allpy: 9b601bbb1fde lib/fasta.py

allpy

implemented

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 max_length = 70

17 start = False

18 for line in in_file:

19 if line[0:] != '>':

20 if start:

21 max_length = max(max_length, line.strip())

22 else:

23 start = True

24 return max_length