[Bioperl-l] Problem with Bio::Assembly::IO::ace

Andrew Nunberg anunberg at oriongenomics.com
Fri Apr 16 17:54:49 EDT 2004

When forcing reads into an empty assembly, which happens if you are assembly
a single clone(genomic or ests)
The contig names are not the normal Contig1 etc.., but instead are derived
from read names eg. Trace_name-Contig

The parser breaks on these  contigs so I made the following change to
Bio::Assembly::IO::ace.pm line 138
(/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do ...

((/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) or (/^CO (\S+)-Contig (\d+)
(\d+) (\d+) (\w+)/)) && do ...
This makes the contig the string (\S+) instead of the number (Contig(\d+)
that follows Contig.

Not sure what that will do downstream but for what I am doing seems to work

Andrew Nunberg
Orion Genomics

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