allpy: ee2c10aa74b8 allpy/fileio.py

allpy

view allpy/fileio.py @ 610:ee2c10aa74b8

paired_cores/score.py: change method of score evaluation Boundary positions of blocks are not considered. Columns represented with one sequence or pure gap columns are not considered. Calculate weighted average of number of connected components in columns. Weight of column = l / sum(l) (l = number of sequnces representing column)

author	boris (kodomo) <bnagaev@gmail.com>
date	Tue, 05 Apr 2011 23:11:41 +0400
parents	ab3f5300bf4e
children	2a119d110ff6

line source

1 import os

2 from tempfile import NamedTemporaryFile

3 import util

5 class File(object):

6 """Automatical file IO."""

7 def __new__(cls, file, format="fasta"):

8 if format == "fasta":

9 return FastaFile(file)

10 else:

11 return EmbossFile(file, format)

13 class FastaFile(object):

14 """Fasta parser & writer."""

16 def __init__(self, file, wrap_column=70):

17 self.file = file

18 self.wrap_column = wrap_column

20 def write_string(self, string, name, description=''):

21 """Append one sequence to file."""

22 if description:

23 name += " " + description

24 self.file.write(">%s\n" % name)

25 if self.wrap_column:

26 while string:

27 self.file.write(string[:self.wrap_column]+"\n")

28 string = string[self.wrap_column:]

29 else:

30 self.file.write(string+"\n")

31 self.file.flush()

33 def write_strings(self, sequences):

34 """Write sequences to file.

36 Sequences are given as list of tuples (string, name, description).

37 """

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(" ")

46 name = name.strip()

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):

55 self.file = file

56 self.format = 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))

63 tmpfile.close()

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)

76 self.file.flush()

77 os.system("seqret %s %s::%s" % (self.file.name, self.format, tmpfile))

78 sequences = FastaFile(tmpfile).read_strings()

79 os.unlink(tmpfile)

80 return sequences

82 # vim: set et ts=4 sts=4 sw=4: