Hello,
Try this:
import sys
fasta_file = sys.argv[1] # should be *.fa
print 'loading dna from', fasta_file
chroms = {}
dna = []
for l in open(fasta_file):
if l.startswith('>'): # new chromosome
if len(dna) > 0:
chroms[chrom] = ''.join(dna)
chrom = l.strip().replace('>', '')
dna = []
else:
dna.append(l.rstrip())
if len(dna) > 0:
chroms[chrom] = ''.join(dna)
--
Vincent Legoll
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