view allpy/fileio.py @ 615:6e93a74d1917
allpy/structure.py: move superimpose(+fix) and save_pdb to AlignmentMixin
move superimpose and save_pdb from BlockMixin to AlignmentMixin
fix of superimpose:
* add extra_columns parameter (allow columns with gaps or without structure)
* add documentation
| author |
boris (kodomo) <bnagaev@gmail.com> |
| date |
Fri, 29 Apr 2011 16:04:51 +0400 |
| parents |
ab3f5300bf4e |
| children |
2a119d110ff6 |
line source
2 from tempfile import NamedTemporaryFile
6 """Automatical file IO."""
7 def __new__(cls, file, format="fasta"):
11 return EmbossFile(file, format)
13 class FastaFile(object):
14 """Fasta parser & writer."""
16 def __init__(self, file, wrap_column=70):
18 self.wrap_column = wrap_column
20 def write_string(self, string, name, description=''):
21 """Append one sequence to file."""
23 name += " " + description
24 self.file.write(">%s\n" % name)
27 self.file.write(string[:self.wrap_column]+"\n")
28 string = string[self.wrap_column:]
30 self.file.write(string+"\n")
33 def write_strings(self, sequences):
34 """Write sequences to file.
36 Sequences are given as list of tuples (string, name, description).
38 for string, name, description in sequences:
39 self.write_string(string, name, description)
41 def read_strings(self):
42 for part in self.file.read().split("\n>"):
43 header, _, body = part.partition("\n")
44 header = header.lstrip(">")
45 name, _, description = header.partition(" ")
47 description = description.strip()
48 body = util.remove_each(body, " \n\r\t\v")
49 yield (name, description, body)
51 class EmbossFile(object):
52 """Parser & writer for file formats supported by EMBOSS."""
54 def __init__(self, file, format):
58 def write_strings(self, sequences):
59 """Write sequences to file."""
60 # XXX: in case of exceptions files are not closed, nor unlinked
61 tmpfile = NamedTemporaryFile('w', delete=False)
62 FastaFile(tmpfile).write_strings(self.fix_sequences(sequences))
64 os.system("seqret %s::%s %s" % (self.format, tmpfile, self.file.name))
65 os.unlink(tmpfile.name)
67 def fix_sequences(self, sequences):
68 """EMBOSS does not permit : in file names. Fix sequences for that."""
69 for name, description, sequence in sequences:
70 yield name.replace(':', '_'), description, sequence
72 def read_strings(self):
73 """Read sequences from file."""
74 # XXX: in case of exceptions files are not closed, nor unlinked
75 tmpfile = NamedTemporaryFile(delete=False)
77 os.system("seqret %s %s::%s" % (self.file.name, self.format, tmpfile))
78 sequences = FastaFile(tmpfile).read_strings()
82 # vim: set et ts=4 sts=4 sw=4:
