allpy: lib/fasta.py annotate

allpy

fix fasta.long_line

author	boris (netbook) <bnagaev@gmail.com>
date	Thu, 28 Oct 2010 19:33:15 +0400
parents	675b402094be
children

rev	line source
bnagaev@151	1 def save_fasta(out_file, string, name, description='', long_line=70):
bnagaev@151	2 """ Saves given string to out_file in fasta_format
bnagaev@151	3
bnagaev@151	4 Splits long lines to substrings of length=long_line
bnagaev@151	5 To prevent this, set long_line=None
bnagaev@151	6 """
bnagaev@151	7 out_file.write(">%(name)s %(description)s \n" % {'name':name, 'description':description})
bnagaev@151	8 if long_line:
bnagaev@151	9 for i in range(0, len(string) // long_line + 1):
bnagaev@151	10 out_file.write("%s \n" % string[ilong_line : ilong_line + long_line])
bnagaev@151	11 else:
bnagaev@151	12 out_file.write("%s \n" % string)
bnagaev@151	13
bnagaev@151	14 def determine_long_line(in_file):
bnagaev@151	15 """ Returns maximum sequence line length in fasta file """
bnagaev@161	16 sequences = in_file.read().split('>')
bnagaev@161	17 for sequence in sequences[1:]:
bnagaev@161	18 lines = sequence.split('\n')[1:]
bnagaev@161	19 if len(lines) >= 2:
bnagaev@161	20 return len(lines[0].strip())
bnagaev@161	21 return 70