioper... at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioper... at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Oct 18 14:35:41 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:41 +0000 Subject: [Bioperl-l] Issues with CLUSTALW In-Reply-To: References: Message-ID: <54A57FF8-5415-4798-89B5-3E256ECDE636@illinois.edu> You need to install BioPerl-Run as well as the core BioPerl modules. chris On Oct 18, 2011, at 12:00 PM, Sarah Tincher wrote: > Hello, > > I am new to BioPerl and have no computer science background. I am taking a > bioinformatics course and I have an assignment to write a BioPerl script to > perform the MSA of a specific six sequences, retrieving the sequences from > NCBI and using CLUSTALW. > > This is the script I wrote based on a lecture from my course: > > #!usr/bin/perl > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > $gb = new Bio::DB::GenBank(); > $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); > $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); > $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); > $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); > $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); > $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); > $factory = Bio::Tools::Run::Alignment::Clustalw->new; > @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); > $seq_array_ref = \@seq_array; > $aln = $factory->align($seq_array_ref); > print "$aln\n"; > > And this is the error that I receive: > > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: > /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 > /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin > /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level > /Library/Perl/Updates/5.8.8 > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) > at HW3_2.pl line 3. > BEGIN failed--compilation aborted at HW3_2.pl line 3. > > I would appreciate any help you can provide. > > Thank you, > Sarah Tincher > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From saxen at lbl.gov Tue Oct 18 20:15:21 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Tue, 18 Oct 2011 17:15:21 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: Thanks Carne and Chris! The problem was with my BioPerl version. Once I used the latest version, the script ran perfectly. Seth 2011/10/17 Fields, Christopher J > On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > > > On 18 October 2011 01:37, Seth D. Axen wrote: > >> Hello, > >> I am having problems using the Bio::DB::EUtilities module to retrieve > >> data from Entrez. The following script is adapted from the code at > >> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO > . > >> The input is a file containing a very long list of GI numbers from NCBI > >> protein. When I run the script, I receive the following error message: > Can't > >> locate object method "get_Response" via package > >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > >> > >> #!/usr/bin/perl -w > >> use warnings; > >> use strict; > >> use Bio::DB::EUtilities; > >> use Bio::SeqIO; > >> use Data::Dumper; > >> > >> my $id_file = $ARGV[0]; > >> my $temp_file = 'temp.gp'; > >> my @ids; > >> > >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > >> @ids = ; > >> close IDFILE; > >> > >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', > >> -db => 'protein', > >> -rettype => 'gb', > >> -email => 'saxen at lbl.gov', > >> -id => \@ids); > >> > >> # dump HTTP::Response content to a file (not retained in memory) > >> $factory->get_Response(-file => $temp_file); > >> > >> my $seqin = Bio::SeqIO->new(-file => $temp_file, > >> -format => 'genbank'); > >> > >> while (my $seq = $seqin->next_seq) { > >> print Dumper($seq); > >> } > >> > >> I would appreciate any insight as to why I am receiving this error. > >> Thanks in advance for your time! > >> Seth Axen > > > > Hi > > > > your code works fine for me. Can the problem be on your IDs or its > > file? By the way, drop the -w from the shebang line, you are alredy > > using warnings. > > > > Carn? > > > Also, check the BioPerl version, there was a very large change in the API > before the v1.6 release. > > chris > > > > From shachigahoimbi at gmail.com Fri Oct 21 01:59:12 2011 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 21 Oct 2011 11:29:12 +0530 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl Message-ID: Dear all, I have fasta format sequence file and I want to extract ORF ID "PITG_14194" from fasta file and then I want to rename same file with that ORF ID "PITG_14194". I have many files and I want to do same exercise with all sequence files. Please tell me how can i do this with perl or bioperl. >tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR NGIAVDHKGVICNGKAPIEIAVDENTLSAAA -- Regards, Shachi From jason.stajich at gmail.com Fri Oct 21 05:56:11 2011 From: jason.stajich at gmail.com (Jason Stajich) Date: Fri, 21 Oct 2011 02:56:11 -0700 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl In-Reply-To: References: Message-ID: easy to do this with a simple regular expression and opening a new file. Have you read up on this concept in Perl. You can use SeqIO to parse FASTA files - did you read the HOWTO and website documentation first? We don't typically do people's work for them on this mailing list so please show some effort first. On Oct 20, 2011, at 10:59 PM, Shachi Gahoi wrote: > Dear all, > > I have fasta format sequence file and I want to extract ORF ID "PITG_14194" > from fasta file and then I want to rename same file with that ORF ID > "PITG_14194". > > I have many files and I want to do same exercise with all sequence files. > > Please tell me how can i do this with perl or bioperl. > >> tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora > infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 > MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL > ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA > RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF > HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM > YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL > TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD > RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR > NGIAVDHKGVICNGKAPIEIAVDENTLSAAA > > > -- > Regards, > Shachi > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Fri Oct 21 11:09:13 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 21 Oct 2011 11:09:13 -0400 Subject: [Bioperl-l] Deobfuscator direct link? Message-ID: Hi everybody, Does anyone object to me changing the center front-page link to the Deobfuscator to go directly to http://bioperl.org/cgi-bin/deob_interface.cgi ? That would still leave the left sidebar link that goes to the wiki page. Dave From cjfields at illinois.edu Fri Oct 21 12:31:45 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 21 Oct 2011 16:31:45 +0000 Subject: [Bioperl-l] Deobfuscator direct link? In-Reply-To: References: Message-ID: <2E2B401F-F358-48AD-880C-3FA9575D9B17@illinois.edu> Go for it. chris On Oct 21, 2011, at 10:09 AM, Dave Messina wrote: > Hi everybody, > > Does anyone object to me changing the center front-page link to the > Deobfuscator to go directly to > > http://bioperl.org/cgi-bin/deob_interface.cgi > > ? > > That would still leave the left sidebar link that goes to the wiki page. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From zheboyang at gmail.com Fri Oct 21 21:38:56 2011 From: zheboyang at gmail.com (boyang zhe) Date: Sat, 22 Oct 2011 03:38:56 +0200 Subject: [Bioperl-l] bioperl-ext installation Message-ID: I try to install bioperl-ext. But I failed. So I try the method suggested by JMF< jeanmarc.frigerio at gmail.com>. made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'' Then I run make. It seems ok for compilation. However, it generate errors when I run make test. No any of the 20 tests passed. it seems that because " Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so" I did not see any Align.so file at those directory. In fact, I can only find a blank directory of blib/arch/auto/Bio/Ext. Hope for your help. It is really hard for me. Thank you very much. boyang info as below: make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic.t .. ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.04 cusr 0.00 csys = 0.08 CPU) Result: PASS make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..20 not ok 1 - use Bio::Ext::Align; # Failed test 'use Bio::Ext::Align;' # at test.pl line 15. # Tried to use 'Bio::Ext::Align'. # Error: Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_access_name_CompMat at /usr/lib/perl/5.10/DynaLoader.pm line 193. # at (eval 4) line 2 # Compilation failed in require at (eval 4) line 2. # BEGIN failed--compilation aborted at (eval 4) line 2. The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed. Please install the bioperl-ext package # Looks like you planned 20 tests but ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test exited with 1 just after 1. make[1]: *** [test_dynamic] Error 1 make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make: *** [subdirs-test] Error 2 This is the info for make. cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h cp Bio/SeqIO/staden/CHANGES blib/lib/Bio/SeqIO/staden/CHANGES cp Bio/Ext/Align/test.pl blib/lib/Bio/Ext/Align/test.pl cp Bio/Ext/Align/libs/wiseoverlay.h blib/lib/Bio/Ext/Align/libs/wiseoverlay.h cp Bio/Ext/Align/libs/proteinsw.h blib/lib/Bio/Ext/Align/libs/proteinsw.h cp Bio/Ext/Align/libs/wisebase.h blib/lib/Bio/Ext/Align/libs/wisebase.h cp Bio/Ext/Align/libs/seqaligndisplay.h blib/lib/Bio/Ext/Align/libs/seqaligndisplay.h cp Bio/Ext/Align/libs/dyna.h blib/lib/Bio/Ext/Align/libs/dyna.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/complexsequence.c blib/lib/Bio/Ext/Align/libs/complexsequence.c cp Bio/Ext/Align/libs/wisestring.h blib/lib/Bio/Ext/Align/libs/wisestring.h cp Bio/Ext/Align/libs/codon.c blib/lib/Bio/Ext/Align/libs/codon.c cp Bio/Ext/Align/libs/linspc.c blib/lib/Bio/Ext/Align/libs/linspc.c cp Bio/Ext/Align/libs/probability.h blib/lib/Bio/Ext/Align/libs/probability.h cp Bio/Ext/Align/Align.xs blib/lib/Bio/Ext/Align/Align.xs cp Bio/SeqIO/staden/t/staden/data/readtest.exp blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.exp cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h cp Bio/Ext/Align/blosum45.mat blib/lib/Bio/Ext/Align/blosum45.mat cp Bio/Ext/Align/libs/dynlibcross.c blib/lib/Bio/Ext/Align/libs/dynlibcross.c cp Bio/Ext/Align/libs/sequencedb.c blib/lib/Bio/Ext/Align/libs/sequencedb.c cp Bio/Ext/Align/libs/sw_wrap.c blib/lib/Bio/Ext/Align/libs/sw_wrap.c cp Bio/Ext/Align/libs/complexsequence.h blib/lib/Bio/Ext/Align/libs/complexsequence.h cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h cp Bio/Ext/Align/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h cp Bio/SeqIO/staden/t/staden/data/readtestabi.fa blib/lib/Bio/SeqIO/staden/t/staden/data/readtestabi.fa cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/SeqIO/staden/t/staden/data/readtest.pln blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.pln cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.c cp Bio/Ext/Align/libs/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/alnrange.c blib/lib/Bio/Ext/Align/libs/alnrange.c cp Bio/Ext/Align/libs/dpenvelope.h blib/lib/Bio/Ext/Align/libs/dpenvelope.h cp Bio/Ext/Align/blosum62.mat blib/lib/Bio/Ext/Align/blosum62.mat cp Bio/Ext/Align/libs/sequence.h blib/lib/Bio/Ext/Align/libs/sequence.h cp Bio/Ext/Align/libs/asciibtcanvas.h blib/lib/Bio/Ext/Align/libs/asciibtcanvas.h cp Bio/Ext/Align/blosum50.mat blib/lib/Bio/Ext/Align/blosum50.mat cp Bio/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm cp Bio/SeqIO/staden/README blib/lib/Bio/SeqIO/staden/README cp Bio/SeqIO/staden/read.xs blib/lib/Bio/SeqIO/staden/read.xs cp Bio/SeqIO/staden/t/staden/data/readtest.abi blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.abi cp Bio/Ext/Align/libs/protein.h blib/lib/Bio/Ext/Align/libs/protein.h cp Bio/Ext/Align/libs/sequencedb.h blib/lib/Bio/Ext/Align/libs/sequencedb.h cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/SeqIO/staden/t/staden/data/readtestref.scf blib/lib/Bio/SeqIO/staden/t/staden/data/readtestref.scf cp Bio/SeqIO/staden/Makefile.PL blib/lib/Bio/SeqIO/staden/Makefile.PL cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c cp Bio/Ext/Align/libs/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/SeqIO/staden/META.yml blib/lib/Bio/SeqIO/staden/META.yml cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/libs/histogram.h blib/lib/Bio/Ext/Align/libs/histogram.h cp Bio/Ext/Align/libs/makefile blib/lib/Bio/Ext/Align/libs/makefile cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap cp Bio/Ext/Align/libs/proteindb.h blib/lib/Bio/Ext/Align/libs/proteindb.h cp Bio/Ext/Align/libs/btcanvas.c blib/lib/Bio/Ext/Align/libs/btcanvas.c cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/dpalign.h blib/lib/Bio/Ext/Align/libs/dpalign.h cp Bio/Ext/Align/libs/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c cp Bio/SeqIO/staden/MANIFEST blib/lib/Bio/SeqIO/staden/MANIFEST cp Bio/Ext/Align/libs/wiserandom.c blib/lib/Bio/Ext/Align/libs/wiserandom.c cp Bio/Ext/Align/libs/btcanvas.h blib/lib/Bio/Ext/Align/libs/btcanvas.h cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/SeqIO/staden/t/staden/data/readtest.ctf blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ctf cp Bio/SeqIO/staden/t/staden/data/readtest.ztr blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ztr cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h cp Bio/Ext/Align/libs/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c cp Bio/Ext/Align/libs/wisememman.c blib/lib/Bio/Ext/Align/libs/wisememman.c cp Bio/Ext/Align/libs/seqaligndisplay.c blib/lib/Bio/Ext/Align/libs/seqaligndisplay.c cp Bio/Ext/Align/libs/commandline.c blib/lib/Bio/Ext/Align/libs/commandline.c cp Bio/Ext/Align/libs/alnconvert.h blib/lib/Bio/Ext/Align/libs/alnconvert.h cp Bio/Ext/Align/libs/compmat.h blib/lib/Bio/Ext/Align/libs/compmat.h cp Bio/Ext/Align/libs/dna.h blib/lib/Bio/Ext/Align/libs/dna.h cp Bio/Ext/Align/libs/basematrix.c blib/lib/Bio/Ext/Align/libs/basematrix.c cp Bio/Ext/Align/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat cp Bio/Ext/Align/libs/aln.h blib/lib/Bio/Ext/Align/libs/aln.h cp Bio/Ext/Align/libs/sequence.c blib/lib/Bio/Ext/Align/libs/sequence.c cp Bio/Ext/Align/scores.lst blib/lib/Bio/Ext/Align/scores.lst cp Bio/Ext/Align/libs/wisememman.h blib/lib/Bio/Ext/Align/libs/wisememman.h cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c cp Bio/Ext/Align/libs/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h cp Bio/SeqIO/staden/t/staden_read.t blib/lib/Bio/SeqIO/staden/t/staden_read.t cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o aln.o aln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnconvert.o alnconvert.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnrange.o alnrange.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o asciibtcanvas.o asciibtcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o basematrix.o basematrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o btcanvas.o btcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o commandline.o commandline.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexconsensi.o complexconsensi.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexevalset.o complexevalset.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexsequence.o complexsequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o compmat.o compmat.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o codon.o codon.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dna.o dna.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dnamatrix.o dnamatrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpenvelope.o dpenvelope.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dynlibcross.o dynlibcross.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o histogram.o histogram.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o hscore.o hscore.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linesubs.o linesubs.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o packaln.o packaln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o probability.o probability.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o protein.o protein.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteindb.o proteindb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteinsw.o proteinsw.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o seqaligndisplay.o seqaligndisplay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequence.o sequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequencedb.o sequencedb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sw_wrap.o sw_wrap.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseerror.o wiseerror.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisefile.o wisefile.c wisefile.dy: In function ?bp_sw_myfclose?: wisefile.dy:66: warning: format ?%d? expects type ?int?, but argument 3 has type ?struct FILE *? cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisememman.o wisememman.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseoverlay.o wiseoverlay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiserandom.o wiserandom.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisestring.o wisestring.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisetime.o wisetime.