view allpy/fileio.py @ 658:1c2f88eedb18
Improve javascript blocks viewer
* mark conservative columns darker
* create script to generate javascript config file with conservative groups
from python config file (from project sequence_based_blocks_search)
* add Makefile
* index.txt: remove unwanted spaces
| author |
boris <bnagaev@gmail.com> |
| date |
Mon, 27 Jun 2011 13:42:42 +0400 |
| parents |
b6a53615f1e9 |
| children |
80043822a41e |
line source
2 from subprocess import Popen, PIPE
3 from tempfile import NamedTemporaryFile
7 """Automatical file IO."""
8 def __new__(cls, file, format="fasta"):
10 return FastaFile(file)
12 return EmbossFile(file, format)
14 class FastaFile(object):
15 """Fasta parser & writer."""
17 def __init__(self, file, wrap_column=70):
19 self.wrap_column = wrap_column
21 def write_string(self, string, name, description=''):
22 """Append one sequence to file."""
24 name += " " + description
25 self.file.write(">%s\n" % name)
28 self.file.write(string[:self.wrap_column]+"\n")
29 string = string[self.wrap_column:]
31 self.file.write(string+"\n")
34 def write_strings(self, sequences):
35 """Write sequences to file.
37 Sequences are given as list of tuples (string, name, description).
39 for string, name, description in sequences:
40 self.write_string(string, name, description)
42 def read_strings(self):
43 for part in self.file.read().split("\n>"):
44 header, _, body = part.partition("\n")
45 header = header.lstrip(">")
46 name, _, description = header.partition(" ")
48 description = description.strip()
49 body = util.remove_each(body, " \n\r\t\v")
50 yield (name, description, body)
52 class EmbossFile(object):
53 """Parser & writer for file formats supported by EMBOSS."""
55 def __init__(self, file, format):
59 def write_strings(self, sequences):
60 """Write sequences to file."""
61 pipe = Popen(['seqret', 'stdin', '%s::stdout' % self.format],
62 stdin=PIPE, stdout=PIPE
64 FastaFile(pipe.stdin).write_strings(self.fix_sequences(sequences))
66 for line in pipe.stdout:
69 def fix_sequences(self, sequences):
70 """EMBOSS does not permit : in file names. Fix sequences for that."""
71 for name, description, sequence in sequences:
72 yield name.replace(':', '_'), description, sequence
74 def read_strings(self):
75 """Read sequences from file."""
76 pipe = Popen(['seqret', '%s::stdin' % self.format, 'stdout'],
77 stdin=PIPE, stdout=PIPE
79 for line in self.file:
80 pipe.stdin.write(line)
82 return FastaFile(pipe.stdout).read_strings()
84 # vim: set et ts=4 sts=4 sw=4:
