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

[Jason Stajich]

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.

-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
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>

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12/