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpalign.o dpalign.c dpalign.c: In function ?dpAlign_fatal?: dpalign.c:43: warning: format not a string literal and no format arguments cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o ar: creating libsw.a make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c cc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.6.0\" -DXS_VERSION=\"1.6.0\" -fPIC "-I/usr/lib/perl/5.10/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c cc -c -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.007000\" -DXS_VERSION=\"1.007000\" -fPIC "-I/usr/lib/perl/5.10/CORE" read.c read.xs: In function ?staden_write_trace?: read.xs:17: warning: cast to pointer from integer of different size read.xs:22: warning: cast to pointer from integer of different size read.xs: In function ?staden_read_graph?: read.xs:204: warning: passing argument 2 of ?Perl_newRV? from incompatible pointer type /usr/lib/perl/5.10/CORE/proto.h:2166: note: expected ?struct SV *? but argument is of type ?struct AV *? Running Mkbootstrap for Bio::SeqIO::staden::read () chmod 644 read.bs rm -f ../blib/arch/auto/Bio/SeqIO/staden/read/read.so LD_RUN_PATH="/usr/local/lib" cc -shared -O2 -g -L/usr/local/lib -fstack-protector read.o -o ../blib/arch/auto/Bio/SeqIO/staden/read/read.so \ -L/usr/local/lib -lz -lm -lread \ chmod 755 ../blib/arch/auto/Bio/SeqIO/staden/read/read.so cp read.bs ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs chmod 644 ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' Manifying blib/man3/Bio::SeqIO::staden::read.3pm From tzhu at mail.bnu.edu.cn Mon Oct 24 07:37:06 2011 From: tzhu at mail.bnu.edu.cn (Tao Zhu) Date: Mon, 24 Oct 2011 19:37:06 +0800 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document Message-ID: <4EA54DE2.1040706@mail.bnu.edu.cn> Here is a script copied totally from documents for module Bio::DB::GenBank, use Bio::DB::GenBank; my $gb = Bio::DB::GenBank->new(); my $seq_obj = $gb->get_Seq_by_acc('J00522'); When I try to run it, it failed. The message appear like this: > Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > Compilation failed in require at (eval 2) line 2. > ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > Compilation failed in require at perlprogram_2.pl line 5. > BEGIN failed--compilation aborted at perlprogram_2.pl line 5. I've never see such error before, how does this come? -- Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing 100875, China Email: tzhu at mail.bnu.edu.cn From cjfields at illinois.edu Mon Oct 24 09:07:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 13:07:56 +0000 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <4EA54DE2.1040706@mail.bnu.edu.cn> References: <4EA54DE2.1040706@mail.bnu.edu.cn> Message-ID: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> As might be implied by the error, you do not have URI::Escape installed, which is a dependency of Bio::DB::GenBank. chris On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > Here is a script copied totally from documents for module Bio::DB::GenBank, > > > use Bio::DB::GenBank; > my $gb = Bio::DB::GenBank->new(); > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > When I try to run it, it failed. The message appear like this: >> Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> Compilation failed in require at (eval 2) line 2. >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. >> Compilation failed in require at perlprogram_2.pl line 5. >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > I've never see such error before, how does this come? > > -- > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > 100875, China > Email: tzhu at mail.bnu.edu.cn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Mon Oct 24 11:10:39 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 16:10:39 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: > Hi, > I am having problems running Bio::Index::Fastq. ?I get the following error > when a quality line begins with '@'. > > ... > > Here is an example of a fastq record that is causing this error, The last > line which starts with an '@' ?is actually the qual line. > @5:105:15806:16092:Y > GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG > + > @9;A565:=8B? > > i see that chris has partially addressed this in the mailing list > http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html > > However as he pointed out at the time, it appears this may be a fairly large > problem. Have you double checked you have the latest BioPerl with that fix Chris mentioned? > My fastq seq and qual lines are alway only one line, so I think that adding > a line count and only checking for @ in the lines that $line_count%4 ==0 > ?would work since the header lines are always the first of 4 lines , 0,4,8, > etc. Yes, *if* you can assume that for your data, which is an assumption I wouldn't like to make a general purpose library like BioPerl (or Biopython) > BioPerl fastq parsing issues aside, is there another tool which allows you > to retrieve arbitrary sequences from a fastq file by sequence ID? > There's one called cdbfasta which looks like it might work ? does anyone > have experience with it? > > Thanks, > sofia > P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? > if so, perhaps their solution could be applied here. If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) or Bio.SeqIO.index_db (using SQLite) functions will give you random access by ID to assorted files including FASTQ, even with nasty line wrapping and quality lines starting with @ or +. The Biopython FASTQ indexer basically tracks the state: @ header, seq line(s), + line, or qual line(s). You pay a slight performance hit when building the index over assuming four lines per record, but it is robust to this kind of nasty data. Peter From cjfields at illinois.edu Mon Oct 24 12:10:38 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 16:10:38 +0000 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >> Hi, >> I am having problems running Bio::Index::Fastq. I get the following error >> when a quality line begins with '@'. >> >> ... >> >> Here is an example of a fastq record that is causing this error, The last >> line which starts with an '@' is actually the qual line. >> @5:105:15806:16092:Y >> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >> + >> @9;A565:=8B?> >> >> i see that chris has partially addressed this in the mailing list >> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >> >> However as he pointed out at the time, it appears this may be a fairly large >> problem. > > Have you double checked you have the latest BioPerl with that > fix Chris mentioned? This should be fixed in both CPAN and bioperl-live. If not let me know. >> My fastq seq and qual lines are alway only one line, so I think that adding >> a line count and only checking for @ in the lines that $line_count%4 ==0 >> would work since the header lines are always the first of 4 lines , 0,4,8, >> etc. > > Yes, *if* you can assume that for your data, which is an assumption I > wouldn't like to make a general purpose library like BioPerl (or Biopython) One could build in an optimization that takes this assumption into account when explicitly requested, something worth looking into. A lot of our short read pipelines use the 4-line format. >> BioPerl fastq parsing issues aside, is there another tool which allows you >> to retrieve arbitrary sequences from a fastq file by sequence ID? >> There's one called cdbfasta which looks like it might work ? does anyone >> have experience with it? >> >> Thanks, >> sofia >> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >> if so, perhaps their solution could be applied here. > > If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) > or Bio.SeqIO.index_db (using SQLite) functions will give you random > access by ID to assorted files including FASTQ, even with nasty line > wrapping and quality lines starting with @ or +. > > The Biopython FASTQ indexer basically tracks the state: @ header, seq > line(s), + line, or qual line(s). You pay a slight performance hit when > building the index over assuming four lines per record, but it is robust > to this kind of nasty data. > > Peter We should really look into a consistent OBDA-like indexing scheme that could work cross-Bio*. Or simply resuscitate OBDA. :) chris From p.j.a.cock at googlemail.com Mon Oct 24 12:17:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 17:17:18 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 5:10 PM, Fields, Christopher J wrote: > On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > >> On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >>> Hi, >>> I am having problems running Bio::Index::Fastq. ?I get the following error >>> when a quality line begins with '@'. >>> >>> ... >>> >>> Here is an example of a fastq record that is causing this error, The last >>> line which starts with an '@' ?is actually the qual line. >>> @5:105:15806:16092:Y >>> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >>> + >>> @9;A565:=8B?>> >>> >>> i see that chris has partially addressed this in the mailing list >>> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >>> >>> However as he pointed out at the time, it appears this may be a fairly large >>> problem. >> >> Have you double checked you have the latest BioPerl with that >> fix Chris mentioned? > > This should be fixed in both CPAN and bioperl-live. ?If not let me know. Good. >>> My fastq seq and qual lines are alway only one line, so I think that adding >>> a line count and only checking for @ in the lines that $line_count%4 ==0 >>> ?would work since the header lines are always the first of 4 lines , 0,4,8, >>> etc. >> >> Yes, *if* you can assume that for your data, which is an assumption I >> wouldn't like to make a general purpose library like BioPerl (or Biopython) > > One could build in an optimization that takes this assumption into account > when explicitly requested, something worth looking into. ?A lot of our short > read pipelines use the 4-line format. That's a sensible compromise. >>> BioPerl fastq parsing issues aside, is there another tool which allows you >>> to retrieve arbitrary sequences from a fastq file by sequence ID? >>> There's one called cdbfasta which looks like it might work ? does anyone >>> have experience with it? >>> >>> Thanks, >>> sofia >>> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >>> if so, perhaps their solution could be applied here. >> >> If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) >> or Bio.SeqIO.index_db (using SQLite) functions will give you random >> access by ID to assorted files including FASTQ, even with nasty line >> wrapping and quality lines starting with @ or +. >> >> The Biopython FASTQ indexer basically tracks the state: @ header, seq >> line(s), + line, or qual line(s). You pay a slight performance hit when >> building the index over assuming four lines per record, but it is robust >> to this kind of nasty data. >> >> Peter > > We should really look into a consistent OBDA-like indexing scheme > that could work cross-Bio*. ?Or simply resuscitate OBDA. :) > > chris +1 Our SQLite index is based on OBDA but replacing the BDB / flat file index with SQLite3. Also we're using the Biopython SeqIO format names which don't 100% align with BioPerl/EMBOSS/etc. Peter From chiragmatkarbioinfo at gmail.com Mon Oct 24 12:38:24 2011 From: chiragmatkarbioinfo at gmail.com (Chirag Matkar) Date: Mon, 24 Oct 2011 22:08:24 +0530 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> References: <4EA54DE2.1040706@mail.bnu.edu.cn> <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> Message-ID: Tao, You can install URI::Escape through CPAN. On Mon, Oct 24, 2011 at 6:37 PM, Fields, Christopher J < cjfields at illinois.edu> wrote: > As might be implied by the error, you do not have URI::Escape installed, > which is a dependency of Bio::DB::GenBank. > > chris > > On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > > > Here is a script copied totally from documents for module > Bio::DB::GenBank, > > > > > > use Bio::DB::GenBank; > > my $gb = Bio::DB::GenBank->new(); > > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > > > When I try to run it, it failed. The message appear like this: > >> Can't locate URI/Escape.pm in @INC (@INC contains: > /home/zhut/bin/PerlModule > /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux > /home/zhut/localperl/lib/site_perl/5.12.3 > /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 > .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> Compilation failed in require at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> Compilation failed in require at (eval 2) line 2. > >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > >> Compilation failed in require at perlprogram_2.pl line 5. > >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > > > I've never see such error before, how does this come? > > > > -- > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > > 100875, China > > Email: tzhu at mail.bnu.edu.cn > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Regards, Chirag From carandraug+dev at gmail.com Mon Oct 31 14:05:35 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Mon, 31 Oct 2011 18:05:35 +0000 Subject: [Bioperl-l] best way to edit sequence features In-Reply-To: References: Message-ID: Hi I've been planning on writing a free (as in freedom) tool to edit sequences and make plamids maps. The idea is to build the command line tool first and maybe later work on a GUI for it. The problem I foresee at the moment while designing it, is how to change a feature of the sequence. I'm not familiar with all sequence formats (only fasta, ensembl and genbank) but I can't see how to specify from the command line what feature to edit since I can't see any unique identifiers for them. Is there a file format that makes this easier? Any tips would be most appreciated. Thank in advance, Carn? Draug From gkuffel22 at gmail.com Thu Oct 20 18:58:07 2011 From: gkuffel22 at gmail.com (Gina) Date: Thu, 20 Oct 2011 15:58:07 -0700 (PDT) Subject: [Bioperl-l] Scripts for the Gene Ontology Database (GO) Message-ID: Is there anyway to use Bioperl to take an accession number of a gene and retrieve gene function information from the GO database? I have tried go-perl but it is not easy to use and doesn't work correctly on windows 7. Thanks for any information and ideas? From sofia2341 at gmail.com Mon Oct 24 10:58:13 2011 From: sofia2341 at gmail.com (Sofia Robb) Date: Mon, 24 Oct 2011 10:58:13 -0400 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual Message-ID: Hi, I am having problems running Bio::Index::Fastq. I get the following error when a quality line begins with '@'. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No description line parsed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368 STACK: Bio::SeqIO::fastq::next_dataset /usr/share/perl5/Bio/SeqIO/fastq.pm:71 STACK: Bio::SeqIO::fastq::next_seq /usr/share/perl5/Bio/SeqIO/fastq.pm:29 STACK: Bio::Index::AbstractSeq::fetch /usr/share/perl5/Bio/Index/AbstractSeq.pm:147 STACK: Bio::Index::AbstractSeq::get_Seq_by_id /usr/share/perl5/Bio/Index/AbstractSeq.pm:198 STACK: /home_stajichlab/robb/bin/clean_pairs_indexed.pl:68 Here is an example of a fastq record that is causing this error, The last line which starts with an '@' is actually the qual line. @5:105:15806:16092:Y GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG + @9;A565:=8B?) { if (/^@/ and $line_count % 4 == 0) { # $begin is the position of the first character after the '@' my $begin = tell($FASTQ) - length( $_ ) + 1; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); $c++; } } $line_count++; } -- BioPerl fastq parsing issues aside, is there another tool which allows you to retrieve arbitrary sequences from a fastq file by sequence ID? There's one called cdbfasta which looks like it might work ? does anyone have experience with it? Thanks, sofia P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? if so, perhaps their solution could be applied here. From rispoli at tigem.it Mon Oct 31 13:19:41 2011 From: rispoli at tigem.it (Rispoli Rossella) Date: Mon, 31 Oct 2011 18:19:41 +0100 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Message-ID: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ---------------------------------------------------------------------------- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ----------------------------------------------------------------------------- From Kevin.M.Brown at asu.edu Mon Oct 31 14:25:40 2011 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 31 Oct 2011 11:25:40 -0700 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro In-Reply-To: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> References: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Message-ID: <1A4207F8295607498283FE9E93B775B407F48285@EX02.asurite.ad.asu.edu> http://search.cpan.org/~cjfields/BioPerl/Bio/DB/TFBS/transfac_pro.pm Did you read the module documentation? -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Rispoli Rossella Sent: Monday, October 31, 2011 10:20 AM To: bioperl-l at bioperl.org Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ------------------------------------------------------------------------ ---- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ------------------------------------------------------------------------ ----- _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From manju.rawat2 at gmail.com Sat Oct 1 07:07:48 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Sat, 1 Oct 2011 12:37:48 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.fa -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin [blastall] WARNING: Unable to open Batu.fa.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau.fa','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); pl tell me what i am doing wrong. Thanks Manju Rawat From Russell.Smithies at agresearch.co.nz Sun Oct 2 23:27:22 2011 From: Russell.Smithies at agresearch.co.nz (Smithies, Russell) Date: Mon, 3 Oct 2011 12:27:22 +1300 Subject: [Bioperl-l] how to blast a seq against multiple dbase In-Reply-To: References: Message-ID: <18DF7D20DFEC044098A1062202F5FFF33C15FA8623@exchsth.agresearch.co.nz> Did you try this? database => 'Chr1.db,Chr2.db,Chr3.db' Blast supports comma-separated database names so thin might have made it into BioPerl. --Russell > -----Original Message----- > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- > bounces at lists.open-bio.org] On Behalf Of Peter Cock > Sent: Wednesday, 28 September 2011 11:02 p.m. > To: Manju Rawat > Cc: bioperl-l at lists.open-bio.org > Subject: Re: [Bioperl-l] how to blast a seq against multiple dbase > > On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat > wrote: > > Hello, > > > > I have downloaded all the chromosome of Bos Taurus and i'd changed > > them in blast format using makeblastdb..and now i want to localy blast > > my sequence against these all chromosome.. > > now i have 29 database.Is there any method by which can i blast my > > sequence against all 29 database in my program.. > > > > > > whta should i write in database???? > > > > @params = ('database' => '????????', 'outfile' => 'blast2.out', > > ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn'); > > > > The simple answer is make a combined database. This works internally with > alias files, have a look at the NR and NT databases for example - they act like > singe databases but are actually a collection of chunks. > > Even simpler would be to combine your Bos taurus sequence files into a > single multi-entry FASTA file, and make that into a single BLAST database. > > Peter > > _______________________________________________ > 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. ======================================================================= From ross at cuhk.edu.hk Mon Oct 3 04:19:52 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 12:19:52 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> Message-ID: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And from NodeI documentation, I cannot identify a way to make a Node object to a NodeI object. By the same token, methods like is_monophyletic or is_paraphyletic are also unable to work on LCA's. Web search does not return any examples about the manipulation of the LCA. Any hints would be highly appreciated so I can continue to dig out the remaining on my own. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; #or by the following _DATA_ my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); } print "$leaf1:LCA:$lca:ACL:$leaf2"; ; #print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } #_DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 00); From David.Messina at sbc.su.se Mon Oct 3 09:17:47 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 11:17:47 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: Hi Ross, Bio::Tree::Node is a NodeI object. It inherits ? or, more accurately, implements ? all of the methods in NodeI. Admittedly, it's a little obscure. The modules ending in 'I' ? the 'I' stands for Interface ? are never meant to be called directly. Rather, they define the methods that other modules, which are called directly, like Bio::Tree::Node, must have in order to be compliant with the Bio::Tree::NodeI interface. If you look at the code for NodeI, you'll that there are only a very few methods actually coded in there; most of them are simply empty placeholders. You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? Dave On Mon, Oct 3, 2011 at 06:19, Ross KK Leung wrote: > The LCA obtained by get_lca from TreeFunctionsI is not a NodeI object. And > from NodeI documentation, I cannot identify a way to make a Node object to > a > NodeI object. By the same token, methods like is_monophyletic or > is_paraphyletic are also unable to work on LCA's. Web search does not > return > any examples about the manipulation of the LCA. Any hints would be highly > appreciated so I can continue to dig out the remaining on my own. > > > > use Bio::TreeIO; > > use Bio::Tree::TreeFunctionsI; > > > > $tab = "\t"; $nl = "\n"; > > my ($testtree) = @ARGV; #or by the following _DATA_ > > my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); > > while( my $tree = $treein->next_tree ){ > > %dist_matrix = (); > > > > my @leaves = $tree->get_leaf_nodes; > > foreach my $leaf1( @leaves ){ > > my $id1 = $leaf1->id; > > foreach my $leaf2( @leaves ){ > > my $id2 = $leaf2->id; > > if ($id1 eq $id2) { > > $dist_matrix{$id1}->{$id2} = 0; > > next; > > } > > my $distance = $tree->distance( -nodes => [$leaf1, > $leaf2] ); > > if ($id1 eq "A" and $id2 eq "B") { > > my $lca = $tree->get_lca(-nodes => [$leaf1, > $leaf2] ); > > } > > print "$leaf1:LCA:$lca:ACL:$leaf2"; ; > > #print $lca->id; ; > > my $distance2 = $tree->distance( -nodes => [$lca, > $leaf2] ); > > print $distance2; ; > > > > $dist_matrix{$id1}->{$id2} = $distance; > > } > > } > > } > > > > #_DATA_ > > > ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000 > > 00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 > > 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,( > > L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 > > .