allpy: 9369dbad919d allpy/fasta.py

allpy

view allpy/fasta.py @ 251:9369dbad919d

Incompatible changes to Monomer interfaces. This branch does not work! - (!!) only changed allpy._monomer, not uses - (!!) removed (temporarily) classes for specific monomer types (DNAMonomer, etc) - refurbished allpy.data.AAcodes to allpy.data.codes with much cleaner interface - refurbished allpy._monomer for simplicity and more friendly interface Now it will (someday) be possible to say: a = Monomer.from_name("alanine") b = protein.Monomer.from_code1("a") c = protein.MonomerType.from_code3("ala") d = dna.Monomer.from_code3("DA") but impossible to say: d = protein.Monomer.from_code3("DA")

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Mon, 13 Dec 2010 20:12:11 +0300
parents	0ffdb88c13bd
children	4e6e85851133

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