[Bioperl-l] Basic Error with Bio::Assembly:IO

[Smithies, Russell]

Have a look in your .ace file and check the contig name.
I think the regex in the old ace.pm was a bit too specific and would only read files with contigs named Contig1, Contig2, etc.. so if your contig is named "contig1" it will fail. 
A quick hack if you only have a few files to do is rename the contigs in your .ace file.
Or tweak the regex at line 142 in ace.pm

Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap
> Sent: Tuesday, 6 January 2009 11:09 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Basic Error with Bio::Assembly:IO
> 
> Hi All
> 
> I am new to Bio::Assembly and the way it is implemented. I am simply
> reading
> an ACE file and getting an error .
> here is the script
> 
> 
> Can't call method "get_consensus_sequence" on an undefined value at
> /usr/lib/perl5/vendor_perl/5.8.8/Bio/Assembly/IO/ace.pm line 167,
> <GEN0>
> line 163.
> 
> 
> Here is the script .
> 
> 
> ==========
> 
> #!/usr/local/bin/perl -w
> 
> my $PROGNAME="$0";
> 
> #my ($infile, $io, $usage
> 
> 
> ###Required Modules
> use strict;
> use Bio::Assembly::IO;
> use Bio::AlignIO;
> use Bio::SeqIO;
> 
> my $usage = <<USAGE;
> 
>     $PROGNAME {acefile name with full path}
> 
> USAGE
> 
> 
>     my $infile = shift or die $usage;
> 
> my $io = Bio::Assembly::IO->new(-file=>"$infile", -format=>"ace");
> 
> #print "IO is $io\n ";
> 
> my $assembly=$io->next_assembly(); ### Pointing to
> Bio::Assembly::Scaffold1
> 
> #print "Assembly : $assembly";
> 
> foreach my $contig ($assembly->all_contigs())  ##Bio::Assembly::Contig
> 
> 
>           {
> 
> 
>               my $contigName=$contig->id;
>               print "Contig Name is \t $contigName";
> 
>           }
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ===========
> 
> 
> 
> --
> -----------------------------
> Abhishek Pratap
> Bioinformatics Software Engineer
> Institute for Genome Sciences
> School of Medicine, Univ of Maryland
> 801, W. Baltimore Street, Baltimore, MD 21209
> Ph: (+1)-410-706-2296
> www.igs.umaryland.edu/
> 
> Chair
> RSG-Worldwide
> ISCB-Student Council
> http://iscbsc.org/rsg
> 
> www.bioinfosolutions.com
> _______________________________________________
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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