Oh thy masters of Perl wisdom, please enlighten me. I am struggling with some problems reading Genebank files (.gbff) through Bioperl.

I am trying to extract CDS and translation sequences using $feat->spliced_seq->seq and $feat->get_tag_values("translation")). My problem is that many of the genebank files are incomplete or are not matching the "correct" (example) format:

LOCUS       SCU49845     5028 bp    DNA             PLN       21-JUN-1
+999
DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds, and 
+Axl2p
            (AXL2) and Rev7p (REV7) genes, complete cds.
...
  JOURNAL   Submitted (22-FEB-1996) Terry Roemer, Biology, Yale Univer
+sity, New
            Haven, CT, USA
FEATURES             Location/Qualifiers
     source          1..5028
                     /organism="Saccharomyces cerevisiae"
                     /db_xref="taxon:4932"
                     /chromosome="IX"
                     /map="9"
     CDS             <1..206
                     /codon_start=3
                     /product="TCP1-beta"
                     /protein_id="AAA98665.1"
                     /db_xref="GI:1293614"
                     /translation="SSIYN...RTANRQHM"
     gene            687..3158
                     /gene="AXL2"
     CDS             687..3158
                     /gene="AXL2"
                     /note="plasma membrane glycoprotein"
                     /codon_start=1
                     /function="required for axial budding pattern of 
+S.
                     cerevisiae"
                     /product="Axl2p"
                     /protein_id="AAA98666.1"
                     /db_xref="GI:1293615"
                     /translation="MTQL...GRIPEML"
     gene            complement(3300..4037)
                     /gene="REV7"
     CDS             complement(3300..4037)
                     /gene="REV7"
                     /codon_start=1
                     /product="Rev7p"
                     /protein_id="AAA98667.1"
                     /db_xref="GI:1293616"
                     /translation="MNRWVEK...IFGSLF"
ORIGIN
        1 gatcctccat ata...tgatc
//

[download]

If all files were in the correct format, it would be relatively straightforward to extract FASTA files with each gene or protein in the format

>FEAT | FEAT | FEAT | FEAT
agcgtgacgattvcatgt...catgcatgcag

[download]

and

>FEAT | FEAT | FEAT | FEAT
AYTKRCL...MRTCKYS

[download]

Many of the files that I have either do not have the "Origin" field at the bottom (example), or have multiple "Origin" fields (example), each just after a "CDS" field, resulting in warnings and die errors that prevent me from doing what I need to do. Most of the warnings indicate that Bioperl hasn't been able to infer the sequence (because they are lacking that "ORIGIN" field)

So my questions are the following:

1. Could you give me any tips on how I can find which of the files have this incorrect file format? I am figuring that a if($feat->spliced_seq->seq) fails, push those filenames to a list and manually download them again :( But I haven't been able to test this correctly yet, and maybe there is something already in Bioperl for these cases?

2. How can I prevent the automatic die everytime a warning comes out, so that I can find the whole list of files that is not designed as it should? Curiously, through the ~1000 files that I am running, the script runs for a few hundreds, outputing those errors but quits at some point. I must say that I have use autodie; in the preamble, but I think the die command is being given by Bioperl.

Note: this was now (27 Oct) crossposted on Biostars in here

In reply to Debugging Bioperl warnings for Genebank files that are missing info by Sosi

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