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#!/usr/bin/env python
import unittest, sys, os
from cogent import DNA, LoadSeqs
from cogent.parse.cigar import map_to_cigar, cigar_to_map, aligned_from_cigar, \
slice_cigar, CigarParser
__author__ = "Hua Ying"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Hua Ying", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Hua Ying"
__email__ = "hua.ying@anu.edu.au"
__status__ = "Production"
class TestCigar(unittest.TestCase):
def setUp(self):
self.cigar_text = '3D2M3D6MDM2D3MD'
self.aln_seq = DNA.makeSequence('---AA---GCTTAG-A--CCT-')
self.aln_seq1 = DNA.makeSequence('CCAAAAAA---TAGT-GGC--G')
self.map, self.seq = self.aln_seq.parseOutGaps()
self.map1, self.seq1 = self.aln_seq1.parseOutGaps()
self.slices = [(1, 4), (0, 8), (7, 12), (0, 1), (3, 5)]
self.aln = LoadSeqs(data = {"FAKE01": self.aln_seq, "FAKE02": self.aln_seq1})
self.cigars = {"FAKE01": self.cigar_text, "FAKE02": map_to_cigar(self.map1)}
self.seqs = {"FAKE01": str(self.seq), "FAKE02": str(self.seq1)}
def test_map_to_cigar(self):
"""convert a Map to cigar string"""
assert map_to_cigar(self.map) == self.cigar_text
def test_cigar_to_map(self):
"""test generating a Map from cigar"""
map = cigar_to_map(self.cigar_text)
assert str(map) == str(self.map)
def test_aligned_from_cigar(self):
"""test generating aligned seq from cigar"""
aligned_seq = aligned_from_cigar(self.cigar_text, self.seq)
assert aligned_seq == self.aln_seq
def test_slice_cigar(self):
"""test slicing cigars"""
for start, end in self.slices:
# test by_align = True
map1, loc1 = slice_cigar(self.cigar_text, start, end)
ori1 = self.aln_seq[start:end]
if loc1:
slicealn1 = self.seq[loc1[0]:loc1[1]].gappedByMap(map1)
assert ori1 == slicealn1
else:
assert map1.length == len(ori1)
# test by_align = False
map2, loc2 = slice_cigar(self.cigar_text, start, end, by_align = False)
slicealn2 = self.seq[start:end].gappedByMap(map2)
ori2 = self.aln_seq[loc2[0]:loc2[1]]
assert slicealn2 == ori2
def test_CigarParser(self):
"""test without slice"""
aln = CigarParser(self.seqs, self.cigars)
assert aln == self.aln
# test slice
i = 1
for start, end in self.slices:
self.aln.getSeq("FAKE01").addFeature("annot%d"%i, "annot", [(start, end)])
annot = self.aln.getAnnotationsFromAnySequence("annot%d"%i)
slice_aln = aln.getRegionCoveringAll(annot).asOneSpan().getSlice()
i += 1
cmp_aln = CigarParser(self.seqs, self.cigars, sliced = True,
ref_seqname = "FAKE01", start = start, end = end)
assert cmp_aln == slice_aln
if __name__ == '__main__':
unittest.main()
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