/usr/lib/python2.7/dist-packages/cogent/align/traceback.py is in python-cogent 1.9-9.
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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 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | #!/usr/bin/env python
"""Conversion of dynamic program results ("arrays of arrows") into gap vectors,
gapped sequences or Cogent Alignment objects"""
from cogent.core.alignment import Alignment, Aligned
from cogent.core.annotation import Map
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Peter Maxwell", "Rob Knight", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
def seq_traceback(s1, s2, aligned_positions, gap_value):
"""Gapped sequences from state matrix and ending point
Gaps are signified by 'gap_value' inserted in the sequences.
"""
seqs = [s1, s2]
alignments = [[], []]
for posn in aligned_positions:
for (dimension, pos) in enumerate(posn):
if pos is not None:
c = seqs[dimension][pos]
else:
c = gap_value
alignments[dimension].append(c)
for dimension in [0,1]:
alignments[dimension].reverse()
if isinstance(s1, basestring):
alignments = [''.join(a) for a in alignments]
return alignments
def gap_traceback(aligned_positions):
"""Gap Vectors from state matrix and ending point"""
consuming = [False, False]
starts = [None, None]
ends = [None, None]
gap_vectors = [[], []]
for (a, posn) in enumerate(aligned_positions):
for dimension in [0, 1]:
delta = posn[dimension] is not None
if delta:
if starts[dimension] is None:
starts[dimension] = posn[dimension]
ends[dimension] = posn[dimension] + 1
if consuming[dimension] != delta:
gap_vectors[dimension].append(a)
consuming[dimension] = delta
a += 1
for dimension in [0,1]:
gv = gap_vectors[dimension]
if consuming[dimension]:
gv.append(a)
gap_vectors[dimension] = [
(gv[i], gv[i+1]) for i in range(0, len(gv), 2)]
return (starts, ends, gap_vectors, a)
def map_traceback(aligned_positions):
# using Map's to keep track of gaps for indel alignment
(starts, ends, gap_vectors, alignment_len) = gap_traceback(
aligned_positions)
#print 'gv', gap_vectors
maps = [Map(gv, parent_length=alignment_len).inverse()
for gv in gap_vectors]
return (starts, ends, maps)
def alignment_traceback(seqs, aligned_positions, word_length):
"""Alignment object from state matrix and ending point.
"""
(starts, ends, maps) = map_traceback(
aligned_positions)
aligneds = []
for (start, end, amap, (name, seq)) in zip(starts, ends, maps, seqs):
gs = Aligned(amap*word_length, seq[start*word_length:end*word_length])
aligneds.append((name, gs))
return Alignment(MolType=None, data=aligneds)
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