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000, > > (Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 > > ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000 > 00); > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From ross at cuhk.edu.hk Mon Oct 3 10:28:38 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Mon, 3 Oct 2011 18:28:38 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> Message-ID: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Dave wrote: >You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design Thanks for this reference, it is very good for me to understand better the architecture of Bioperl. >So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right? But the following codes will generate errors because lca cannot be identified. my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; my $distance = $tree->distance( -nodes => [$leaf1,$leaf2] ); if ($id1 eq "A" and $id2 eq "B") { my $lca = $tree->get_lca(-nodes => [$leaf1,$leaf2] ); } print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca,$leaf2] ); print $distance2; ; } } } _DATA_ ((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.00000000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00 000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0 .00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000 ):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.00000000); My ultimate goal is just to conveniently derive the information that nodes M and L share the same LCA O for the following tree. +---I | +---M | | | +---H | +---O | | | | +---G | | | | +---L | | | +---F A | +---E | | | +---K | | | | | +---D | | +---N | | +---C | | +---J | +---B From David.Messina at sbc.su.se Mon Oct 3 11:28:41 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Mon, 3 Oct 2011 13:28:41 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: Hi Ross, >So, if I understand your question correctly, you should be able to use all > of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit > confused, is_monophyletic is something you'd call on a Tree object, not on a > Node object, right?**** > > But the following codes will generate errors because lca cannot be > identified. > Right, but there are some compile-time errors in your code. I changed a few things so I could get it to run: http://cl.ly/AdzH In my hands, there is a Node object returned as $lca. However, it doesn't have an id so the next line where you try to print $lca->id, I get an undefined value error. When I look at $lca, it doesn't seems to be equivalent to node C, which, based on the tree you supplied, I would expect to be the LCA. SO there may in fact be something wrong in the BioPerl code here, too. However, I'm not that familiar with these modules, and I know there's been some recent work done on them, so perhaps someone else can chime in here. **** > > My ultimate goal is just to conveniently derive the information that nodes > M and L share the same LCA O for the following tree. > Ok, thanks for that clarification. I think the code should be able to do that. Incidentally, the tree you provided in Newick format does not appear to me to be the same tree you drew as ASCII art ? is that right? Dave From thomas.sharpton at gmail.com Mon Oct 3 14:35:33 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 07:35:33 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: On Mon, Oct 3, 2011 at 4:28 AM, Dave Messina wrote: In my hands, there is a Node object returned as $lca. However, it doesn't > have an id so the next line where you try to print $lca->id, I get an > undefined value error. > > When I look at $lca, it doesn't seems to be equivalent to node C, which, > based on the tree you supplied, I would expect to be the LCA. SO there may > in fact be something wrong in the BioPerl code here, too. > > However, I'm not that familiar with these modules, and I know there's been > some recent work done on them, so perhaps someone else can chime in here. > Dave is (as usual) right: $lca is a Node object. He's also right that the node $lca doesn't have an id. But I don't think this is a problem with BioPerl, but rather with how the newick tree in question is formatted. Specifically, the tree that Ross provided only has ids at the leaf nodes, which is why $lca->id() is returning an error (the internal node ids are thus undefined). Ross, you'll need to adopt the following format for your trees if you want to call internal node ids, at least as I understand how these BioPerl modules work. Instead of: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5); Structure your newick trees like this: (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F; ** The above trees are identical, with the exception that the internal nodes E and F have identifiers (names) associated with them. Does that make sense? You might check the wikipedia page for more information (http://en.wikipedia.org/wiki/Newick_format) and you can quickly view both of the above trees through the web-based tool PhyloWidget ( http://www.phylowidget.org) to get a better understanding of what I'm talking above. Best, Tom From ross at cuhk.edu.hk Mon Oct 3 17:41:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 01:41:27 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> Message-ID: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Thanks Tom. This is the 2nd time you help me. Suppose I change the structure to: ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; I have identified two problems. 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? From kboggavarapu2 at uh.edu Sun Oct 2 17:40:53 2011 From: kboggavarapu2 at uh.edu (krishna mohan) Date: Sun, 2 Oct 2011 12:40:53 -0500 Subject: [Bioperl-l] extract fasta headers of genes Message-ID: hi, How to obtain FASTA headers of genes associated to particular genomen using eUtils and BIOPERL From angel at mpi-marburg.mpg.de Mon Oct 3 17:27:07 2011 From: angel at mpi-marburg.mpg.de (roey.angel) Date: Mon, 3 Oct 2011 10:27:07 -0700 (PDT) Subject: [Bioperl-l] saving amino acids sequence to file Message-ID: <32583843.post@talk.nabble.com> Hi, I'm trying to save the amino acid sequence from a sequence object I retrieved from GenBank. I can easily save the nucleotide sequence with: my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); $out_nuc -> write_seq($seq_object); And I also managed to extract the amino acid sequence with: for my $feat_object ($seq_object->get_SeqFeatures) { # obtain features from seq object if ($feat_object->primary_tag eq "CDS") { # look for CDS features if ($feat_object->has_tag('translation')) { # look for amino acids for my $val ($feat_object->get_tag_values('translation')){ } } } } But is there a way to save that sequence into a file using write_seq or a similar method? Thanks in advance, Roey -- View this message in context: http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. From thomas.sharpton at gmail.com Mon Oct 3 18:24:32 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Mon, 3 Oct 2011 11:24:32 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: Hi Ross, On Mon, Oct 3, 2011 at 10:41 AM, Ross KK Leung wrote: > Thanks Tom. This is the 2nd time you help me. > This list has been a vital resource for me, so I'm happy to contribute when I can. > Suppose I change the structure to:**** > > ** ** > > ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G;**** > > ** ** > > I have identified two problems.**** > > ** ** > > 1) The distance of A and F, I suppose to be 0.1, cannot be calculated (a warning will prompt and the value shown is wrong). > > Can you provide the code you are using and the result and error it produces in your next email? This will help diagnose the problem. > **** > > 2) Nodes F, E and G are annotated by me, but in fact the newick tree generated does not contain any ID. So that means I have to manually supplement ID's for such intermediate nodes before further processing (this is indeed dealing with "recursive descent parsing" myself...)? **** > > Yes, this is unfortunate, but you can automate the labeling of internal node ids using something like the following: #$tree_in is a TreeIO object while( my $tree = $tree_in->next_tree() ){ my $id_basename = "intnode_"; my $id_count = 0; my @nodes = $tree->get_nodes(); foreach my $node( @nodes ){ next if $node->is_Leaf(); my $id = $node->id(); if( !(defined( $id ) ) ){ $id = $id_basename . $id_count; $node->id( $id ); $id_count++; } } #print the new tree or continue processing it } Now all of the nodes in the tree will have some identifier associated with it. I haven't tried the above code block so I can't verify that it works perfectly. One issue I foresee is that node ids will be added to the tree in the order in which they appear in @nodes; you will have to cross reference a tree to interpret your results. Others might have better solutions to this problem. Let me know if you have questions. Best, Tom From ross at cuhk.edu.hk Tue Oct 4 01:53:29 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Tue, 4 Oct 2011 09:53:29 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> Message-ID: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From cjfields at illinois.edu Tue Oct 4 02:23:28 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 4 Oct 2011 02:23:28 +0000 Subject: [Bioperl-l] extract fasta headers of genes In-Reply-To: References: Message-ID: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook -c On Oct 2, 2011, at 12:40 PM, krishna mohan wrote: > hi, > How to obtain FASTA headers of genes associated to > particular genomen using eUtils and BIOPERL > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From jluis.lavin at unavarra.es Tue Oct 4 09:48:31 2011 From: jluis.lavin at unavarra.es (=?ISO-8859-1?Q?Jos=E9_Luis_Lav=EDn?=) Date: Tue, 4 Oct 2011 11:48:31 +0200 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: It seems that all installation atempts failed for Perl 5.10...I'll have to upgrade my Perl version unless there'd be another Graphical module in Bioperl tah any of you could recommend. 2011/9/30 Fields, Christopher J > It's available for all perl versions from 5.8.8 up. I have it running with > perl 5.14. Now, I recall there being problems with installation on Mac OS > X, though I think that was mainly due to GD.pm and libgd. > > chris > > On Sep 30, 2011, at 3:23 AM, > wrote: > > > > > Dear All, > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > windows machine. > > > > I read about the Bio-Graphics module and it'd be wonderful to install it, > > but seems like it is only available for Perl 5.8... > > Is there any other Perl and/or Bioperl module to do the same kind of > > genomic and Blast report representation currently available? > > > > Thanks in advance > > > > -- > > Dr. Jos? Luis Lav?n Trueba > > > > Dpto. de Producci?n Agraria > > Grupo de Gen?tica y Microbiolog?a > > Universidad P?blica de Navarra > > 31006 Pamplona > > Navarra > > SPAIN > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > -- -- Dr. Jos? Luis Lav?n Trueba Dpto. de Producci?n Agraria Grupo de Gen?tica y Microbiolog?a Universidad P?blica de Navarra 31006 Pamplona Navarra SPAIN From David.Messina at sbc.su.se Tue Oct 4 10:12:51 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Tue, 4 Oct 2011 12:12:51 +0200 Subject: [Bioperl-l] saving amino acids sequence to file In-Reply-To: References: <32583843.post@talk.nabble.com> Message-ID: [Sent this yesterday just to Roey by accident; reposting to the list now.] Hi Roey, >From the feature table, I think you can only get the amino acid sequence as a string. If you'd like to be able to use the SeqIO methods on it, you'll need to create a Bio::Seq object from it first. For examples, look at the 'To and From a String' section of the SeqIO HOWTO: http://www.bioperl.org/wiki/HOWTO:SeqIO But if you just want Fasta, plain ol' print statements are often sufficient. Dave On Mon, Oct 3, 2011 at 19:27, roey.angel wrote: > Hi, > >> I'm trying to save the amino acid sequence from a sequence object I > >> retrieved from GenBank. > >> I can easily save the nucleotide sequence with: > >> > my $out_nuc = Bio::SeqIO->new(-format => 'fasta', -file => '>out.nuc'); > >> $out_nuc -> write_seq($seq_object); > >> > And I also managed to extract the amino acid sequence with: > >> > for my $feat_object ($seq_object->get_SeqFeatures) { # obtain > >> features from seq object > >> if ($feat_object->primary_tag eq "CDS") { # look for CDS > >> features > >> if ($feat_object->has_tag('translation')) { # look for > >> amino acids > >> for my $val > >> ($feat_object->get_tag_values('translation')){ > >> } > >> } > >> } > >> } > >> > But is there a way to save that sequence into a file using write_seq or a > >> similar method? > >> > Thanks in advance, > >> Roey > -- > View this message in context: > http://old.nabble.com/saving-amino-acids-sequence-to-file-tp32583843p32583843.html > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From lincoln.stein at gmail.com Tue Oct 4 11:51:49 2011 From: lincoln.stein at gmail.com (Lincoln Stein) Date: Tue, 4 Oct 2011 07:51:49 -0400 Subject: [Bioperl-l] Bio-Graphics module In-Reply-To: References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es> Message-ID: Exactly what problems are you encountering? Are you using ActiveState Perl, and if so, at what step is the install failing? Lincoln 2011/10/4 Jos? Luis Lav?n > It seems that all installation atempts failed for Perl 5.10...I'll have to > upgrade my Perl version unless there'd be another Graphical module in > Bioperl tah any of you could recommend. > > 2011/9/30 Fields, Christopher J > > > It's available for all perl versions from 5.8.8 up. I have it running > with > > perl 5.14. Now, I recall there being problems with installation on Mac > OS > > X, though I think that was mainly due to GD.pm and libgd. > > > > chris > > > > On Sep 30, 2011, at 3:23 AM, > > wrote: > > > > > > > > Dear All, > > > > > > I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a > > > windows machine. > > > > > > I read about the Bio-Graphics module and it'd be wonderful to install > it, > > > but seems like it is only available for Perl 5.8... > > > Is there any other Perl and/or Bioperl module to do the same kind of > > > genomic and Blast report representation currently available? > > > > > > Thanks in advance > > > > > > -- > > > Dr. Jos? Luis Lav?n Trueba > > > > > > Dpto. de Producci?n Agraria > > > Grupo de Gen?tica y Microbiolog?a > > > Universidad P?blica de Navarra > > > 31006 Pamplona > > > Navarra > > > SPAIN > > > > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > -- > -- > Dr. Jos? Luis Lav?n Trueba > > Dpto. de Producci?n Agraria > Grupo de Gen?tica y Microbiolog?a > Universidad P?blica de Navarra > 31006 Pamplona > Navarra > SPAIN > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa From thomas.sharpton at gmail.com Tue Oct 4 18:05:27 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 11:05:27 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> Message-ID: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > Hi, Tom. Let me formally define my problem because this would be > more effective for communication. My objective is to assign a state > for intermediate nodes. For the following example, nodes M and J can > be assigned with (Wing). After assignment (forget the unassigned > first), the pairwise distances of these intermediate nodes and any > other nodes may be compared (e.g. Nodes M and L; Nodes J and E). > > > +---I (Wing) > | > +---M > | | > | +---H (Wing) > | > +---O > | | > | | > | | > | +---L (No-Wing) > | > | > Z > | +---E (Wing) > | | > | +---K > | | | > | | +---D (No-Wing) > | | > +---N > | > | +---C (Wing) > | | > +---J > | > +---B (Wing) > > Technically, I can either use TreeFunctionsI's method add_trait to > the leaves first. Then I back trace the ancestral nodes. While nodes > K and J are pictorially displayed to be nicely at the same level, in > fact besides exhaustively testing NodeI's methods ancestor or > get_all_Descendants etc, I cannot come up with a better idea. As you > have mentioned before, when the tree is big, this curse is > amplified, not to say "Wing" is just one of several hundred > properties to test. > > That's why I'm posting this question to see whether any convenient > data structures already exist to tackle this kind of "graph- > traversing" process. From ross at cuhk.edu.hk Tue Oct 4 23:32:42 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 07:32:42 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> Message-ID: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Hi Tom, I shall infer the state based on descendant's states. In my example, Nodes H and I belong to "Wing", then their ancestor M is also assigned "Wing". After assigning these states to all the nodes of the tree, I shall calculate the distances between these nodes. Switching to C is only the last option because that involves another 2 months, not to include the time if C does not have any libraries to deal with Newick Tree. Best, Ross From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] Sent: 2011?10?5? 2:05 To: Ross KK Leung Cc: bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree Hi Ross, I understand that you want to infer ancestral states on your tree, but I'm unclear about how you want to do so. Can you clarify how you infer the state for node K on your example tree? In particular, is your method of inference dependent on the branch lengths? The answers to these questions will (hopefully) help guide you to methods that can assist you. Unfortunately, Perl is not the most efficient language for tree/graph traversal. It can certainly be done, but for very, very large trees, I tend to roll over to C (but only if I have to as I am not proficient in C). Best, Tom On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: Hi, Tom. Let me formally define my problem because this would be more effective for communication. My objective is to assign a state for intermediate nodes. For the following example, nodes M and J can be assigned with (Wing). After assignment (forget the unassigned first), the pairwise distances of these intermediate nodes and any other nodes may be compared (e.g. Nodes M and L; Nodes J and E). +---I (Wing) | +---M | | | +---H (Wing) | +---O | | | | | | | +---L (No-Wing) | | Z | +---E (Wing) | | | +---K | | | | | +---D (No-Wing) | | +---N | | +---C (Wing) | | +---J | +---B (Wing) Technically, I can either use TreeFunctionsI's method add_trait to the leaves first. Then I back trace the ancestral nodes. While nodes K and J are pictorially displayed to be nicely at the same level, in fact besides exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I cannot come up with a better idea. As you have mentioned before, when the tree is big, this curse is amplified, not to say "Wing" is just one of several hundred properties to test. That's why I'm posting this question to see whether any convenient data structures already exist to tackle this kind of "graph-traversing" process. From R.A.Vos at reading.ac.uk Tue Oct 4 23:59:52 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 01:59:52 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011?10?5? 