[Bioperl-l] Assembly error when parsing .ace files

[Wes Barris]

Jason Stajich wrote:

> Maybe you can make the changes locally, get it to work , then post a  
> patch?  Assuming the authors were writing it for phrap ace assemblies  
> and coded it as such.

Ok.  I'm not sure about how you want this formated but here is my fix:

Bio/Assembly/IO/ace.pm line 384
Old:
           my ($phdfilename,$chromatfilename);
New:
           my ($phdfilename,$chromatfilename) = qw(unset unset);

> 
> -jason
> 
> On Sep 22, 2005, at 9:19 PM, Wes Barris wrote:
> 
>> Hi,
>>
>> I have a .ace (and associated files) that I want to parse with  bioperl.
>> The following code produces the displayed error when run:
>>
>> #!/usr/bin/perl -w
>> use strict;
>> use Bio::Assembly::IO;
>> my $usage = "Usage: $0 <infile.ace>\n";
>> my $infile = shift or die $usage;
>> my $io = new Bio::Assembly::IO(-file=>$infile, -format=>'ace');
>> my $assembly = $io->next_assembly();
>>
>> Use of uninitialized value in concatenation (.) or string at /usr/ 
>> lib/perl5/site_perl/5.8.5/Bio/Assembly/IO/ace.pm line 392, <GEN1>  
>> line 1.
>> Use of uninitialized value in concatenation (.) or string at /usr/ 
>> lib/perl5/site_perl/5.8.5/Bio/Assembly/IO/ace.pm line 392, <GEN1>  
>> line 2.
>>
>> The problem is in the following code fragment from ace.pm:
>>
>>           my ($phdfilename,$chromatfilename);
>>           if ($seq->desc() =~ /PHD_FILE: (\S+)/) {
>>               $phdfilename = $1;
>>           }
>>           if ($seq->desc() =~ /CHROMAT_FILE: (\S+)/)  {
>>                $chromatfilename = $1;
>>           }
>>           (my $phdfile = $singletsfilename) =~ s/edit_dir.*//;
>>           $phdfile .= "phd_dir/$phdfilename";
>>
>> The above code is reading the .singlets file and looking for the  string
>> "PHD_FILE:" in the defline.  That string does not exist in my singlets
>> deflines.  My .ace (and associated files) are created using the cap3
>> application.
>>
>> Perhaps ace.pm should be modified to gracefully handle the case where
>> singlet deflines do not contain the "PHD_FILE:" string.
>>
>> I am running a CVS version of bioperl updated on Sep 22 on a Linux
>> RHEL 4.1 system.  Perl version 5.8.5.  The defline of my singlet file
>> is:
>>
>> >BF654941 11920073 | BF654941.1 CLONE: unknown CLONE_LIB: MARC 3BOV  
>> LEN: 491 bp FILE: 284.fa 5-PRIME DEFN: 279305 MARC 3BOV Bos taurus  
>> cDNA 5', mRNA sequence. tissuetype=[pooled] organism=[Bos taurus]
>>
>> -- 
>> Wes Barris
>> E-Mail: Wes.Barris at csiro.au
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> -- 
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12/
> 


-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au