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

[Wes Barris]

Wes Barris wrote:

> 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);

Hi Jason,

I notice that this has not yet made its way into the bioperl source.
I don't have CVS access.  Can you make the change?

> 
>>
>> -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