1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
|
#!/usr/bin/env python
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def phylip_from_alignment(aln, generic_label=True, make_seqlabel=None):
"""returns a phylip formatted string and an ID map of new to original
sequence names. Sequences are sequential.
Fails if all sequences are not the same length.
Arguments:
- generic_label: if true then numbered seq labels are generated
- make_seqlabel: callback function that takes the seq object and
returns a label str. The user must ensure these are correct for Phylip
format.
"""
assert generic_label or make_seqlabel is not None
if aln.isRagged():
raise ValueError, "Sequences in alignment are not all the same " +\
"length. Cannot generate PHYLIP format."
num_seqs = len(aln.Seqs)
if not aln or not num_seqs:
return ""
phylip_out = ["%d %d" % (num_seqs, aln.SeqLen)]
id_map = {}
cur_seq_id = 1
for seq_name, seq in zip(aln.Names, aln.Seqs):
if make_seqlabel is not None:
label = make_seqlabel(seq)
elif generic_label:
label = "seq%07d" % cur_seq_id
id_map[label] = seq_name
phylip_out.append("%s %s" % (label, seq))
cur_seq_id += 1
return '\n'.join(phylip_out), id_map
|
