BioPerl

Thanks Chris, the module you mentioned can only calculate score for nucleic acids, and I am in fact working with aminoacids alignment. However, I've written the sub for my needs (it's below, in case someone else needs it). sub score_aln { ... [More] #Takes two alignment lines AS STRINGS; #Assumes $matrix (Bio::Matrix::Generic), $open_penalty and $extend_penalty to be declared as global variables die "Different lengths of sequences:\n$_[0]\n$_[1]\n" if length$_[0]!=length$_[1]; my < at >line1=split(//,$_[0]); my < at >line2=split(//,$_[0]); my $score=0; my $extend=0; #Below we count score for each pair (two AA, new gap or gap extension) CHAR:for (my $j=0;$j<scalar(< at >line1);$j++) { if (($line1[$j] eq '-')or($line2[$j] eq '-')) { next CHAR if ($line1[$j] eq $line2[$j]); #Skip positions with both sequences containing gaps (in case we haven't filtered [Less]

Dear colleagues, Is there a method in bioperl that will calculate pairwise alignment scores for any given pair of genes in MSA (according to a given matrix and gap opening/extension cost)? It seems that Bio::SimpleAlign methods only work with score ... [More] if it has been described in MSA file and can only hold a general multiple sequence alignment score. -- Alexey Morozov, LIN SB RAS, bioinformatics group. Irkutsk, Russia. Bio::Align::PairwiseStatistics appears to deal with this, see if it fits your needs. You may need to extract the pairwise alignment of the two genes if they are in a multiple sequence alignment. chris _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l [Less]

Dear colleagues, Is there a method in bioperl that will calculate pairwise alignment scores for any given pair of genes in MSA (according to a given matrix and gap opening/extension cost)? It seems that Bio::SimpleAlign methods only work with score ... [More] if it has been described in MSA file and can only hold a general multiple sequence alignment score. [Less]

Very cool! Nice work Mark!! On Mon, Sep 29, 2014 at 11:30 PM, Mark A. Jensen <maj< at >fortinbras.us> wrote: _______________________________________________ Bioperl-l mailing list Bioperl-l< at >mailman.open-bio.org http://mailman.open-bio.org/mailman/listinfo/bioperl-l

(minus damn linebreaks) All (esp. George)- My work on Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) has metastasized. The proximate problem was tests that fail because of once-local prerequisites. The ultimate problems are - Why ... [More] should I have to install every single wrapper when I only want X? - Why should I care about any test that doesn't deal with X? - Why doesn't X bring along its own prereq metadata (including Bio prereqs), rather than tag along with the distro and hope for the best? (And I think these are the ultimate problems across BioPerl in terms of decentralized distribution.) My solution was - Add to the distro real, manually prepared metadata on prerequisites for all the tools - Add an interactive selector that allows a user to pick their desired tools at perl Build.PL-time - Have Module::Build check only (and ALL) the prereqs of the desired tools, and inform user of missing ones at perl Build.PL-time - Make use of the persistence of the config information to skip/r [Less]

All (esp. George)- My work on Issue #11 (https://github.com/bioperl/bioperl-run/issues/11) has metastasized. The proximate problem was tests that fail because of once-local prerequisites. The ultimate problems are - Why should I have to install ... [More] every single wrapper when I only want X? - Why should I care about any test that doesn't deal with X? - Why doesn't X bring along its own prereq metadata (including Bio prereqs), rather than tag along with the distro and hope for the best? (And I think these are the ultimate problems across BioPerl in terms of decentralized distribution.) My solution was - Add to the distro real, manually prepared metadata on prerequisites for all the tools - Add an interactive selector that allows a user to pick their desired tools at perl Build.PL-time - Have Module::Build check only (and ALL) the prereqs of the desired tools, and inform user of missing ones at perl Build.PL-time - Make use of the persistence of the config information to skip/run .t files a [Less]

Yes, it looks like a corner case that I was "unlucky" enough to hit. Certainly: https://github.com/bioperl/bioperl-live/issues/84 Best regards, Adam

I can reproduce that on master branch. It’s a weird consequence/side-effect of the text wrapping I think; if you remove the space at the end of the string of X’s and allow the module to text wrap the line it works fine. I don’t think we’ve ever run ... [More] into it frankly. If possible can you file it as a bug on GitHub? chris On Sep 29, 2014, at 10:17 AM, Adam Sjøgren <adsj< at >novozymes.com> wrote: [Less]

Hi. If you craft a tag on a feature sneakily (or if you are unlucky) Bio::SeqIO will create invalid EMBL, separating the "/" from the qualifier name: ID unknown; SV 1; linear; unassigned DNA; STD; UNC; 4 BP. XX AC unknown; XX ... [More] XX XX FH Key Location/Qualifiers FH FT CDS 1..4 FT / FT note="XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX FT X" XX SQ Sequence 4 BP; 1 A; 1 C; 1 G; 1 T; 0 other; actg 4 // In this example "/" and "note" are on separate lines, which is wrong; at least BioPerl does not accept it itself. Here is a script to create the above output (BioPerl 1.6.901 used): #!/usr/bin/perl use strict; use warnings; use Bio::Seq::RichSeq; use Bio::SeqFeature::Generic; use IO::String; use Bio::SeqIO; my $seq=Bio::Seq::RichSeq->new(-display [Less]

Hi, I'm using bioperl 1.6.923-1 (Ubuntu Trusty package) and Bio::DB::SeqFeature to store and manipulate GFF3 files. I'm wondering why the "Parent" GFF3 attributes are stored as parent_id values in the feature objects, but not returned as such in ... [More] the gff3_string? GFF3: Chr01 transdecoder mRNA 5216 5627 . + . ID=T1.Chr01.mRNA.1;Parent=T1.Chr01.gene.1;Alias=T1.asmbl_1|m.6484,T1.ORF;Name=T1.Chr01.mRNA.1 Example debugger trace after fetching stored feature: x $f 0 Bio::DB::SeqFeature=HASH(0x3e3a798) 'attributes' => HASH(0x3e3a858) 'Alias' => ARRAY(0x3e3a8b8) 0 'T1.asmbl_1|m.6484' 1 'T1.ORF' 'load_id' => ARRAY(0x3e3aca8) 0 'T1.Chr01.mRNA.1' 'parent_id' => ARRAY(0x3e3acf0) 0 'T1.Chr01.gene.1' 'is_circular' => 0 'name' => 'T1.Chr01.mRNA.1' 'phase' => undef 'primary_id' => 2428 'ref' => 'Chr01' 'score' => undef 'source' => 'transdecoder' 'start' => 5216 'stop' => 5627 'store' => Bio::DB::SeqFeatu [Less]