[Bioperl-l] ace.pm

Wes Barris wes.barris at csiro.au
Mon Feb 16 18:19:02 EST 2004


ACE files generated by an application called tgicl have "CO"
lines of the form:

CO CL15Contig2 794 4 0 U

This line is not parsed properly by the ace.pm bioperl module.
Notice this line from Bio/Assembly/IO/ace.pm .

         (/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New 
contig found!

Bioperl expects the second "word" in the line to be "Contig\d+" where
the number is used as the "contigID".  Is there a reason why
"contigID" must be a number?  Why can't it be the whole second
"word" of the "CO" line?
Wes Barris
E-Mail: Wes.Barris at csiro.au

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