2:05 > To: Ross KK Leung > Cc: bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > > > > Hi Ross, > > > > I understand that you want to infer ancestral states on your tree, but I'm > unclear about how you want to do so. Can you clarify how you infer the state > for node K on your example tree? In particular, is your method of inference > dependent on the branch lengths? The answers to these questions will > (hopefully) help guide you to methods that can assist you. > > > > Unfortunately, Perl is not the most efficient language for tree/graph > traversal. It can certainly be done, but for very, very large trees, I tend > to roll over to C (but only if I have to as I am not proficient in C). > > > > Best, > > Tom > > > > On Oct 3, 2011, at 6:53 PM, Ross KK Leung wrote: > > > > > > Hi, Tom. Let me formally define my problem because this would be more > effective for communication. My objective is to assign a state for > intermediate nodes. For the following example, nodes M and J can be assigned > with (Wing). After assignment (forget the unassigned first), the pairwise > distances of these intermediate nodes and any other nodes may be compared > (e.g. Nodes M and L; Nodes J and E). > > > > > > +---I (Wing) > > | > > +---M > > | | > > | +---H (Wing) > > | > > +---O > > | | > > | | > > | | > > | +---L (No-Wing) > > | > > | > > Z > > | +---E (Wing) > > | | > > | +---K > > | | | > > | | +---D (No-Wing) > > | | > > +---N > > | > > | +---C (Wing) > > | | > > +---J > > | > > +---B (Wing) > > > > Technically, I can either use TreeFunctionsI's method add_trait to the > leaves first. Then I back trace the ancestral nodes. While nodes K and J are > pictorially displayed to be nicely at the same level, in fact besides > exhaustively testing NodeI's methods ancestor or get_all_Descendants etc, I > cannot come up with a better idea. As you have mentioned before, when the > tree is big, this curse is amplified, not to say "Wing" is just one of > several hundred properties to test. > > > > That's why I'm posting this question to see whether any convenient data > structures already exist to tackle this kind of "graph-traversing" process. > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Wed Oct 5 00:04:22 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 08:04:22 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> Message-ID: <002201cc82f2$565c2e40$03148ac0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011?10?5? 8:00 To: Ross KK Leung Cc: Thomas Sharpton; bioperl-l Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree > I shall infer the state based on descendant's states. In my example, Nodes H > and I belong to "Wing", then their ancestor M is also assigned "Wing". After > assigning these states to all the nodes of the tree, I shall calculate the > distances between these nodes. What is your approach for when internal states are equivocal? I will assign "undetermined" and the detailed plan of assignment is too much to mention here. From R.A.Vos at reading.ac.uk Wed Oct 5 00:42:08 2011 From: R.A.Vos at reading.ac.uk (Rutger Vos) Date: Wed, 5 Oct 2011 02:42:08 +0200 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002201cc82f2$565c2e40$03148ac0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. 2011/10/5 Ross KK Leung : > -----Original Message----- > From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger > Vos > Sent: 2011?10?5? 8:00 > To: Ross KK Leung > Cc: Thomas Sharpton; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes > from a tree > >> I shall infer the state based on descendant's states. In my example, Nodes > H >> and I belong to "Wing", then their ancestor M is also assigned "Wing". > After >> assigning these states to all the nodes of the tree, I shall calculate the >> distances between these nodes. > > What is your approach for when internal states are equivocal? > > I will assign "undetermined" and the detailed plan of assignment is too much > to mention here. > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com From ross at cuhk.edu.hk Wed Oct 5 01:10:33 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Wed, 5 Oct 2011 09:10:33 +0800 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> Message-ID: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> -----Original Message----- From: rutgeraldo at gmail.com [mailto:rutgeraldo at gmail.com] On Behalf Of Rutger Vos Sent: 2011?10?5? 8:42 To: Ross KK Leung Cc: bioperl-l; Thomas Sharpton Subject: Re: [Bioperl-l] Find distances between LCA's and the other nodes from a tree You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way. Thanks, Rutger. While there is a convenient function to help calculate the distances between leaf nodes, I find it difficult for ancestors. After using get_lca, it seems that bioperl has no data structures to help manipulate these LCA's. From thomas.sharpton at gmail.com Wed Oct 5 01:43:38 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Tue, 4 Oct 2011 18:43:38 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <002801cc82fb$951b53a0$bf51fae0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> Message-ID: Hi Ross, I think Rutger has given you a good idea and it is certainly simpler than the solution I just concocted (no surprise there). Regarding your most recent note: 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help calculate the > distances between leaf nodes, I find it difficult for ancestors. After > using > get_lca, it seems that bioperl has no data structures to help manipulate > these LCA's. > > >From what I understand, the get_lca does return a node object, specifically an internal node. The following is from the BioPerl documentation (note the "Returns" line): Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no common ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes You can get the distance between any two nodes, including an internal node, using the distance method. Note that the nodes you input into the distance function do not need to have ids associated with them. For example, #$nodeA and $nodeB are BioPerl node objects that correspond to any node on the tree my $lca = get_lca( $nodeA, $nodeB ); my $distance = distance( $nodeA, $lca ); $distance will now contain the total branch length between nodeA and the last common ancestor between nodes A and B. At no point are node ids used to conduct calculation; only the node objects themselves are needed. Anything that you can do to a node, you can do to $lca. This is how I understand the functions, at least. Someone please correct me if I'm wrong, as I fear I sound like a broken record at this point.... Best, Tom From thomas.sharpton at gmail.com Wed Oct 5 17:47:53 2011 From: thomas.sharpton at gmail.com (Thomas Sharpton) Date: Wed, 5 Oct 2011 10:47:53 -0700 Subject: [Bioperl-l] Find distances between LCA's and the other nodes from a tree In-Reply-To: <004101cc836f$6a4a6250$3edf26f0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: Hi Ross, Let's keep this discussion on the listserv so that others can benefit from and contribute to it. I just executed your script using the tree you provided (for those following along, I have copied the script and tree below my signature). It produces no warnings or errors on my machine. Look below my signature to see the terminal output of this test run on my computer. Are you working with the latest version of bioperl? What version of perl are you using? I see that the warning (which is distinct from an error) that you are getting is: "MSG: At least some nodes do not have a branch length, the distance returned could be wrong" I also see in your newick tree that you have given the root node (node G) an ID, but no branch length. I'm thinking that you may have an old version of bioperl, which might bark at you when you have a root node with an id but no branch length. Note that the distances being printed in my output (which is not the distance between the node ids that precede the value printed, but instead the distance between the LCA of these node ids and the second of the two ids printed) are indeed correct. Can you provide information on the version of BioPerl and Perl that you are trying this on? Best, Tom ########## testtree.nwk ------------------ ((A:0.1,B:0.2)F:0.3,(C:0.3,D:0.4)E:0.5)G; ########## test.pl ----------------- use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; $tab = "\t"; $nl = "\n"; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } # next if( defined( $dist_matrix{$id1}->{$id2} ) || defined ( $dist_matrix{$id2}->{$id1} ) ); my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); #print "$leaf1 and $leaf2 distance: $distance\n"; # print "$id1 and $id2 distance: $distance\n"; #=pod print $id1; ; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); # print $lca->id; #; my $distance2 = $tree->distance( -nodes => [$lca, $leaf2] ); print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; #=cut } } } ######### output --------------- [sharpton at kazushi ~]$perl test.pl test.nwk A B 0.2 A C 0.8 A D 0.9 B A 0.1 B C 0.8 B D 0.9 C A 0.4 C B 0.5 C D 0.4 D A 0.4 D B 0.5 D C 0.3 [sharpton at kazushi ~]$ On Oct 5, 2011, at 7:59 AM, Ross KK Leung wrote: > Hi Tom, > > I personally attach this program and tree files to you and see > whether you can run the program without any error (mine does, I > can't use Modern perl as I can't request the admin to install/update > anything).... > > Thanks a lot, Ross > > > > > > > > From: Thomas Sharpton [mailto:thomas.sharpton at gmail.com] > Sent: 2011?10?5? 9:44 > To: Ross KK Leung > Cc: Rutger Vos; bioperl-l > Subject: Re: [Bioperl-l] Find distances between LCA's and the other > nodes from a tree > > Hi Ross, > > I think Rutger has given you a good idea and it is certainly simpler > than the solution I just concocted (no surprise there). > > Regarding your most recent note: > > 2011/10/4 Ross KK Leung > Thanks, Rutger. While there is a convenient function to help > calculate the > distances between leaf nodes, I find it difficult for ancestors. > After using > get_lca, it seems that bioperl has no data structures to help > manipulate > these LCA's. > > > From what I understand, the get_lca does return a node object, > specifically an internal node. The following is from the BioPerl > documentation (note the "Returns" line): > > > > Title : get_lca > Usage : get_lca(-nodes => \@nodes ); OR > get_lca(@nodes); > Function: given two or more nodes, returns the lowest common > ancestor (aka most > recent common ancestor) > > > Returns : node object or undef if there is no common ancestor > Args : -nodes => arrayref of nodes to test, OR > just a list of nodes > > You can get the distance between any two nodes, including an > internal node, using the distance method. Note that the nodes you > input into the distance function do not need to have ids associated > with them. For example, > > #$nodeA and $nodeB are BioPerl node objects that correspond to any > node on the tree > my $lca = get_lca( $nodeA, $nodeB ); > my $distance = distance( $nodeA, $lca ); > > $distance will now contain the total branch length between nodeA and > the last common ancestor between nodes A and B. At no point are node > ids used to conduct calculation; only the node objects themselves > are needed. Anything that you can do to a node, you can do to $lca. > > This is how I understand the functions, at least. Someone please > correct me if I'm wrong, as I fear I sound like a broken record at > this point.... > > Best, > Tom > From ross at cuhk.edu.hk Thu Oct 6 07:07:11 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Thu, 6 Oct 2011 15:07:11 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> Message-ID: <006501cc83f6$91830ca0$b48925e0$@edu.hk> Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } From ross at cuhk.edu.hk Fri Oct 7 08:49:27 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 16:49:27 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <006501cc83f6$91830ca0$b48925e0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> Message-ID: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> each_Descendent documentation mentions "not a recursive fetchall" and I find out a method called "recursion" may solve my problem. the principle is to first force_binary, then start from root and go down along the tree until Is_Leaf, and then assign ancestor and continue the "recursion". -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Ross KK Leung Sent: 2011?10?6? 15:07 To: 'Thomas Sharpton' Cc: 'bioperl-l' Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree Hi Tom, With Dave's and your help, I'm moving forward to the core part. The previous problem was indeed due to old versions of Perl/Bioperl. Sorry for being unaware that perl interpreter can be a problem... -_- Rutger tipped previously: " You should probably pre-compute the distances from each node to all its ancestors (post-order traversal) and attach those values as hashes to the internal nodes. Then, for any assigned node, you just traverse from it to the root, look up those hashes along the way and compute the distance from the assigned node to all others that way." Yet, we still do not have any information about the level of hierarchy. For the following tree, we say nodes E and F ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; are at the same level. get_lca, ancestor, get_descendant etc cannot help solve the problem easily because they either return LCA regardless of level (get_lca(A,C) will return G) or throw exception (by the following codes and the above tree). I notice that splice() may actually be dealing one level (ancestor/descent) by one level but it's a bit complicated for me to hack it... use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf1( @leaves ){ my $id1 = $leaf1->id; foreach my $leaf2( @leaves ){ my $id2 = $leaf2->id; if ($id1 eq $id2) { $dist_matrix{$id1}->{$id2} = 0; next; } my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] ); print "L1: "; print $id1; ; print "L2: "; print $id2; ; my $lca = $tree->get_lca(-nodes => [$leaf1, $leaf2] ); my $anc = $lca->ancestor; print "LCA: "; print $lca->id; ; my $distance2 = $tree->distance( -nodes => [$lca, $anc] ); print "LCA-L2: "; print $distance2; ; $dist_matrix{$id1}->{$id2} = $distance; } } } _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From ross at cuhk.edu.hk Fri Oct 7 13:16:12 2011 From: ross at cuhk.edu.hk (Ross KK Leung) Date: Fri, 7 Oct 2011 21:16:12 +0800 Subject: [Bioperl-l] Check the hierarchy (level) of nodes in a Newick tree In-Reply-To: <00db01cc84ce$0592d4e0$10b87ea0$@edu.hk> References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com> <003e01cc8183$b2d5d9c0$18818d40$@edu.hk> <006d01cc81b7$36ee0ab0$a4ca2010$@edu.hk> <009e01cc81f3$adc7a4c0$0956ee40$@edu.hk> <00bb01cc8238$6a3e9ed0$3ebbdc70$@edu.hk> <5C47B07F-E0FF-42AF-AF3B-B985F2513EB3@gmail.com> <001701cc82ed$e9ebda70$bdc38f50$@edu.hk> <002201cc82f2$565c2e40$03148ac0$@edu.hk> <002801cc82fb$951b53a0$bf51fae0$@edu.hk> <004101cc836f$6a4a6250$3edf26f0$@edu.hk> <006501cc83f6$91830ca0$b 48925e0$@edu.hk> <00d b01cc84ce$0592d4e0$10b87ea0$@edu.hk> Message-ID: <00f601cc84f3$49406ca0$dbc145e0$@edu.hk> I use the following codes to test and find that the root node G is not assigned state "Opter". Moreover, I find that when a tree looks like this, +---I (Wing) | +---M | | | +---H (Wing) | O | | | +---L (No-Wing) L cannot match with internal node M as L is already a leaf node. use Bio::TreeIO; use Bio::Tree::TreeFunctionsI; my ($testtree) = @ARGV; system("cat $testtree"); my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' ); while( my $tree = $treein->next_tree ){ %dist_matrix = (); my @leaves = $tree->get_leaf_nodes; foreach my $leaf( @leaves ){ $leaf->add_tag_value("state", "Wing"); } $rootnode=$tree->get_root_node; Traverse($rootnode); @tmpnodes = $tree->get_nodes; foreach $prnnode (@tmpnodes) { $prnval = $prnnode->get_tag_values("state"); print $prnnode->id, "\t"; print $prnval, "\n"; } } sub Traverse { ($node) = @_; my $state = "dummy"; foreach my $desnode ( $node->each_Descendent() ) { if (!($desnode->is_Leaf)) { Traverse($desnode); } push @cmpnodes, $desnode; } #assume binary? if ($cmpnodes[0]->get_tag_values("state") eq $cmpnodes[1]->get_tag_values("state")) { # $node->add_tag_value("state", $cmpnodes[0]->get_tag_values("state")); $node->add_tag_value("state", "Opter"); } } __DATA__ ((A:0.1,B:0.2)E:0.3,(C:0.3,D:0.4)F:0.5)G; From maquino at knome.com Tue Oct 11 14:44:06 2011 From: maquino at knome.com (Mark Aquino) Date: Tue, 11 Oct 2011 10:44:06 -0400 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues Message-ID: Hi, I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. Code: #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -usehistory => 'y'); $esearch->get_Response || die; my @h_genes = $esearch->get_ids; print "@h_genes\n"; my $history = $esearch->next_History || die "elink failed"; my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', -history => $history, -cmd => 'neighbor_history'); $elink->get_Response; my $hist1 = $elink->next_History; my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', -history => $hist1, -cookie => $elink->next_cookie); $esum->get_Response || die "esum failed"; while (my $docsum = $esum->next_DocSum){ print $docsum->get_id,"\n"; print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; } [According to what I can find, the method get_Content_by_name should work but I am getting the error: Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From cjfields at illinois.edu Tue Oct 11 20:16:00 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 11 Oct 2011 20:16:00 +0000 Subject: [Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues In-Reply-To: References: Message-ID: <85FDDEF8-1522-4209-AA21-E51E436E6158@illinois.edu> Mark, Some odd things going on with homologen data, but I wanted to address a few points first. The code has a number of issues: * Missing email (warnings pop up). This will be required in future releases of Bio::DB::EUtilities, it's already technically required by NCBI * 'perldoc Bio::Tools::EUtilities::Summary::DocSum' indicates the method name is 'get_contents_by_name' (note lower-case and plural). As the name implies, it returns a list of raw data * Missing the elink databases. The history will capture the original queried database, but not the database linked to; the default on NCBI's end is pubmed when db is not set), which leads to... * The last EUtilities call is to 'pubmed', from the history. If you dump the docsum output (add a 'print $docsum->to_string) this is apparent. * Content key is wrong. Dumping the raw data initially is a good idea for debugging to ensure you are capturing the correct key. In this case, the key is 'TaxId' (note the case). * Calls to get_Response() are unnecessary; this just returns the HTTP::Response object from the user agent if you need the raw output. Calls to the eutilities-specific methods will lazily grab incoming data and parse as needed, so get_ids() alone will work as you would expect. Note the homologene data is hierarchical; there is more than one gene per linked ID, so the item data is nested. The tools are meant to be fairly generic, so you could just retrieve all the TaxID information, but it might be more relevant to get the GeneIDs to go along with them for more context. The following works for me. chris =================================================== #!/usr/bin/perl use strict; use warnings; use Bio::DB::EUtilities; my $eutil = Bio::DB::EUtilities->new(-eutil => 'esearch', -db => 'homologene', -term => 'Copg AND mouse', -email => , -usehistory => 'y'); my @h_genes = $eutil->get_ids; print "@h_genes\n"; my $history = $eutil->next_History || die "esearch failed"; $eutil->reset_parameters(-eutil => 'elink', -history => $history, -email => , -db => 'homologene', -cmd => 'neighbor_history'); $history = $eutil->next_History || die "elink failed"; $eutil->reset_parameters(-eutil => 'esummary', -email => , -history => $history); while (my $docsum = $eutil->next_DocSum) { print "Homologen ID:".$docsum->get_id."\n"; print "Label: ".($docsum->get_contents_by_name('Caption'))[0]."\n"; while (my $item = $docsum->next_Item) { # HomoloGeneDataList while (my $sub = $item->next_subItem) { # HomoloGeneData print "\tGeneId: ".($sub->get_contents_by_name('GeneID'))[0]."\n"; print "\tTaxId: ".($sub->get_contents_by_name('TaxId'))[0]."\n"; } } } On Oct 11, 2011, at 9:44 AM, Mark Aquino wrote: > Hi, > > I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues. However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated. > > Code: > > #!