allpy: 3ab611713d35 lib/fasta.py

allpy

wt: compile.sh script improvements create build/ if not exists

author	boris (netbook) <bnagaev@gmail.com>
date	Sun, 31 Oct 2010 17:36:04 +0300
parents	675b402094be
children

line source

1 def save_fasta(out_file, string, name, description='', long_line=70):

2 """ Saves given string to out_file in fasta_format

4 Splits long lines to substrings of length=long_line

5 To prevent this, set long_line=None

6 """

7 out_file.write(">%(name)s %(description)s \n" % {'name':name, 'description':description})

8 if long_line:

9 for i in range(0, len(string) // long_line + 1):

10 out_file.write("%s \n" % string[i*long_line : i*long_line + long_line])

11 else:

12 out_file.write("%s \n" % string)

14 def determine_long_line(in_file):

15 """ Returns maximum sequence line length in fasta file """

16 sequences = in_file.read().split('>')

17 for sequence in sequences[1:]:

18 lines = sequence.split('\n')[1:]

19 if len(lines) >= 2:

20 return len(lines[0].strip())

21 return 70