[Bioperl-l] Parsing CAP3 output to Fasta

[Dave Messina]

Hi Ki,

Hopefully someone who (unlike me) uses these modules regularly will chime
in, but in the meantime, here are some ideas:

The Bio::AssemblyIO module can read and write ace files, which CAP3 can
produce as output. I don't think there is an explicit means to dump to a
multi-fasta file like you want.

But you could probably write a Bio::AssemblyIO::Fasta class which could
write the multi-Fasta format you want. Then you could use Bio::AssemblyIO
objects to read in ace files from CAP3 and write out to multi-fasta.

Look at

Bio::AssemblyIO::*
Bio::Assembly::ScaffoldI
Bio::Assembly::Contig
Bio::LocatableSeq
Bio::AlignIO

Assemblies are made of scaffolds, scaffolds are made of contigs, and contigs
are made of sequences which can be manipulated like any old seq in BioPerl.
Bio::AlignIO can read and write multiple sequence alignments and
multi-fastas, so that should help you to get from AssemblyIO to your desired
output format.



Hope this helps,
Dave