/usr/bin/perl > use strict; > use warnings; > use Bio::DB::EUtilities; > my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch', > -db => 'homologene', > -term => 'Copg AND mouse', > -usehistory => 'y'); > $esearch->get_Response || die; > my @h_genes = $esearch->get_ids; > print "@h_genes\n"; > my $history = $esearch->next_History || die "elink failed"; > my $elink = Bio::DB::EUtilities->new(-eutil => 'elink', > -history => $history, > -cmd => 'neighbor_history'); > > $elink->get_Response; > my $hist1 = $elink->next_History; > my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary', > -history => $hist1, > -cookie => $elink->next_cookie); > $esum->get_Response || die "esum failed"; > while (my $docsum = $esum->next_DocSum){ > print $docsum->get_id,"\n"; > print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n"; > } > > [According to what I can find, the method get_Content_by_name should work but I am getting the error: > Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.] From manju.rawat2 at gmail.com Wed Oct 12 05:32:06 2011 From: manju.rawat2 at gmail.com (Manju Rawat) Date: Wed, 12 Oct 2011 11:02:06 +0530 Subject: [Bioperl-l] [blastall] WARNING: Unable to open Batu.fa.nin In-Reply-To: References: Message-ID: I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux*. * I created the database for Bos_taurus using Formatdb commamd of blast. *agl at agl-desktop:~/blast-2.2.25/data$ formatdb -i Btau.txt -p F -o T* database was create sucessfully and working properly in terminal.. but when i am using this database in bioperl programming it showing me balst output with this warning that [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin [blastall] WARNING: Unable to open Batu.nin and this is my program which i am running in terminal.. @params = ('database' => 'Btau','outfile' => 'bla.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'test_query.fa' , '-format' => 'Fasta' ); $input = $str->next_seq(); $factory->blastall($input); it working fine in terminal with following command but showing error in programming.. agl at agl-desktop:~/BP$ blastall -p blastn -d btau -i test_query.fa -o test.out pl tell me what i am doing wrong. Thanks Manju Rawat From rajasimhah at nei.nih.gov Wed Oct 12 16:07:03 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 12:07:03 -0400 Subject: [Bioperl-l] Installation problem Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> I am trying to install Bioperl since yesterday without any luck. I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. I am attaching errors encountered during one such attempt below. Please help. root at comp1z BioPerl-1.6.1]# perl Build.PL This package requires Module::Build v0.2805 or greater to install itself. Base class package "Module::Build" is empty. (Perhaps you need to 'use' the module which defines that package first.) at (eval 2) line 1 BEGIN failed--compilation aborted at (eval 2) line 1. BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. Compilation failed in require at Build.PL line 14. BEGIN failed--compilation aborted at Build.PL line 14. I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). Please help!!! Harsha National Eye Institute, Bethesda, MD 301-402-5734 From cjfields at illinois.edu Wed Oct 12 19:37:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:37:35 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov> Message-ID: Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Wed Oct 12 19:41:05 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 12 Oct 2011 19:41:05 +0000 Subject: [Bioperl-l] Installation problem In-Reply-To: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> Message-ID: <54A3917D-C212-4219-9C29-8285F3254EA5@illinois.edu> Possibly, though hard to say unless you give it a try. It does have a lot of bug fixes though. chris On Oct 12, 2011, at 2:38 PM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > No Christopher, I am trying the latest stable version 1.6.1 > Should I expect a smoother install with 1.6.901? > > Harsha > > ________________________________________ > From: Fields, Christopher J [cjfields at illinois.edu] > Sent: Wednesday, October 12, 2011 3:37 PM > To: Rajasimha, Harsha (NIH/NEI) [C] > Cc: bioperl-l at bioperl.org > Subject: Re: [Bioperl-l] Installation problem > > Have you tried the latest version from CPAN (v1.6.901)? > > chris > > On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > >> I am trying to install Bioperl since yesterday without any luck. >> I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. >> I am attaching errors encountered during one such attempt below. Please help. >> >> root at comp1z BioPerl-1.6.1]# perl Build.PL >> This package requires Module::Build v0.2805 or greater to install itself. >> Base class package "Module::Build" is empty. >> (Perhaps you need to 'use' the module which defines that package first.) >> at (eval 2) line 1 >> BEGIN failed--compilation aborted at (eval 2) line 1. >> BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. >> Compilation failed in require at Build.PL line 14. >> BEGIN failed--compilation aborted at Build.PL line 14. >> >> I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). >> >> Please help!!! >> Harsha >> National Eye Institute, Bethesda, MD >> 301-402-5734 >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From rajasimhah at nei.nih.gov Wed Oct 12 19:38:43 2011 From: rajasimhah at nei.nih.gov (Rajasimha, Harsha (NIH/NEI) [C]) Date: Wed, 12 Oct 2011 15:38:43 -0400 Subject: [Bioperl-l] Installation problem In-Reply-To: References: <3130CC3EDB107548B508BDD41A619F1F09C94BC11B@NIHMLBX02.nih.gov>, Message-ID: <3130CC3EDB107548B508BDD41A619F1F09C94BC11F@NIHMLBX02.nih.gov> No Christopher, I am trying the latest stable version 1.6.1 Should I expect a smoother install with 1.6.901? Harsha ________________________________________ From: Fields, Christopher J [cjfields at illinois.edu] Sent: Wednesday, October 12, 2011 3:37 PM To: Rajasimha, Harsha (NIH/NEI) [C] Cc: bioperl-l at bioperl.org Subject: Re: [Bioperl-l] Installation problem Have you tried the latest version from CPAN (v1.6.901)? chris On Oct 12, 2011, at 11:07 AM, Rajasimha, Harsha (NIH/NEI) [C] wrote: > I am trying to install Bioperl since yesterday without any luck. > I have tried exact same instructions for multiple ways of installing from the bioperl wiki - but no luck. > I am attaching errors encountered during one such attempt below. Please help. > > root at comp1z BioPerl-1.6.1]# perl Build.PL > This package requires Module::Build v0.2805 or greater to install itself. > Base class package "Module::Build" is empty. > (Perhaps you need to 'use' the module which defines that package first.) > at (eval 2) line 1 > BEGIN failed--compilation aborted at (eval 2) line 1. > BEGIN failed--compilation aborted at Bio/Root/Build.pm line 83. > Compilation failed in require at Build.PL line 14. > BEGIN failed--compilation aborted at Build.PL line 14. > > I have tried installing Module::Build using CPAN, but that installation fails too due to dependencies (even though I say "yes" to all prepend dependencies questions during install). > > Please help!!! > Harsha > National Eye Institute, Bethesda, MD > 301-402-5734 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 13:07:18 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 09:07:18 -0400 Subject: [Bioperl-l] Fwd: [bioperl-network] Not indexed by CPAN (#1) References: Message-ID: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> bioperl-l, It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. Brian O. Begin forwarded message: > From: "Chad A. Davis" > Date: October 13, 2011 7:40:27 AM EDT > To: bosborne > Subject: [bioperl-network] Not indexed by CPAN (#1) > > I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. > > This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi > > CPAN 1.9800 > > -- > Reply to this email directly or view it on GitHub: > https://github.com/bioperl/bioperl-network/issues/1 From cjfields at illinois.edu Thu Oct 13 15:47:33 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 15:47:33 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> Message-ID: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Brian, If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. chris On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > bioperl-l, > > It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. > > Brian O. > > Begin forwarded message: > >> From: "Chad A. Davis" >> Date: October 13, 2011 7:40:27 AM EDT >> To: bosborne >> Subject: [bioperl-network] Not indexed by CPAN (#1) >> >> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >> >> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >> >> CPAN 1.9800 >> >> -- >> Reply to this email directly or view it on GitHub: >> https://github.com/bioperl/bioperl-network/issues/1 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From bosborne11 at verizon.net Thu Oct 13 15:52:55 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 11:52:55 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> Message-ID: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Yes, BOSBORNE. On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > Brian, > > If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? > > It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. > > chris > > On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: > >> bioperl-l, >> >> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >> >> Brian O. >> >> Begin forwarded message: >> >>> From: "Chad A. Davis" >>> Date: October 13, 2011 7:40:27 AM EDT >>> To: bosborne >>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>> >>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>> >>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>> >>> CPAN 1.9800 >>> >>> -- >>> Reply to this email directly or view it on GitHub: >>> https://github.com/bioperl/bioperl-network/issues/1 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Thu Oct 13 17:03:49 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 13 Oct 2011 17:03:49 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> Message-ID: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. chris On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > Yes, BOSBORNE. > > On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: > >> Brian, >> >> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >> >> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >> >> chris >> >> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >> >>> bioperl-l, >>> >>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>> >>> Brian O. >>> >>> Begin forwarded message: >>> >>>> From: "Chad A. Davis" >>>> Date: October 13, 2011 7:40:27 AM EDT >>>> To: bosborne >>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>> >>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>> >>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>> >>>> CPAN 1.9800 >>>> >>>> -- >>>> Reply to this email directly or view it on GitHub: >>>> https://github.com/bioperl/bioperl-network/issues/1 >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > From bosborne11 at verizon.net Fri Oct 14 01:45:56 2011 From: bosborne11 at verizon.net (Brian Osborne) Date: Thu, 13 Oct 2011 21:45:56 -0400 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> Message-ID: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Chris, OK, tell me what they say when you hear from them. BIO On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. > > chris > > On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: > >> Yes, BOSBORNE. >> >> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >> >>> Brian, >>> >>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>> >>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>> >>> chris >>> >>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>> >>>> bioperl-l, >>>> >>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>> >>>> Brian O. >>>> >>>> Begin forwarded message: >>>> >>>>> From: "Chad A. Davis" >>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>> To: bosborne >>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>> >>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>> >>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>> >>>>> CPAN 1.9800 >>>>> >>>>> -- >>>>> Reply to this email directly or view it on GitHub: >>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Fri Oct 14 12:48:19 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Fri, 14 Oct 2011 14:48:19 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: Because it may be related, I wanted to mention that I am having the same problem with Bioperl-Run. In this case, however, I can find the distribution via: i /bioperl-run/ But searching for a containing module does not return the distribution: i /clustalw/ Chad On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: > Chris, > > OK, tell me what they say when you hear from them. > > BIO > > > On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: > >> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >> >> chris >> >> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >> >>> Yes, BOSBORNE. >>> >>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>> >>>> Brian, >>>> >>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>> >>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>> >>>>> bioperl-l, >>>>> >>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>> >>>>> Brian O. >>>>> >>>>> Begin forwarded message: >>>>> >>>>>> From: "Chad A. Davis" >>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>> To: bosborne >>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>> >>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>> >>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>> >>>>>> CPAN 1.9800 >>>>>> >>>>>> -- >>>>>> Reply to this email directly or view it on GitHub: >>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > From cjfields at illinois.edu Fri Oct 14 13:34:22 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 14 Oct 2011 13:34:22 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> Message-ID: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). chris On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > Because it may be related, I wanted to mention that I am having the > same problem with Bioperl-Run. In this case, however, I can find the > distribution via: > > i /bioperl-run/ > > But searching for a containing module does not return the distribution: > > i /clustalw/ > > Chad > > On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >> Chris, >> >> OK, tell me what they say when you hear from them. >> >> BIO >> >> >> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >> >>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>> >>> chris >>> >>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>> >>>> Yes, BOSBORNE. >>>> >>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>> >>>>> Brian, >>>>> >>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>> >>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>> >>>>>> bioperl-l, >>>>>> >>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>> >>>>>> Brian O. >>>>>> >>>>>> Begin forwarded message: >>>>>> >>>>>>> From: "Chad A. Davis" >>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>> To: bosborne >>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>> >>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>> >>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>> >>>>>>> CPAN 1.9800 >>>>>>> >>>>>>> -- >>>>>>> Reply to this email directly or view it on GitHub: >>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Oct 17 03:12:59 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 03:12:59 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? chris On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). > > chris > > On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: > >> Because it may be related, I wanted to mention that I am having the >> same problem with Bioperl-Run. In this case, however, I can find the >> distribution via: >> >> i /bioperl-run/ >> >> But searching for a containing module does not return the distribution: >> >> i /clustalw/ >> >> Chad >> >> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>> Chris, >>> >>> OK, tell me what they say when you hear from them. >>> >>> BIO >>> >>> >>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>> >>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>> >>>> chris >>>> >>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>> >>>>> Yes, BOSBORNE. >>>>> >>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>> >>>>>> Brian, >>>>>> >>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>> >>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>> >>>>>>> bioperl-l, >>>>>>> >>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>> >>>>>>> Brian O. >>>>>>> >>>>>>> Begin forwarded message: >>>>>>> >>>>>>>> From: "Chad A. Davis" >>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>> To: bosborne >>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>> >>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>> >>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>> >>>>>>>> CPAN 1.9800 >>>>>>>> >>>>>>>> -- >>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 08:08:16 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Mon, 17 Oct 2011 10:08:16 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: The index looks good now, I'm able to get the bioperl-network distro by depending on a module within it. Would it be possible to do the same for a bioperl-run 1.6.901 release? Cheers, Chad On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J wrote: > This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. > > Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? > > chris > > On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: > >> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >> >> chris >> >> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >> >>> Because it may be related, I wanted to mention that I am having the >>> same problem with Bioperl-Run. In this case, however, I can find the >>> distribution via: >>> >>> i /bioperl-run/ >>> >>> But searching for a containing module does not return the distribution: >>> >>> i /clustalw/ >>> >>> Chad >>> >>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>> Chris, >>>> >>>> OK, tell me what they say when you hear from them. >>>> >>>> BIO >>>> >>>> >>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>> >>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>> >>>>> chris >>>>> >>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>> >>>>>> Yes, BOSBORNE. >>>>>> >>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>> >>>>>>> Brian, >>>>>>> >>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>> >>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> bioperl-l, >>>>>>>> >>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>> >>>>>>>> Brian O. >>>>>>>> >>>>>>>> Begin forwarded message: >>>>>>>> >>>>>>>>> From: "Chad A. Davis" >>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>> To: bosborne >>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>> >>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>> >>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>> >>>>>>>>> CPAN 1.9800 >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From cjfields at illinois.edu Mon Oct 17 18:02:35 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 18:02:35 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. chris On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > The index looks good now, I'm able to get the bioperl-network distro > by depending on a module within it. > Would it be possible to do the same for a bioperl-run 1.6.901 release? > > Cheers, > Chad > > > On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J > wrote: >> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >> >> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >> >> chris >> >> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >> >>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>> >>> chris >>> >>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>> >>>> Because it may be related, I wanted to mention that I am having the >>>> same problem with Bioperl-Run. In this case, however, I can find the >>>> distribution via: >>>> >>>> i /bioperl-run/ >>>> >>>> But searching for a containing module does not return the distribution: >>>> >>>> i /clustalw/ >>>> >>>> Chad >>>> >>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>> Chris, >>>>> >>>>> OK, tell me what they say when you hear from them. >>>>> >>>>> BIO >>>>> >>>>> >>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>> >>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>> >>>>>> chris >>>>>> >>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>> >>>>>>> Yes, BOSBORNE. >>>>>>> >>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> Brian, >>>>>>>> >>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>> >>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> bioperl-l, >>>>>>>>> >>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>> >>>>>>>>> Brian