allpy
view allpy/fileio.py @ 444:36095a51e4c0
Tested and fixed Block.process(*, False, False)
In this ivokation process only copies gap patterns, not sequence names. It is
equivalent to calling Block._replace_column_contents.
Previously this function assumed self is Alignment and that each monomer in
self.sequences is visible in columns. This is false for Blocks.
author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
---|---|
date | Tue, 15 Feb 2011 22:45:34 +0300 |
parents | 0bd118c2d72b |
children | 5dfb9b9761d5 |
line source
7 """ Base class providing alignment/sequence import and export
9 Data:
10 * file - file object
11 """
17 """ Saves given string to file
19 Splits long lines to substrings of length=long_line
20 To prevent this, set long_line=None
21 """
22 pass
25 """Parse fasta file, remove spaces and newlines from sequence bodies.
27 Return a list of tuples (name, description, sequence_body).
28 """
29 pass
32 """ return tuple (name, description, string) for sequence with name name """
38 """ Fasta import and export
40 Additional data:
41 * long_line - max length of file line while export
42 Splits long lines to substrings of length=long_line
43 To prevent this, set long_line=None
44 """
78 """ Msf import and export """