Skip Menu |
 

This queue is for tickets about the bioperl-run CPAN distribution.

Report information
The Basics
Id: 56576
Status: open
Priority: 0/
Queue: bioperl-run

People
Owner: Nobody in particular
Requestors: dimitark [...] bii.a-star.edu.sg
Cc:
AdminCc:

Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)



From dimitark [...] bii.a-star.edu.sg Tue Apr 13 23: 42:46 2010
MIME-Version: 1.0
X-Spam-Status: No, score=-10.599 tagged_above=-99.9 required=10 tests=[BAYES_00=-2.599, RCVD_IN_DNSWL_HI=-8] autolearn=ham
X-Spam-Flag: NO
content-type: text/plain; charset="utf-8"; format="flowed"
Message-ID: <4BC5396E.3090800 [...] bii.a-star.edu.sg>
X-Virus-Scanned: Debian amavisd-new at bestpractical.com
X-Spam-Score: -10.599
Received: from localhost (localhost [127.0.0.1]) by hipster.bestpractical.com (Postfix) with ESMTP id 19065240615 for <cpan-bug+bioperl-run [...] hipster.bestpractical.com>; Tue, 13 Apr 2010 23:42:46 -0400 (EDT)
Received: from hipster.bestpractical.com ([127.0.0.1]) by localhost (hipster.bestpractical.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id CPpqhoTNJq+g for <cpan-bug+bioperl-run [...] hipster.bestpractical.com>; Tue, 13 Apr 2010 23:42:42 -0400 (EDT)
Received: from la.mx.develooper.com (x1.develooper.com [207.171.7.70]) by hipster.bestpractical.com (Postfix) with SMTP id A34372405BD for <bug-bioperl-run [...] rt.cpan.org>; Tue, 13 Apr 2010 23:42:41 -0400 (EDT)
Received: (qmail 13926 invoked by uid 103); 14 Apr 2010 03:42:48 -0000
Received: from x16.dev (10.0.100.26) by x1.dev with QMQP; 14 Apr 2010 03:42:48 -0000
Received: from exchange.bii.a-star.edu.sg (HELO exchange.bii.a-star.edu.sg) (123.136.68.157) by 16.mx.develooper.com (qpsmtpd/0.80) with ESMTP; Tue, 13 Apr 2010 20:42:43 -0700
Received: from [172.20.130.104] (ip130-104-v219.level7.bii [172.20.130.104]) by exchange.bii.a-star.edu.sg (Postfix) with ESMTPA id 602A06A565 for <bug-bioperl-run [...] rt.cpan.org>; Wed, 14 Apr 2010 11:42:33 +0800 (SGT)
Delivered-To: cpan-bug+bioperl-run [...] hipster.bestpractical.com
Subject: bug in Bio::Tools::Run::Alignment::StandAloneFasta
User-Agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.1.7) Gecko/20100121 Thunderbird/3.0.1
Return-Path: <dimitark [...] bii.a-star.edu.sg>
X-RT-Mail-Extension: bioperl-run
X-Original-To: cpan-bug+bioperl-run [...] hipster.bestpractical.com
X-Spam-Check-BY: 16.mx.develooper.com
Date: Wed, 14 Apr 2010 11:41:34 +0800
X-Spam-Level:
To: bug-bioperl-run [...] rt.cpan.org
Content-Transfer-Encoding: 7bit
From: Dimitar Kenanov <dimitark [...] bii.a-star.edu.sg>
X-RT-Original-Encoding: ISO-8859-1
Content-Length: 1808
Download (untitled) / with headers
text/plain 1.7k
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
MIME-Version: 1.0
In-Reply-To: <4BC5396E.3090800 [...] bii.a-star.edu.sg>
X-Mailer: MIME-tools 5.427 (Entity 5.427)
Content-Disposition: inline
References: <4BC5396E.3090800 [...] bii.a-star.edu.sg>
Content-Type: text/plain; charset="UTF-8"
Message-ID: <rt-3.8.HEAD-26540-1271249301-1447.56576-0-0 [...] rt.cpan.org>
Content-Transfer-Encoding: binary
X-RT-Original-Encoding: utf-8
Content-Length: 1978
Download (untitled) / with headers
text/plain 1.9k
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
MIME-Version: 1.0
In-Reply-To: <rt-3.8.HEAD-26540-1271249301-1447.56576-0-0 [...] rt.cpan.org>
X-Mailer: MIME-tools 5.504 (Entity 5.504)
Content-Disposition: inline
X-RT-Interface: Web
References: <4BC5396E.3090800 [...] bii.a-star.edu.sg> <rt-3.8.HEAD-26540-1271249301-1447.56576-0-0 [...] rt.cpan.org>
Content-Type: text/plain; charset="utf-8"
Message-ID: <rt-4.0.18-20864-1505671032-451.56576-0-0 [...] rt.cpan.org>
Content-Transfer-Encoding: binary
X-RT-Original-Encoding: utf-8
X-RT-Encrypt: 0
X-RT-Sign: 0
Content-Length: 2303
Download (untitled) / with headers
text/plain 2.2k
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 > >


This service is sponsored and maintained by Best Practical Solutions and runs on Perl.org infrastructure.

Please report any issues with rt.cpan.org to rt-cpan-admin@bestpractical.com.