O. >>>>>>>>> >>>>>>>>> Begin forwarded message: >>>>>>>>> >>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>> To: bosborne >>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>> >>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>> >>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>> >>>>>>>>>> CPAN 1.9800 >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioperl-l mailing list >>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Mon Oct 17 19:40:26 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 17 Oct 2011 19:40:26 +0000 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. chris On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > Yes, I planned on that but wanted to make sure everything was working from your end. Will upload that in a bit. > > chris > > On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: > >> The index looks good now, I'm able to get the bioperl-network distro >> by depending on a module within it. >> Would it be possible to do the same for a bioperl-run 1.6.901 release? >> >> Cheers, >> Chad >> >> >> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >> wrote: >>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>> >>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>> >>> chris >>> >>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>> >>>> It's very likely related; bioperl-db suffers the same thing. I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>> >>>>> Because it may be related, I wanted to mention that I am having the >>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>> distribution via: >>>>> >>>>> i /bioperl-run/ >>>>> >>>>> But searching for a containing module does not return the distribution: >>>>> >>>>> i /clustalw/ >>>>> >>>>> Chad >>>>> >>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>> Chris, >>>>>> >>>>>> OK, tell me what they say when you hear from them. >>>>>> >>>>>> BIO >>>>>> >>>>>> >>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>> >>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. I've emailed modules at perl to see if they can diagnose it. It's likely due to the version in that section. >>>>>>> >>>>>>> chris >>>>>>> >>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>> >>>>>>>> Yes, BOSBORNE. >>>>>>>> >>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>> >>>>>>>>> Brian, >>>>>>>>> >>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). Is yours BOSBORNE? >>>>>>>>> >>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. I did notice that cpanm attempted to install an older version (1.6.0). I'll try a new upload (1.6.901), see if that helps. >>>>>>>>> >>>>>>>>> chris >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>> >>>>>>>>>> bioperl-l, >>>>>>>>>> >>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>> >>>>>>>>>> Brian O. >>>>>>>>>> >>>>>>>>>> Begin forwarded message: >>>>>>>>>> >>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>> To: bosborne >>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>> >>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>> >>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>> >>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioperl-l mailing list >>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From chad.a.davis at gmail.com Mon Oct 17 22:33:00 2011 From: chad.a.davis at gmail.com (Chad Davis) Date: Tue, 18 Oct 2011 00:33:00 +0200 Subject: [Bioperl-l] [bioperl-network] Not indexed by CPAN (#1) In-Reply-To: References: <57A1CB6E-9E3F-439E-A386-1422B9362231@verizon.net> <2F666B50-B169-495F-9287-EE91A109CE26@illinois.edu> <69E4F64F-C3A6-4602-8BC0-AB4FCAA7D8B6@verizon.net> <7F50BF17-0304-49D7-BB85-FB9FD658E03F@illinois.edu> <0DB21458-E729-4E9C-A324-89C3B9805113@verizon.net> <0D146132-82AB-4BF9-8E9B-7A925BE7C300@illinois.edu> Message-ID: Chris, Looks good. I find Bioperl-Run by querying one of the contained modules now. Thank you for sorting that out. Chad On Mon, Oct 17, 2011 at 21:40, Fields, Christopher J wrote: > I actually tested out simply reindexing the current bioperl-run and bioperl-db distributions (v.1.6.900), they both succeeded. ?It may take a little time to propagate, but try it out in a couple of hours, it should be fixed. > > chris > > On Oct 17, 2011, at 1:02 PM, Fields, Christopher J wrote: > >> Yes, I planned on that ?but wanted to make sure everything was working from your end. ? Will upload that in a bit. >> >> chris >> >> On Oct 17, 2011, at 3:08 AM, Chad Davis wrote: >> >>> The index looks good now, I'm able to get the bioperl-network distro >>> by depending on a module within it. >>> Would it be possible to do the same for a bioperl-run 1.6.901 release? >>> >>> Cheers, >>> Chad >>> >>> >>> On Mon, Oct 17, 2011 at 05:12, Fields, Christopher J >>> wrote: >>>> This appears to be due to a bug in a few places, primarily Module::Build and the CPAN indexer (the former is assigning a default version of '0' to modules, which is breaking the CPAN indexer). ?We should be assigning the default version to the modules, though; this can be fixed a bit more easily if we migrate over to Dist::Zilla for releases, something that Rob Buels implemented in a branch of the github repo. >>>> >>>> Anyway, for immediate concern Andreas fixed the indexer and reindexed BioPerl-Network (now at v. 1.6.901), can you retry an installation after updating your local index? >>>> >>>> chris >>>> >>>> On Oct 14, 2011, at 8:34 AM, Fields, Christopher J wrote: >>>> >>>>> It's very likely related; bioperl-db suffers the same thing. ?I asked about this previously with brian d foy (on modules at perl.org) re: bioperl-db, they didn't know what the problem was. ?We're working on a fix though, might be up in a couple of days (uses Dist::Zilla for releases, which I know works). >>>>> >>>>> chris >>>>> >>>>> On Oct 14, 2011, at 7:48 AM, Chad Davis wrote: >>>>> >>>>>> Because it may be related, I wanted to mention that I am having the >>>>>> same problem with Bioperl-Run. In this case, however, I can find the >>>>>> distribution via: >>>>>> >>>>>> i /bioperl-run/ >>>>>> >>>>>> But searching for a containing module does not return the distribution: >>>>>> >>>>>> i /clustalw/ >>>>>> >>>>>> Chad >>>>>> >>>>>> On Fri, Oct 14, 2011 at 03:45, Brian Osborne wrote: >>>>>>> Chris, >>>>>>> >>>>>>> OK, tell me what they say when you hear from them. >>>>>>> >>>>>>> BIO >>>>>>> >>>>>>> >>>>>>> On Oct 13, 2011, at 1:03 PM, Fields, Christopher J wrote: >>>>>>> >>>>>>>> There is apparently some funkiness with the indexing and the META.yml file 'provides' section. ?I've emailed modules at perl to see if they can diagnose it. ?It's likely due to the version in that section. >>>>>>>> >>>>>>>> chris >>>>>>>> >>>>>>>> On Oct 13, 2011, at 10:52 AM, Brian Osborne wrote: >>>>>>>> >>>>>>>>> Yes, BOSBORNE. >>>>>>>>> >>>>>>>>> On Oct 13, 2011, at 11:47 AM, Fields, Christopher J wrote: >>>>>>>>> >>>>>>>>>> Brian, >>>>>>>>>> >>>>>>>>>> If you have a PAUSE ID, I think I can set this up so you can submit new releases (just need to add you as a secondary maintainer). ?Is yours BOSBORNE? >>>>>>>>>> >>>>>>>>>> It's odd that CPAN isn't indexing this, though; it's popping up on search.cpan.org. ?I did notice that cpanm attempted to install an older version (1.6.0). ?I'll try a new upload (1.6.901), see if that helps. >>>>>>>>>> >>>>>>>>>> chris >>>>>>>>>> >>>>>>>>>> On Oct 13, 2011, at 8:07 AM, Brian Osborne wrote: >>>>>>>>>> >>>>>>>>>>> bioperl-l, >>>>>>>>>>> >>>>>>>>>>> It looks like bioperl-network is not indexed by CPAN, I don't think I have the privileges at CPAN to do this. >>>>>>>>>>> >>>>>>>>>>> Brian O. >>>>>>>>>>> >>>>>>>>>>> Begin forwarded message: >>>>>>>>>>> >>>>>>>>>>>> From: "Chad A. Davis" >>>>>>>>>>>> Date: October 13, 2011 7:40:27 AM EDT >>>>>>>>>>>> To: bosborne >>>>>>>>>>>> Subject: [bioperl-network] Not indexed by CPAN (#1) >>>>>>>>>>>> >>>>>>>>>>>> I have code managed by Module::Install that depends on Bio::Network::ProteinNet. Module::Install cannot automatically fetch and install the dependency. It seems that the bioperl-network modules are not indexed by CPAN at the moment. You should see the problem if you try to "install Bio::Network::ProteinNet" from the CPAN shell. My workaround is currently to "install CJFIELDS/BioPerl-Network-1.006900.tar.gz" from the CPAN shell. That works, but I cannot give a name like that to Module::Install in my Makefile.PL. Users of my code have to install bioperl-network as an additional step. >>>>>>>>>>>> >>>>>>>>>>>> This is perl 5, version 12, subversion 4 (v5.12.4) built for x86_64-linux-gnu-thread-multi >>>>>>>>>>>> >>>>>>>>>>>> CPAN 1.9800 >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Reply to this email directly or view it on GitHub: >>>>>>>>>>>> https://github.com/bioperl/bioperl-network/issues/1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Bioperl-l mailing list >>>>>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioperl-l mailing list >>>>>>>> Bioperl-l at lists.open-bio.org >>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioperl-l mailing list >>>>>>> Bioperl-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >>>> >>>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioperl-l > > From saxen at lbl.gov Tue Oct 18 00:37:59 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Mon, 17 Oct 2011 17:37:59 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch Message-ID: Hello, I am having problems using the Bio::DB::EUtilities module to retrieve data from Entrez. The following script is adapted from the code at http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. The input is a file containing a very long list of GI numbers from NCBI protein. When I run the script, I receive the following error message: Can't locate object method "get_Response" via package "Bio::DB::EUtilities::efetch" at getGP.pl line 23. #!/usr/bin/perl -w use warnings; use strict; use Bio::DB::EUtilities; use Bio::SeqIO; use Data::Dumper; my $id_file = $ARGV[0]; my $temp_file = 'temp.gp'; my @ids; open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; @ids = ; close IDFILE; my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', -db => 'protein', -rettype => 'gb', -email => 'saxen at lbl.gov', -id => \@ids); # dump HTTP::Response content to a file (not retained in memory) $factory->get_Response(-file => $temp_file); my $seqin = Bio::SeqIO->new(-file => $temp_file, -format => 'genbank'); while (my $seq = $seqin->next_seq) { print Dumper($seq); } I would appreciate any insight as to why I am receiving this error. Thanks in advance for your time! Seth Axen From carandraug+dev at gmail.com Tue Oct 18 01:16:40 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Tue, 18 Oct 2011 02:16:40 +0100 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On 18 October 2011 01:37, Seth D. Axen wrote: > Hello, > ? I am having problems using the Bio::DB::EUtilities module to retrieve > data from Entrez. The following script is adapted from the code at > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. > The input is a file containing a very long list of GI numbers from NCBI > protein. When I run the script, I receive the following error message: Can't > locate object method "get_Response" via package > "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > > #!/usr/bin/perl -w > use warnings; > use strict; > use Bio::DB::EUtilities; > use Bio::SeqIO; > use Data::Dumper; > > my $id_file = $ARGV[0]; > my $temp_file = 'temp.gp'; > my @ids; > > open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > @ids = ; > close IDFILE; > > my $factory = Bio::DB::EUtilities->new(-eutil ? => 'efetch', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -db ? ? ?=> 'protein', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -rettype => 'gb', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -email ? => 'saxen at lbl.gov', > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? -id ? ? ?=> \@ids); > > # dump HTTP::Response content to a file (not retained in memory) > $factory->get_Response(-file => $temp_file); > > my $seqin = Bio::SeqIO->new(-file ? => $temp_file, > ? ? ? ? ? ? ? ? ? ? ? ? ? ?-format => 'genbank'); > > while (my $seq = $seqin->next_seq) { > ? print Dumper($seq); > } > > ? I would appreciate any insight as to why I am receiving this error. > Thanks in advance for your time! > ? Seth Axen Hi your code works fine for me. Can the problem be on your IDs or its file? By the way, drop the -w from the shebang line, you are alredy using warnings. Carn? From cjfields at illinois.edu Tue Oct 18 01:33:13 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 01:33:13 +0000 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > On 18 October 2011 01:37, Seth D. Axen wrote: >> Hello, >> I am having problems using the Bio::DB::EUtilities module to retrieve >> data from Entrez. The following script is adapted from the code at >> http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO. >> The input is a file containing a very long list of GI numbers from NCBI >> protein. When I run the script, I receive the following error message: Can't >> locate object method "get_Response" via package >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. >> >> #!/usr/bin/perl -w >> use warnings; >> use strict; >> use Bio::DB::EUtilities; >> use Bio::SeqIO; >> use Data::Dumper; >> >> my $id_file = $ARGV[0]; >> my $temp_file = 'temp.gp'; >> my @ids; >> >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; >> @ids = ; >> close IDFILE; >> >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', >> -db => 'protein', >> -rettype => 'gb', >> -email => 'saxen at lbl.gov', >> -id => \@ids); >> >> # dump HTTP::Response content to a file (not retained in memory) >> $factory->get_Response(-file => $temp_file); >> >> my $seqin = Bio::SeqIO->new(-file => $temp_file, >> -format => 'genbank'); >> >> while (my $seq = $seqin->next_seq) { >> print Dumper($seq); >> } >> >> I would appreciate any insight as to why I am receiving this error. >> Thanks in advance for your time! >> Seth Axen > > Hi > > your code works fine for me. Can the problem be on your IDs or its > file? By the way, drop the -w from the shebang line, you are alredy > using warnings. > > Carn? Also, check the BioPerl version, there was a very large change in the API before the v1.6 release. chris From jeanmarc.frigerio at gmail.com Tue Oct 18 12:43:51 2011 From: jeanmarc.frigerio at gmail.com (jmf) Date: Tue, 18 Oct 2011 05:43:51 -0700 (PDT) Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> Message-ID: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Hi I agree that it'd be nice to see it revived. I made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', Thanks Dave for the topic ! Chris can you correct the file or should I submit the patch (I don't know where ?) On 2 sep, 17:20, Jack Tanner wrote: > I also see that someone's forked it on Github and made some packaging fixes. > > It'd be nice to see it revived. > > On 9/2/2011 9:00 AM, Fields, Christopher J wrote: > > > > > > > > > > > I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. ?Otherwise I worry about the long-term support for it/ > > > chris > > > On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: > > >> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: > >>http://toolkit.tuebingen.mpg.de/hhpred > > >> He got it working thus: > >> Hi Dave, > >> thanks a lot. i made it work. The error i got later on was: > >> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; > >> recompile with -fPIC > > >> the solution is: > >> perl Makefile.PL PREFIX= ?/fftwsingle --enable-shared --with-pic --enable-single > >> > >> make > >> make install > >>http://forums.fedoraforum.org/showthread.php?t=232607 > > >> Dave > > >> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J ?wrote: > >> Yes, it's essentially deprecated (unmaintained). ?I don't know of anyone who has packaged that up in a while, if ever. > > >> chris > > >> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: > > >>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? > > >>> Does anyone have a spec file for building an SRPM for it for RHEL 6? > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioper... at lists.open-bio.org > >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioper... at lists.open-bio.org > >>http://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l From sarah.tincher at gmail.com Tue Oct 18 17:00:46 2011 From: sarah.tincher at gmail.com (Sarah Tincher) Date: Tue, 18 Oct 2011 12:00:46 -0500 Subject: [Bioperl-l] Issues with CLUSTALW Message-ID: Hello, I am new to BioPerl and have no computer science background. I am taking a bioinformatics course and I have an assignment to write a BioPerl script to perform the MSA of a specific six sequences, retrieving the sequences from NCBI and using CLUSTALW. This is the script I wrote based on a lecture from my course: #!usr/bin/perl use Bio::DB::GenBank; use Bio::Tools::Run::Alignment::Clustalw; $gb = new Bio::DB::GenBank(); $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); $factory = Bio::Tools::Run::Alignment::Clustalw->new; @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); print "$aln\n"; And this is the error that I receive: Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level /Library/Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) at HW3_2.pl line 3. BEGIN failed--compilation aborted at HW3_2.pl line 3. I would appreciate any help you can provide. Thank you, Sarah Tincher From cjfields at illinois.edu Tue Oct 18 18:35:08 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:08 +0000 Subject: [Bioperl-l] Bio::Ext::Align? In-Reply-To: <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> References: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu> <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu> <7f619fb4-8cc4-456c-a89e-3b3ce7b5cabb@h5g2000vbf.googlegroups.com> Message-ID: <364EF42F-D067-40B5-9B92-7D36ED22B6E1@illinois.edu> A patch is fine. Also, it might be worth talking to the WUSTL group on merging those changes from their fork in (fairly easy to do). At some point, if this code looks as if it needs to exist independently of bioperl-ext we can create a new repo for it. I think it will see more use that way. chris On Oct 18, 2011, at 7:43 AM, jmf wrote: > Hi > I agree that it'd be nice to see it revived. I made a patch to the Bio/ > Ext/Align/Makefile.PL to make the compiler happy, just by changing: > > 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', > to > 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'', > > Thanks Dave for the topic ! > > Chris can you correct the file or should I submit the patch (I don't > know where ?) > > On 2 sep, 17:20, Jack Tanner wrote: >> I also see that someone's forked it on Github and made some packaging fixes. >> >> It'd be nice to see it revived. >> >> On 9/2/2011 9:00 AM, Fields, Christopher J wrote: >> >> >> >> >> >> >> >> >> >>> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own. Otherwise I worry about the long-term support for it/ >> >>> chris >> >>> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote: >> >>>> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred: >>>> http://toolkit.tuebingen.mpg.de/hhpred >> >>>> He got it working thus: >>>> Hi Dave, >>>> thanks a lot. i made it work. The error i got later on was: >>>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; >>>> recompile with -fPIC >> >>>> the solution is: >>>> perl Makefile.PL PREFIX= /fftwsingle --enable-shared --with-pic --enable-single >>>> >>>> make >>>> make install >>>> http://forums.fedoraforum.org/showthread.php?t=232607 >> >>>> Dave >> >>>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J wrote: >>>> Yes, it's essentially deprecated (unmaintained). I don't know of anyone who has packaged that up in a while, if ever. >> >>>> chris >> >>>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote: >> >>>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead? >> >>>>> Does anyone have a spec file for building an SRPM for it for RHEL 6? >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioper... at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioper... at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioper... at lists.open-bio.orghttp://lists.