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#!/usr/bin/env python
from Bio import pairwise2
def _pretty_print_align(align1, align2, score, begin, end):
s = pairwise2.format_alignment(align1, align2, score, begin, end)
print s,
def _pretty_print_all(aligns):
aligns.sort()
for align in aligns:
_pretty_print_align(*align)
def _align_and_print(fn, *args, **keywds):
print fn.__name__
_pretty_print_all(fn(*args, **keywds))
a = pairwise2.align
print "### Test the function generation code"
fn = a.globalxx
print fn.__name__ # globalxx
print fn.__doc__ # globalxx(sequenceA, sequenceB) -> alignments
print a.localcd.__doc__ # localxx(...match_fn, openA, ...) -> alignments
try:
a.blah
except:
print "correctly failed"
print "#### Let's start with a simple global alignment."
_align_and_print(a.globalxx, "GAACT", "GAT") # 2 aligns, 3
print "#### Try a local alignment."
_align_and_print(a.localxs, "AxBx", "zABz", -0.1, 0) # 2 aligns, 1.9
print "#### Test match score, open penalty."
_align_and_print(a.globalms, "AA", "A", 2.0, -1, -0.1, 0) # 2 aligns, 1.9
_align_and_print(a.globalms, "GAA", "GA", 1.5, 0, -0.1, 0) # 2 aligns, 2.9
_align_and_print(a.globalxs, "GAACT", "GAT", -0.1, 0) # 1 align, 2.9
_align_and_print(a.globalms, "GCT", "GATA", 1, -2, -0.1, 0) # 1 align, -0.1
print "#### Test the extend penalty."
_align_and_print(a.globalxs, "GACT", "GT", -0.2, -0.5) # 1 align, 1.3
_align_and_print(a.globalxs, "GACT", "GT", -0.2, -1.5) # 2 aligns, 0.6
print "#### Test penalize_extend_when_opening"
_align_and_print(a.globalxs, "GACT", "GT", -0.2, -1.5,
penalize_extend_when_opening=1) # 1 align, -1.2
print "#### Test penalize_end_gaps"
_align_and_print(a.globalxs, "GACT", "GT", -0.2, -0.8,
penalize_end_gaps=0) # 3 aligns, 1
print "#### Test separate gap penalties"
_align_and_print(a.localxd, "GAT", "GTCT", -0.3, 0, -0.8, 0) # 2 aligns, 1.7
_align_and_print(a.localxd, "GAT", "GTCT", -0.5, 0, -0.2, 0) # 1 aligns, 1.8
print "#### Test separate gap penalties, with extension. Test align list"
_align_and_print(a.localxd, list("GAAT"), list("GTCCT"), -0.1, 0, -0.1, -0.1,
gap_char=["-"]) # 3 aligns, 1.9
print "#### Test match dictionary"
match_dict = {
("A", "A") : 1.5,
("A", "T") : 0.5,
("T", "T") : 1.0
}
_align_and_print(a.localds, "ATAT", "ATT", match_dict, -.5, 0) # 2 aligns, 3
_align_and_print(a.localds, "ATAT", "ATT", match_dict, -1, 0) # 1 align, 3
_align_and_print(a.localds, "ATT", "ATAT", match_dict, -1, 0) # 1 align, 3
print "#### This used to cause errors, reported by Daishi"
_align_and_print(a.localxs, "abcde", "c", -0.3, -0.1) # 1 align, 1.0, 1 char
_align_and_print(a.localxs, "abcce", "c", -0.3, -0.1) # 2 aligns, 1.0, 1 char
_align_and_print(a.globalxs, "abcde", "c", -0.3, -0.1) # 1 aligns, 0.2, 1 char
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