[Bioperl-l] ace to fasta conversion

scrosson scrosson at uchicago.edu
Fri Jul 13 23:43:59 EDT 2007


This problem now makes sense.  I've been playing with Bio::Assembly::IO,
which does indeed read phrap .ace files.  Does anyone have an idea how to
pull the assembled contigs out of a Bio::Assembly object and write them out
as multi-fasta (or strings for that matter)?  None of our workstations are
running phrap/consed and I'd love to see these contigs.

Sean 
       


Hello,
	the SeqIO 'ace' is an AceDB file, the 454*ace you are trying to use
is a phrap/consed ace file.  They aren't related at all. You might try
poking
around in Bio::AssemblyIO which should read assembly ace files.

Joel

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