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From cjfields at illinois.edu Tue Oct 18 18:35:41 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 18 Oct 2011 18:35:41 +0000 Subject: [Bioperl-l] Issues with CLUSTALW In-Reply-To: References: Message-ID: <54A57FF8-5415-4798-89B5-3E256ECDE636@illinois.edu> You need to install BioPerl-Run as well as the core BioPerl modules. chris On Oct 18, 2011, at 12:00 PM, Sarah Tincher wrote: > Hello, > > I am new to BioPerl and have no computer science background. I am taking a > bioinformatics course and I have an assignment to write a BioPerl script to > perform the MSA of a specific six sequences, retrieving the sequences from > NCBI and using CLUSTALW. > > This is the script I wrote based on a lecture from my course: > > #!usr/bin/perl > use Bio::DB::GenBank; > use Bio::Tools::Run::Alignment::Clustalw; > $gb = new Bio::DB::GenBank(); > $seq1 = $gb->get_Seq_by_acc('NP_000509.1'); > $seq2 = $gb->get_Seq_by_acc('XP_508242.1'); > $seq3 = $gb->get_Seq_by_acc('XP_537902.1'); > $seq4 = $gb->get_Seq_by_acc('XP_001252211.2'); > $seq5 = $gb->get_Seq_by_acc('NP_032246.2'); > $seq6 = $gb->get_Seq_by_acc('NP_942071.1'); > $factory = Bio::Tools::Run::Alignment::Clustalw->new; > @seq_array = ($seq1, $seq2, $seq3, $seq4, $seq5, $seq6); > $seq_array_ref = \@seq_array; > $aln = $factory->align($seq_array_ref); > print "$aln\n"; > > And this is the error that I receive: > > Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: > /sw/lib/perl5/5.8.8/darwin-thread-multi-2level /sw/lib/perl5/5.8.8 > /sw/lib/perl5/darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin > /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level > /Library/Perl/Updates/5.8.8 > /System/Library/Perl/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level > /Library/Perl/5.8.8 /Library/Perl > /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > /Network/Library/Perl/5.8.8 /Network/Library/Perl > /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1 .) > at HW3_2.pl line 3. > BEGIN failed--compilation aborted at HW3_2.pl line 3. > > I would appreciate any help you can provide. > > Thank you, > Sarah Tincher > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From saxen at lbl.gov Wed Oct 19 00:15:21 2011 From: saxen at lbl.gov (Seth D. Axen) Date: Tue, 18 Oct 2011 17:15:21 -0700 Subject: [Bioperl-l] Error While Using Bio::DB::EUtilities::efetch In-Reply-To: References: Message-ID: Thanks Carne and Chris! The problem was with my BioPerl version. Once I used the latest version, the script ran perfectly. Seth 2011/10/17 Fields, Christopher J > On Oct 17, 2011, at 8:16 PM, Carn? Draug wrote: > > > On 18 October 2011 01:37, Seth D. Axen wrote: > >> Hello, > >> I am having problems using the Bio::DB::EUtilities module to retrieve > >> data from Entrez. The following script is adapted from the code at > >> > http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2C_then_parse_via_Bio::SeqIO > . > >> The input is a file containing a very long list of GI numbers from NCBI > >> protein. When I run the script, I receive the following error message: > Can't > >> locate object method "get_Response" via package > >> "Bio::DB::EUtilities::efetch" at getGP.pl line 23. > >> > >> #!/usr/bin/perl -w > >> use warnings; > >> use strict; > >> use Bio::DB::EUtilities; > >> use Bio::SeqIO; > >> use Data::Dumper; > >> > >> my $id_file = $ARGV[0]; > >> my $temp_file = 'temp.gp'; > >> my @ids; > >> > >> open (IDFILE, "<$id_file") || die "Could not open $id_file\n"; > >> @ids = ; > >> close IDFILE; > >> > >> my $factory = Bio::DB::EUtilities->new(-eutil => 'efetch', > >> -db => 'protein', > >> -rettype => 'gb', > >> -email => 'saxen at lbl.gov', > >> -id => \@ids); > >> > >> # dump HTTP::Response content to a file (not retained in memory) > >> $factory->get_Response(-file => $temp_file); > >> > >> my $seqin = Bio::SeqIO->new(-file => $temp_file, > >> -format => 'genbank'); > >> > >> while (my $seq = $seqin->next_seq) { > >> print Dumper($seq); > >> } > >> > >> I would appreciate any insight as to why I am receiving this error. > >> Thanks in advance for your time! > >> Seth Axen > > > > Hi > > > > your code works fine for me. Can the problem be on your IDs or its > > file? By the way, drop the -w from the shebang line, you are alredy > > using warnings. > > > > Carn? > > > Also, check the BioPerl version, there was a very large change in the API > before the v1.6 release. > > chris > > > > From shachigahoimbi at gmail.com Fri Oct 21 05:59:12 2011 From: shachigahoimbi at gmail.com (Shachi Gahoi) Date: Fri, 21 Oct 2011 11:29:12 +0530 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl Message-ID: Dear all, I have fasta format sequence file and I want to extract ORF ID "PITG_14194" from fasta file and then I want to rename same file with that ORF ID "PITG_14194". I have many files and I want to do same exercise with all sequence files. Please tell me how can i do this with perl or bioperl. >tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR NGIAVDHKGVICNGKAPIEIAVDENTLSAAA -- Regards, Shachi From jason.stajich at gmail.com Fri Oct 21 09:56:11 2011 From: jason.stajich at gmail.com (Jason Stajich) Date: Fri, 21 Oct 2011 02:56:11 -0700 Subject: [Bioperl-l] extract ORF ID from fasta file using bioperl In-Reply-To: References: Message-ID: easy to do this with a simple regular expression and opening a new file. Have you read up on this concept in Perl. You can use SeqIO to parse FASTA files - did you read the HOWTO and website documentation first? We don't typically do people's work for them on this mailing list so please show some effort first. On Oct 20, 2011, at 10:59 PM, Shachi Gahoi wrote: > Dear all, > > I have fasta format sequence file and I want to extract ORF ID "PITG_14194" > from fasta file and then I want to rename same file with that ORF ID > "PITG_14194". > > I have many files and I want to do same exercise with all sequence files. > > Please tell me how can i do this with perl or bioperl. > >> tr|D0NNU7|D0NNU7_PHYIT Carbohydrate esterase, putative OS=Phytophthora > infestans (strain T30-4) GN=PITG_14194 PE=4 SV=1 > MVKLSIVSSTMQSLLAPLLRVWTDPERRRKFLRWLFGGTSGAIALLLILEATRGFCRTPL > ETAQLLAGISWTLCKITVQFVARGFKPKFAKWTLRYELLHGLMRTAATMFGERIVDLQHA > RVIRHHTGMFGTVLGSFARWQNEMRLESVRLNGLEHIWLKSSTCTTETKSERKRLVVLFF > HGGGYAVLSPRMYISFCSAVAGAIRQQLASDDVDVDVFLANYRKLPEHKFPVPAEDAVAM > YEYLLQHEKLEPSQIILAGDSAGGGLVMSTLLRVRDGLSSWKSKLPLPLAAIVMCPLADL > TWDEDEIAGQHCVLPLNMTAASVLTYHPTRDDPSTWADASPVHCNLQGLPPVFLQSATLD > RLFQHSVRLAAKAKADGLVNWEVDIHEGVPHVFMVIPAYVLPYARVGVGRMAAFAAKQFR > NGIAVDHKGVICNGKAPIEIAVDENTLSAAA > > > -- > Regards, > Shachi > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From David.Messina at sbc.su.se Fri Oct 21 15:09:13 2011 From: David.Messina at sbc.su.se (Dave Messina) Date: Fri, 21 Oct 2011 11:09:13 -0400 Subject: [Bioperl-l] Deobfuscator direct link? Message-ID: Hi everybody, Does anyone object to me changing the center front-page link to the Deobfuscator to go directly to http://bioperl.org/cgi-bin/deob_interface.cgi ? That would still leave the left sidebar link that goes to the wiki page. Dave From cjfields at illinois.edu Fri Oct 21 16:31:45 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 21 Oct 2011 16:31:45 +0000 Subject: [Bioperl-l] Deobfuscator direct link? In-Reply-To: References: Message-ID: <2E2B401F-F358-48AD-880C-3FA9575D9B17@illinois.edu> Go for it. chris On Oct 21, 2011, at 10:09 AM, Dave Messina wrote: > Hi everybody, > > Does anyone object to me changing the center front-page link to the > Deobfuscator to go directly to > > http://bioperl.org/cgi-bin/deob_interface.cgi > > ? > > That would still leave the left sidebar link that goes to the wiki page. > > > Dave > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From zheboyang at gmail.com Sat Oct 22 01:38:56 2011 From: zheboyang at gmail.com (boyang zhe) Date: Sat, 22 Oct 2011 03:38:56 +0200 Subject: [Bioperl-l] bioperl-ext installation Message-ID: I try to install bioperl-ext. But I failed. So I try the method suggested by JMF< jeanmarc.frigerio at gmail.com>. made a patch to the Bio/ Ext/Align/Makefile.PL to make the compiler happy, just by changing: 'MYEXTLIB' => 'libs/libsw$(LIB_EXT)', to 'MYEXTLIB' => '\'-fPIC libs/libsw$(LIB_EXT)\'' Then I run make. It seems ok for compilation. However, it generate errors when I run make test. No any of the 20 tests passed. it seems that because " Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so" I did not see any Align.so file at those directory. In fact, I can only find a blank directory of blib/arch/auto/Bio/Ext. Hope for your help. It is really hard for me. Thank you very much. boyang info as below: make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/basic.t .. ok All tests successful. Files=1, Tests=1, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.04 cusr 0.00 csys = 0.08 CPU) Result: PASS make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..20 not ok 1 - use Bio::Ext::Align; # Failed test 'use Bio::Ext::Align;' # at test.pl line 15. # Tried to use 'Bio::Ext::Align'. # Error: Can't load '../blib/arch/auto/Bio/Ext/Align/Align.so' for module Bio::Ext::Align: ../blib/arch/auto/Bio/Ext/Align/Align.so: undefined symbol: bp_sw_access_name_CompMat at /usr/lib/perl/5.10/DynaLoader.pm line 193. # at (eval 4) line 2 # Compilation failed in require at (eval 4) line 2. # BEGIN failed--compilation aborted at (eval 4) line 2. The C-compiled engine for Smith Waterman alignments (Bio::Ext::Align) has not been installed. Please install the bioperl-ext package # Looks like you planned 20 tests but ran 1. # Looks like you failed 1 test of 1 run. # Looks like your test exited with 1 just after 1. make[1]: *** [test_dynamic] Error 1 make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make: *** [subdirs-test] Error 2 This is the info for make. cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h cp Bio/Ext/Align/libs/probability.c blib/lib/Bio/Ext/Align/libs/probability.c cp Bio/Ext/Align/libs/linesubs.h blib/lib/Bio/Ext/Align/libs/linesubs.h cp Bio/SeqIO/staden/CHANGES blib/lib/Bio/SeqIO/staden/CHANGES cp Bio/Ext/Align/test.pl blib/lib/Bio/Ext/Align/test.pl cp Bio/Ext/Align/libs/wiseoverlay.h blib/lib/Bio/Ext/Align/libs/wiseoverlay.h cp Bio/Ext/Align/libs/proteinsw.h blib/lib/Bio/Ext/Align/libs/proteinsw.h cp Bio/Ext/Align/libs/wisebase.h blib/lib/Bio/Ext/Align/libs/wisebase.h cp Bio/Ext/Align/libs/seqaligndisplay.h blib/lib/Bio/Ext/Align/libs/seqaligndisplay.h cp Bio/Ext/Align/libs/dyna.h blib/lib/Bio/Ext/Align/libs/dyna.h cp Bio/Ext/Align/libs/wiseerror.c blib/lib/Bio/Ext/Align/libs/wiseerror.c cp Bio/Ext/Align/libs/commandline.h blib/lib/Bio/Ext/Align/libs/commandline.h cp Bio/Ext/Align/libs/aln.c blib/lib/Bio/Ext/Align/libs/aln.c cp Bio/Ext/Align/libs/packaln.c blib/lib/Bio/Ext/Align/libs/packaln.c cp Bio/Ext/Align/libs/dpenvelope.c blib/lib/Bio/Ext/Align/libs/dpenvelope.c cp Bio/Ext/Align/libs/complexsequence.c blib/lib/Bio/Ext/Align/libs/complexsequence.c cp Bio/Ext/Align/libs/wisestring.h blib/lib/Bio/Ext/Align/libs/wisestring.h cp Bio/Ext/Align/libs/codon.c blib/lib/Bio/Ext/Align/libs/codon.c cp Bio/Ext/Align/libs/linspc.c blib/lib/Bio/Ext/Align/libs/linspc.c cp Bio/Ext/Align/libs/probability.h blib/lib/Bio/Ext/Align/libs/probability.h cp Bio/Ext/Align/Align.xs blib/lib/Bio/Ext/Align/Align.xs cp Bio/SeqIO/staden/t/staden/data/readtest.exp blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.exp cp Bio/Ext/Align/libs/packaln.h blib/lib/Bio/Ext/Align/libs/packaln.h cp Bio/Ext/Align/blosum45.mat blib/lib/Bio/Ext/Align/blosum45.mat cp Bio/Ext/Align/libs/dynlibcross.c blib/lib/Bio/Ext/Align/libs/dynlibcross.c cp Bio/Ext/Align/libs/sequencedb.c blib/lib/Bio/Ext/Align/libs/sequencedb.c cp Bio/Ext/Align/libs/sw_wrap.c blib/lib/Bio/Ext/Align/libs/sw_wrap.c cp Bio/Ext/Align/libs/complexsequence.h blib/lib/Bio/Ext/Align/libs/complexsequence.h cp Bio/Ext/Align/libs/wiseerror.h blib/lib/Bio/Ext/Align/libs/wiseerror.h cp Bio/Ext/Align/Makefile.PL blib/lib/Bio/Ext/Align/Makefile.PL cp Bio/Ext/Align/libs/wiseconfig.h blib/lib/Bio/Ext/Align/libs/wiseconfig.h cp Bio/SeqIO/staden/t/staden/data/readtestabi.fa blib/lib/Bio/SeqIO/staden/t/staden/data/readtestabi.fa cp Bio/Ext/Align/libs/dynlibcross.h blib/lib/Bio/Ext/Align/libs/dynlibcross.h cp Bio/SeqIO/staden/t/staden/data/readtest.pln blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.pln cp Bio/Ext/Align/libs/complexconsensi.c blib/lib/Bio/Ext/Align/libs/complexconsensi.c cp Bio/Ext/Align/libs/hscore.c blib/lib/Bio/Ext/Align/libs/hscore.c cp Bio/Ext/Align/libs/alnrange.c blib/lib/Bio/Ext/Align/libs/alnrange.c cp Bio/Ext/Align/libs/dpenvelope.h blib/lib/Bio/Ext/Align/libs/dpenvelope.h cp Bio/Ext/Align/blosum62.mat blib/lib/Bio/Ext/Align/blosum62.mat cp Bio/Ext/Align/libs/sequence.h blib/lib/Bio/Ext/Align/libs/sequence.h cp Bio/Ext/Align/libs/asciibtcanvas.h blib/lib/Bio/Ext/Align/libs/asciibtcanvas.h cp Bio/Ext/Align/blosum50.mat blib/lib/Bio/Ext/Align/blosum50.mat cp Bio/Ext/Align/blosum62.bla blib/lib/Bio/Ext/Align/blosum62.bla cp Bio/SeqIO/staden/read.pm blib/lib/Bio/SeqIO/staden/read.pm cp Bio/SeqIO/staden/README blib/lib/Bio/SeqIO/staden/README cp Bio/SeqIO/staden/read.xs blib/lib/Bio/SeqIO/staden/read.xs cp Bio/SeqIO/staden/t/staden/data/readtest.abi blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.abi cp Bio/Ext/Align/libs/protein.h blib/lib/Bio/Ext/Align/libs/protein.h cp Bio/Ext/Align/libs/sequencedb.h blib/lib/Bio/Ext/Align/libs/sequencedb.h cp Bio/Ext/Align/Align.pm blib/lib/Bio/Ext/Align/Align.pm cp Bio/Ext/Align/libs/complexconsensi.h blib/lib/Bio/Ext/Align/libs/complexconsensi.h cp Bio/Ext/Align/libs/dna.c blib/lib/Bio/Ext/Align/libs/dna.c cp Bio/Ext/Align/libs/sw.h blib/lib/Bio/Ext/Align/libs/sw.h cp Bio/SeqIO/staden/t/staden/data/readtestref.scf blib/lib/Bio/SeqIO/staden/t/staden/data/readtestref.scf cp Bio/SeqIO/staden/Makefile.PL blib/lib/Bio/SeqIO/staden/Makefile.PL cp Bio/Ext/Align/libs/wisestring.c blib/lib/Bio/Ext/Align/libs/wisestring.c cp Bio/Ext/Align/libs/alnrange.h blib/lib/Bio/Ext/Align/libs/alnrange.h cp Bio/Ext/Align/libs/sw_wrap.h blib/lib/Bio/Ext/Align/libs/sw_wrap.h cp Bio/Ext/Align/libs/complexevalset.c blib/lib/Bio/Ext/Align/libs/complexevalset.c cp Bio/Ext/Align/libs/complexevalset.h blib/lib/Bio/Ext/Align/libs/complexevalset.h cp Bio/SeqIO/staden/META.yml blib/lib/Bio/SeqIO/staden/META.yml cp Bio/Ext/Align/libs/wiseconfig.c blib/lib/Bio/Ext/Align/libs/wiseconfig.c cp Bio/Ext/Align/libs/wisefile.c blib/lib/Bio/Ext/Align/libs/wisefile.c cp Bio/Ext/Align/libs/alnconvert.c blib/lib/Bio/Ext/Align/libs/alnconvert.c cp Bio/Ext/Align/libs/histogram.h blib/lib/Bio/Ext/Align/libs/histogram.h cp Bio/Ext/Align/libs/makefile blib/lib/Bio/Ext/Align/libs/makefile cp Bio/Ext/Align/typemap blib/lib/Bio/Ext/Align/typemap cp Bio/Ext/Align/libs/proteindb.h blib/lib/Bio/Ext/Align/libs/proteindb.h cp Bio/Ext/Align/libs/btcanvas.c blib/lib/Bio/Ext/Align/libs/btcanvas.c cp Bio/Ext/Align/libs/dpalign.c blib/lib/Bio/Ext/Align/libs/dpalign.c cp Bio/Ext/Align/libs/database.h blib/lib/Bio/Ext/Align/libs/database.h cp Bio/Ext/Align/libs/dpalign.h blib/lib/Bio/Ext/Align/libs/dpalign.h cp Bio/Ext/Align/libs/wisetime.c blib/lib/Bio/Ext/Align/libs/wisetime.c cp Bio/Ext/Align/libs/proteinsw.c blib/lib/Bio/Ext/Align/libs/proteinsw.c cp Bio/SeqIO/staden/MANIFEST blib/lib/Bio/SeqIO/staden/MANIFEST cp Bio/Ext/Align/libs/wiserandom.c blib/lib/Bio/Ext/Align/libs/wiserandom.c cp Bio/Ext/Align/libs/btcanvas.h blib/lib/Bio/Ext/Align/libs/btcanvas.h cp Bio/Ext/Align/libs/proteindb.c blib/lib/Bio/Ext/Align/libs/proteindb.c cp Bio/Ext/Align/libs/compmat.c blib/lib/Bio/Ext/Align/libs/compmat.c cp Bio/Ext/Align/libs/codon.h blib/lib/Bio/Ext/Align/libs/codon.h cp Bio/Ext/Align/libs/linesubs.c blib/lib/Bio/Ext/Align/libs/linesubs.c cp Bio/SeqIO/staden/t/staden/data/readtest.ctf blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ctf cp Bio/SeqIO/staden/t/staden/data/readtest.ztr blib/lib/Bio/SeqIO/staden/t/staden/data/readtest.ztr cp Bio/Ext/Align/libs/basematrix.h blib/lib/Bio/Ext/Align/libs/basematrix.h cp Bio/Ext/Align/libs/wiserandom.h blib/lib/Bio/Ext/Align/libs/wiserandom.h cp Bio/Ext/Align/libs/dnamatrix.h blib/lib/Bio/Ext/Align/libs/dnamatrix.h cp Bio/Ext/Align/libs/histogram.c blib/lib/Bio/Ext/Align/libs/histogram.c cp Bio/Ext/Align/libs/wisememman.c blib/lib/Bio/Ext/Align/libs/wisememman.c cp Bio/Ext/Align/libs/seqaligndisplay.c blib/lib/Bio/Ext/Align/libs/seqaligndisplay.c cp Bio/Ext/Align/libs/commandline.c blib/lib/Bio/Ext/Align/libs/commandline.c cp Bio/Ext/Align/libs/alnconvert.h blib/lib/Bio/Ext/Align/libs/alnconvert.h cp Bio/Ext/Align/libs/compmat.h blib/lib/Bio/Ext/Align/libs/compmat.h cp Bio/Ext/Align/libs/dna.h blib/lib/Bio/Ext/Align/libs/dna.h cp Bio/Ext/Align/libs/basematrix.c blib/lib/Bio/Ext/Align/libs/basematrix.c cp Bio/Ext/Align/md_20.mat blib/lib/Bio/Ext/Align/md_20.mat cp Bio/Ext/Align/libs/aln.h blib/lib/Bio/Ext/Align/libs/aln.h cp Bio/Ext/Align/libs/sequence.c blib/lib/Bio/Ext/Align/libs/sequence.c cp Bio/Ext/Align/scores.lst blib/lib/Bio/Ext/Align/scores.lst cp Bio/Ext/Align/libs/wisememman.h blib/lib/Bio/Ext/Align/libs/wisememman.h cp Bio/Ext/Align/libs/protein.c blib/lib/Bio/Ext/Align/libs/protein.c cp Bio/Ext/Align/libs/wisetime.h blib/lib/Bio/Ext/Align/libs/wisetime.h cp Bio/SeqIO/staden/t/staden_read.t blib/lib/Bio/SeqIO/staden/t/staden_read.t cp Bio/Ext/Align/libs/wiseoverlay.c blib/lib/Bio/Ext/Align/libs/wiseoverlay.c cp Bio/Ext/Align/libs/dnamatrix.c blib/lib/Bio/Ext/Align/libs/dnamatrix.c cp Bio/Ext/Align/libs/asciibtcanvas.c blib/lib/Bio/Ext/Align/libs/asciibtcanvas.c cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' cp Align.pm ../blib/lib/Bio/Ext/Align.pm DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o aln.o aln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnconvert.o alnconvert.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o alnrange.o alnrange.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o asciibtcanvas.o asciibtcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o basematrix.o basematrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o btcanvas.o btcanvas.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o commandline.o commandline.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexconsensi.o complexconsensi.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexevalset.o complexevalset.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o complexsequence.o complexsequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o compmat.o compmat.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o codon.o codon.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dna.o dna.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dnamatrix.o dnamatrix.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpenvelope.o dpenvelope.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dynlibcross.o dynlibcross.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o histogram.o histogram.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o hscore.o hscore.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linesubs.o linesubs.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o packaln.o packaln.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o probability.o probability.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o protein.o protein.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteindb.o proteindb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o proteinsw.o proteinsw.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o seqaligndisplay.o seqaligndisplay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequence.o sequence.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sequencedb.o sequencedb.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o sw_wrap.o sw_wrap.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseerror.o wiseerror.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisefile.o wisefile.c wisefile.dy: In function ?bp_sw_myfclose?: wisefile.dy:66: warning: format ?%d? expects type ?int?, but argument 3 has type ?struct FILE *? cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisememman.o wisememman.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiseoverlay.o wiseoverlay.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wiserandom.o wiserandom.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisestring.o wisestring.