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

[Andrew Nunberg]

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
from
(/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do ...

To
((/^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
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com