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Id: 56576
Status: open
Priority: 0/
Queue: bioperl-run

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Requestors: dimitark [...] bii.a-star.edu.sg
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Subject: bug in Bio::Tools::Run::Alignment::StandAloneFasta
Date: Wed, 14 Apr 2010 11:41:34 +0800
To: bug-bioperl-run [...] rt.cpan.org
From: Dimitar Kenanov <dimitark [...] bii.a-star.edu.sg>
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Hello guys, i found some strange behavior of the the module "Bio::Tools::Run::Alignment::StandAloneFasta" and i was told to report it as a bug. So here it is. I am trying to run "ssearch36" or "fasta36" locally and parse the report. I want to get the hits name, e-values, and sequences out of the report and print them to another file which i can process further. Below is the code where - $fh_dbs=file with a list of fasta libraries; $line=my current fasta library; $seq=my query. my @arg=( 'E' => '0.01', 'd' => '0', #problem here 'H' => '', 'w' => '100', 'O' => "$output", 'program' => 'ssearch36', ); my $line; while($line=<$fh_dbs>){ chomp($line); print "DB:$line:\n"; my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg); $factory->library($line); my @fastreport=$factory->run($seq); foreach (@fastreport) { print "Parsed fasta report:\n"; my $result = $_->next_result; while( my $hit = $result->next_hit()) { print "\thit name: ", $hit->name(); while( my $hsp = $hit->next_hsp()) { my $e_val=$hsp->evalue; my $qseq=$hsp->query_string; my $hseq=$hsp->hit_string; print "E:$e_val:\n", print "Q-SEQ:$qseq:\n"; print "HIT-SEQ:$hseq:\n"; } } } } Now the problem is that if i mark the line 'd' => '0' then i can get the HIT and QUERY sequences but not the E-value and if its unmarked as i want it then i can get the E-value but not the sequences. Dimitar -- Dimitar Kenanov Postdoctoral research fellow Protein Sequence Analysis Group Bioinformatics Institute A*STAR, Singapore email: dimitark@bii.a-star.edu.sg tel: +65 6478 8514
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On Tue Apr 13 23:42:55 2010, dimitark@bii.a-star.edu.sg wrote: Show quoted text
> Hello guys, > i found some strange behavior of the the module > "Bio::Tools::Run::Alignment::StandAloneFasta" and i was told to report > it as a bug. So here it is. > > I am trying to run "ssearch36" or "fasta36" locally and parse the > report. I want to get the hits name, e-values, and sequences out of the > report and print them to another file which i can process further. > > Below is the code where - $fh_dbs=file with a list of fasta libraries; > $line=my current fasta library; $seq=my query. > > my @arg=( > 'E' => '0.01', > 'd' => '0', #problem here > 'H' => '', > 'w' => '100', > 'O' => "$output", > 'program' => 'ssearch36', > ); > > my $line; > while($line=<$fh_dbs>){ > chomp($line); > print "DB:$line:\n"; > > > my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg); > $factory->library($line); > my @fastreport=$factory->run($seq); > > foreach (@fastreport) { > print "Parsed fasta report:\n"; > my $result = $_->next_result; > > while( my $hit = $result->next_hit()) { > print "\thit name: ", $hit->name(); > while( my $hsp = $hit->next_hsp()) { > my $e_val=$hsp->evalue; > my $qseq=$hsp->query_string; > my $hseq=$hsp->hit_string; > print "E:$e_val:\n", > print "Q-SEQ:$qseq:\n"; > print "HIT-SEQ:$hseq:\n"; > > > } > } > } > } > > Now the problem is that if i mark the line 'd' => '0' then i can get the > HIT and QUERY sequences but not the E-value and if its unmarked as i > want it then i can get the E-value but not the sequences. > > Dimitar
Mail list threads on this bug: http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032771.html http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032775.html
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Trace back from https://github.com/bioperl/bioperl-run/issues/53 Also appear to be issues with the most recent fasta releases that needs debugging. On Wed Apr 14 07:48:21 2010, cjfields wrote: Show quoted text
> On Tue Apr 13 23:42:55 2010, dimitark@bii.a-star.edu.sg wrote:
> > Hello guys, > > i found some strange behavior of the the module > > "Bio::Tools::Run::Alignment::StandAloneFasta" and i was told to report > > it as a bug. So here it is. > > > > I am trying to run "ssearch36" or "fasta36" locally and parse the > > report. I want to get the hits name, e-values, and sequences out of the > > report and print them to another file which i can process further. > > > > Below is the code where - $fh_dbs=file with a list of fasta libraries; > > $line=my current fasta library; $seq=my query. > > > > my @arg=( > > 'E' => '0.01', > > 'd' => '0', #problem here > > 'H' => '', > > 'w' => '100', > > 'O' => "$output", > > 'program' => 'ssearch36', > > ); > > > > my $line; > > while($line=<$fh_dbs>){ > > chomp($line); > > print "DB:$line:\n"; > > > > > > my $factory=Bio::Tools::Run::Alignment::StandAloneFasta->new(@arg); > > $factory->library($line); > > my @fastreport=$factory->run($seq); > > > > foreach (@fastreport) { > > print "Parsed fasta report:\n"; > > my $result = $_->next_result; > > > > while( my $hit = $result->next_hit()) { > > print "\thit name: ", $hit->name(); > > while( my $hsp = $hit->next_hsp()) { > > my $e_val=$hsp->evalue; > > my $qseq=$hsp->query_string; > > my $hseq=$hsp->hit_string; > > print "E:$e_val:\n", > > print "Q-SEQ:$qseq:\n"; > > print "HIT-SEQ:$hseq:\n"; > > > > > > } > > } > > } > > } > > > > Now the problem is that if i mark the line 'd' => '0' then i can get the > > HIT and QUERY sequences but not the E-value and if its unmarked as i > > want it then i can get the E-value but not the sequences. > > > > Dimitar
> > Mail list threads on this bug: > > http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032771.html > http://lists.open-bio.org/pipermail/bioperl-l/2010-April/032775.html > >


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