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o wisetime.o wisetime.c cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o dpalign.o dpalign.c dpalign.c: In function ?dpAlign_fatal?: dpalign.c:43: warning: format not a string literal and no format arguments cc -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR -c -o linspc.o linspc.c ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o btcanvas.o commandline.o complexconsensi.o complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o ar: creating libsw.a make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' DEFINE='-DPOSIX -DNOERROR'; CC='cc'; CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'; export DEFINE INC CC CFLAGS; \ cd libs && make CC='cc' CFLAGS='-D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DPOSIX -DNOERROR' DEFINE='-DPOSIX -DNOERROR' libsw.a -e ; \ : libsw.a make[2]: Entering directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' make[2]: `libsw.a' is up to date. make[2]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align/libs' /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap -typemap typemap Align.xs > Align.xsc && mv Align.xsc Align.c cc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.6.0\" -DXS_VERSION=\"1.6.0\" -fPIC "-I/usr/lib/perl/5.10/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib -fstack-protector Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so '-fPIC libs/libsw.a' \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/Ext/Align' make[1]: Entering directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm /usr/bin/perl /usr/share/perl/5.10.1/ExtUtils/xsubpp -typemap /usr/share/perl/5.10/ExtUtils/typemap read.xs > read.xsc && mv read.xsc read.c cc -c -I/usr/local/include -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"1.007000\" -DXS_VERSION=\"1.007000\" -fPIC "-I/usr/lib/perl/5.10/CORE" read.c read.xs: In function ?staden_write_trace?: read.xs:17: warning: cast to pointer from integer of different size read.xs:22: warning: cast to pointer from integer of different size read.xs: In function ?staden_read_graph?: read.xs:204: warning: passing argument 2 of ?Perl_newRV? from incompatible pointer type /usr/lib/perl/5.10/CORE/proto.h:2166: note: expected ?struct SV *? but argument is of type ?struct AV *? Running Mkbootstrap for Bio::SeqIO::staden::read () chmod 644 read.bs rm -f ../blib/arch/auto/Bio/SeqIO/staden/read/read.so LD_RUN_PATH="/usr/local/lib" cc -shared -O2 -g -L/usr/local/lib -fstack-protector read.o -o ../blib/arch/auto/Bio/SeqIO/staden/read/read.so \ -L/usr/local/lib -lz -lm -lread \ chmod 755 ../blib/arch/auto/Bio/SeqIO/staden/read/read.so cp read.bs ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs chmod 644 ../blib/arch/auto/Bio/SeqIO/staden/read/read.bs Manifying ../blib/man3/Bio::SeqIO::staden::read.3pm make[1]: Leaving directory `/home/bji/Software/bioperl-ext/Bio/SeqIO/staden' Manifying blib/man3/Bio::SeqIO::staden::read.3pm From tzhu at mail.bnu.edu.cn Mon Oct 24 11:37:06 2011 From: tzhu at mail.bnu.edu.cn (Tao Zhu) Date: Mon, 24 Oct 2011 19:37:06 +0800 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document Message-ID: <4EA54DE2.1040706@mail.bnu.edu.cn> Here is a script copied totally from documents for module Bio::DB::GenBank, use Bio::DB::GenBank; my $gb = Bio::DB::GenBank->new(); my $seq_obj = $gb->get_Seq_by_acc('J00522'); When I try to run it, it failed. The message appear like this: > Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > Compilation failed in require at (eval 2) line 2. > ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > Compilation failed in require at perlprogram_2.pl line 5. > BEGIN failed--compilation aborted at perlprogram_2.pl line 5. I've never see such error before, how does this come? -- Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing 100875, China Email: tzhu at mail.bnu.edu.cn From cjfields at illinois.edu Mon Oct 24 13:07:56 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 13:07:56 +0000 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <4EA54DE2.1040706@mail.bnu.edu.cn> References: <4EA54DE2.1040706@mail.bnu.edu.cn> Message-ID: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> As might be implied by the error, you do not have URI::Escape installed, which is a dependency of Bio::DB::GenBank. chris On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > Here is a script copied totally from documents for module Bio::DB::GenBank, > > > use Bio::DB::GenBank; > my $gb = Bio::DB::GenBank->new(); > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > When I try to run it, it failed. The message appear like this: >> Can't locate URI/Escape.pm in @INC (@INC contains: /home/zhut/bin/PerlModule /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux /home/zhut/localperl/lib/site_perl/5.12.3 /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. >> Compilation failed in require at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. >> Compilation failed in require at (eval 2) line 2. >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. >> BEGIN failed--compilation aborted at /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. >> Compilation failed in require at perlprogram_2.pl line 5. >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > I've never see such error before, how does this come? > > -- > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > 100875, China > Email: tzhu at mail.bnu.edu.cn > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l From p.j.a.cock at googlemail.com Mon Oct 24 15:10:39 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 16:10:39 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: > Hi, > I am having problems running Bio::Index::Fastq. ?I get the following error > when a quality line begins with '@'. > > ... > > Here is an example of a fastq record that is causing this error, The last > line which starts with an '@' ?is actually the qual line. > @5:105:15806:16092:Y > GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG > + > @9;A565:=8B? > > i see that chris has partially addressed this in the mailing list > http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html > > However as he pointed out at the time, it appears this may be a fairly large > problem. Have you double checked you have the latest BioPerl with that fix Chris mentioned? > My fastq seq and qual lines are alway only one line, so I think that adding > a line count and only checking for @ in the lines that $line_count%4 ==0 > ?would work since the header lines are always the first of 4 lines , 0,4,8, > etc. Yes, *if* you can assume that for your data, which is an assumption I wouldn't like to make a general purpose library like BioPerl (or Biopython) > BioPerl fastq parsing issues aside, is there another tool which allows you > to retrieve arbitrary sequences from a fastq file by sequence ID? > There's one called cdbfasta which looks like it might work ? does anyone > have experience with it? > > Thanks, > sofia > P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? > if so, perhaps their solution could be applied here. If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) or Bio.SeqIO.index_db (using SQLite) functions will give you random access by ID to assorted files including FASTQ, even with nasty line wrapping and quality lines starting with @ or +. The Biopython FASTQ indexer basically tracks the state: @ header, seq line(s), + line, or qual line(s). You pay a slight performance hit when building the index over assuming four lines per record, but it is robust to this kind of nasty data. Peter From cjfields at illinois.edu Mon Oct 24 16:10:38 2011 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 24 Oct 2011 16:10:38 +0000 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >> Hi, >> I am having problems running Bio::Index::Fastq. I get the following error >> when a quality line begins with '@'. >> >> ... >> >> Here is an example of a fastq record that is causing this error, The last >> line which starts with an '@' is actually the qual line. >> @5:105:15806:16092:Y >> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >> + >> @9;A565:=8B?> >> >> i see that chris has partially addressed this in the mailing list >> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >> >> However as he pointed out at the time, it appears this may be a fairly large >> problem. > > Have you double checked you have the latest BioPerl with that > fix Chris mentioned? This should be fixed in both CPAN and bioperl-live. If not let me know. >> My fastq seq and qual lines are alway only one line, so I think that adding >> a line count and only checking for @ in the lines that $line_count%4 ==0 >> would work since the header lines are always the first of 4 lines , 0,4,8, >> etc. > > Yes, *if* you can assume that for your data, which is an assumption I > wouldn't like to make a general purpose library like BioPerl (or Biopython) One could build in an optimization that takes this assumption into account when explicitly requested, something worth looking into. A lot of our short read pipelines use the 4-line format. >> BioPerl fastq parsing issues aside, is there another tool which allows you >> to retrieve arbitrary sequences from a fastq file by sequence ID? >> There's one called cdbfasta which looks like it might work ? does anyone >> have experience with it? >> >> Thanks, >> sofia >> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >> if so, perhaps their solution could be applied here. > > If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) > or Bio.SeqIO.index_db (using SQLite) functions will give you random > access by ID to assorted files including FASTQ, even with nasty line > wrapping and quality lines starting with @ or +. > > The Biopython FASTQ indexer basically tracks the state: @ header, seq > line(s), + line, or qual line(s). You pay a slight performance hit when > building the index over assuming four lines per record, but it is robust > to this kind of nasty data. > > Peter We should really look into a consistent OBDA-like indexing scheme that could work cross-Bio*. Or simply resuscitate OBDA. :) chris From p.j.a.cock at googlemail.com Mon Oct 24 16:17:18 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 24 Oct 2011 17:17:18 +0100 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual In-Reply-To: References: Message-ID: On Mon, Oct 24, 2011 at 5:10 PM, Fields, Christopher J wrote: > On Oct 24, 2011, at 10:10 AM, Peter Cock wrote: > >> On Mon, Oct 24, 2011 at 3:58 PM, Sofia Robb wrote: >>> Hi, >>> I am having problems running Bio::Index::Fastq. ?I get the following error >>> when a quality line begins with '@'. >>> >>> ... >>> >>> Here is an example of a fastq record that is causing this error, The last >>> line which starts with an '@' ?is actually the qual line. >>> @5:105:15806:16092:Y >>> GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG >>> + >>> @9;A565:=8B?>> >>> >>> i see that chris has partially addressed this in the mailing list >>> http://bioperl.org/pipermail/bioperl-l/2011-January/034481.html >>> >>> However as he pointed out at the time, it appears this may be a fairly large >>> problem. >> >> Have you double checked you have the latest BioPerl with that >> fix Chris mentioned? > > This should be fixed in both CPAN and bioperl-live. ?If not let me know. Good. >>> My fastq seq and qual lines are alway only one line, so I think that adding >>> a line count and only checking for @ in the lines that $line_count%4 ==0 >>> ?would work since the header lines are always the first of 4 lines , 0,4,8, >>> etc. >> >> Yes, *if* you can assume that for your data, which is an assumption I >> wouldn't like to make a general purpose library like BioPerl (or Biopython) > > One could build in an optimization that takes this assumption into account > when explicitly requested, something worth looking into. ?A lot of our short > read pipelines use the 4-line format. That's a sensible compromise. >>> BioPerl fastq parsing issues aside, is there another tool which allows you >>> to retrieve arbitrary sequences from a fastq file by sequence ID? >>> There's one called cdbfasta which looks like it might work ? does anyone >>> have experience with it? >>> >>> Thanks, >>> sofia >>> P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? >>> if so, perhaps their solution could be applied here. >> >> If you want a Python solution, Biopython's Bio.SeqIO.index (in memory) >> or Bio.SeqIO.index_db (using SQLite) functions will give you random >> access by ID to assorted files including FASTQ, even with nasty line >> wrapping and quality lines starting with @ or +. >> >> The Biopython FASTQ indexer basically tracks the state: @ header, seq >> line(s), + line, or qual line(s). You pay a slight performance hit when >> building the index over assuming four lines per record, but it is robust >> to this kind of nasty data. >> >> Peter > > We should really look into a consistent OBDA-like indexing scheme > that could work cross-Bio*. ?Or simply resuscitate OBDA. :) > > chris +1 Our SQLite index is based on OBDA but replacing the BDB / flat file index with SQLite3. Also we're using the Biopython SeqIO format names which don't 100% align with BioPerl/EMBOSS/etc. Peter From chiragmatkarbioinfo at gmail.com Mon Oct 24 16:38:24 2011 From: chiragmatkarbioinfo at gmail.com (Chirag Matkar) Date: Mon, 24 Oct 2011 22:08:24 +0530 Subject: [Bioperl-l] Fail to run a script in Bio::DB::GenBank's document In-Reply-To: <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> References: <4EA54DE2.1040706@mail.bnu.edu.cn> <6160084C-8FA3-49EB-A27D-CEC390FBB622@illinois.edu> Message-ID: Tao, You can install URI::Escape through CPAN. On Mon, Oct 24, 2011 at 6:37 PM, Fields, Christopher J < cjfields at illinois.edu> wrote: > As might be implied by the error, you do not have URI::Escape installed, > which is a dependency of Bio::DB::GenBank. > > chris > > On Oct 24, 2011, at 6:37 AM, Tao Zhu wrote: > > > Here is a script copied totally from documents for module > Bio::DB::GenBank, > > > > > > use Bio::DB::GenBank; > > my $gb = Bio::DB::GenBank->new(); > > my $seq_obj = $gb->get_Seq_by_acc('J00522'); > > > > When I try to run it, it failed. The message appear like this: > >> Can't locate URI/Escape.pm in @INC (@INC contains: > /home/zhut/bin/PerlModule > /home/zhut/localperl/lib/site_perl/5.12.3/x86_64-linux > /home/zhut/localperl/lib/site_perl/5.12.3 > /home/zhut/localperl/lib/5.12.3/x86_64-linux /home/zhut/localperl/lib/5.12.3 > .) at /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/Query/GenBank.pm line 100. > >> Compilation failed in require at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/NCBIHelper.pm line 91. > >> Compilation failed in require at (eval 2) line 2. > >> ...propagated at /home/zhut/localperl/lib/5.12.3/base.pm line 94. > >> BEGIN failed--compilation aborted at > /home/zhut/bin/PerlModule/Bio/DB/GenBank.pm line 171. > >> Compilation failed in require at perlprogram_2.pl line 5. > >> BEGIN failed--compilation aborted at perlprogram_2.pl line 5. > > > > I've never see such error before, how does this come? > > > > -- > > Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing > > 100875, China > > Email: tzhu at mail.bnu.edu.cn > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- Regards, Chirag From carandraug+dev at gmail.com Mon Oct 31 18:05:35 2011 From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=) Date: Mon, 31 Oct 2011 18:05:35 +0000 Subject: [Bioperl-l] best way to edit sequence features In-Reply-To: References: Message-ID: Hi I've been planning on writing a free (as in freedom) tool to edit sequences and make plamids maps. The idea is to build the command line tool first and maybe later work on a GUI for it. The problem I foresee at the moment while designing it, is how to change a feature of the sequence. I'm not familiar with all sequence formats (only fasta, ensembl and genbank) but I can't see how to specify from the command line what feature to edit since I can't see any unique identifiers for them. Is there a file format that makes this easier? Any tips would be most appreciated. Thank in advance, Carn? Draug From gkuffel22 at gmail.com Thu Oct 20 22:58:07 2011 From: gkuffel22 at gmail.com (Gina) Date: Thu, 20 Oct 2011 15:58:07 -0700 (PDT) Subject: [Bioperl-l] Scripts for the Gene Ontology Database (GO) Message-ID: Is there anyway to use Bioperl to take an accession number of a gene and retrieve gene function information from the GO database? I have tried go-perl but it is not easy to use and doesn't work correctly on windows 7. Thanks for any information and ideas? From sofia2341 at gmail.com Mon Oct 24 14:58:13 2011 From: sofia2341 at gmail.com (Sofia Robb) Date: Mon, 24 Oct 2011 10:58:13 -0400 Subject: [Bioperl-l] Bio::Index::Fastq '@' in qual Message-ID: Hi, I am having problems running Bio::Index::Fastq. I get the following error when a quality line begins with '@'. ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No description line parsed STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368 STACK: Bio::SeqIO::fastq::next_dataset /usr/share/perl5/Bio/SeqIO/fastq.pm:71 STACK: Bio::SeqIO::fastq::next_seq /usr/share/perl5/Bio/SeqIO/fastq.pm:29 STACK: Bio::Index::AbstractSeq::fetch /usr/share/perl5/Bio/Index/AbstractSeq.pm:147 STACK: Bio::Index::AbstractSeq::get_Seq_by_id /usr/share/perl5/Bio/Index/AbstractSeq.pm:198 STACK: /home_stajichlab/robb/bin/clean_pairs_indexed.pl:68 Here is an example of a fastq record that is causing this error, The last line which starts with an '@' is actually the qual line. @5:105:15806:16092:Y GTGGCGCGGAACAGAGGAGGAATGTTCAGGAGAGGGGGCATGTGTTGTTACCGAGTACTTGGAAACGACG + @9;A565:=8B?) { if (/^@/ and $line_count % 4 == 0) { # $begin is the position of the first character after the '@' my $begin = tell($FASTQ) - length( $_ ) + 1; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); $c++; } } $line_count++; } -- BioPerl fastq parsing issues aside, is there another tool which allows you to retrieve arbitrary sequences from a fastq file by sequence ID? There's one called cdbfasta which looks like it might work ? does anyone have experience with it? Thanks, sofia P.S. I am CCing Peter Cock in case BioPython has solved this issue already ? if so, perhaps their solution could be applied here. From rispoli at tigem.it Mon Oct 31 17:19:41 2011 From: rispoli at tigem.it (Rispoli Rossella) Date: Mon, 31 Oct 2011 18:19:41 +0100 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Message-ID: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ---------------------------------------------------------------------------- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ----------------------------------------------------------------------------- From Kevin.M.Brown at asu.edu Mon Oct 31 18:25:40 2011 From: Kevin.M.Brown at asu.edu (Kevin Brown) Date: Mon, 31 Oct 2011 11:25:40 -0700 Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro In-Reply-To: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> References: <0C8566F4-A89F-40C4-8AD1-63ED2812BB7A@tigem.it> Message-ID: <1A4207F8295607498283FE9E93B775B407F48285@EX02.asurite.ad.asu.edu> http://search.cpan.org/~cjfields/BioPerl/Bio/DB/TFBS/transfac_pro.pm Did you read the module documentation? -----Original Message----- From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Rispoli Rossella Sent: Monday, October 31, 2011 10:20 AM To: bioperl-l at bioperl.org Subject: [Bioperl-l] about module Bio::DB::TFBS::transfac_pro Hi, I'm Rossella Rispoli and I work in research institute in Naples. I'm trying to use the module Bio::DB::TFBS::transfac_pro to get some information from the transfac.dat file( that I downloaded from their web site). But It didn't work because it doesn't found the module Bio/DB/Taxonomy/ transfac_pro.pm, but I didn't understand how to have this module???? Can you help me? Thanks in advances Rossella Rispoli ------------------------------------------------------------------------ ---- Rossella Rispoli, Bioinformatics Core Group Telethon Institute of Genetics and Medicine (TIGEM) Via P. Castellino 111, 80131, Naples, Italy Tel: +39 081 6132 498 Fax: +39 081 6132 351 Web: http://bioinformatics.tigem.it/ ------------------------------------------------------------------------ ----- _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l