allpy: lib/fasta.py annotate

allpy

fix. delete sequence.pdb_files on pdb_unload. however memory leak remains

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@151	16 max_length = 70
bnagaev@151	17 start = False
bnagaev@151	18 for line in in_file:
bnagaev@151	19 if line[0:] != '>':
bnagaev@151	20 if start:
bnagaev@151	21 max_length = max(max_length, line.strip())
bnagaev@151	22 else:
bnagaev@151	23 start = True
bnagaev@151	24 return max_length