root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/align/sitemask/sitemask_tests.py

リビジョン 3, 2.5 KB (コミッタ: kohda, 14 年 前)

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1"""
2Tests for `bx.align.maf.sitemask`.
3"""
4
5import sys,tempfile
6import unittest
7from StringIO import StringIO
8import cpg
9import bx.align.maf
10
11test_maf_cpg = """##maf version=1 scoring=none
12a score=0
13s apple  34 64 + 110 AGGGA---GTTCGTCACT------GTCGTAAGGGTTCAGA--CTGTCTATGTATACACAAGTTGTGTTGCA--ACCG
14s orange 19 61 - 100 AGGGATGCGTT--TCACTGCTATCGTCGTA----TTCAGACTTCG-CTATCT------GAGTTGT---GCATTACCG
15"""
16
17cpg_inclusive_result = [
18"##maf,version=1",
19"a,score=0",
20"s,apple,34,64,+,110,AGGGA---GTTCGTCACT------GT##TAAGGGTTCAGA--CTGTCTATGTATACACAAGTTGTGTTGCA--ACCG",
21"s,orange,19,61,-,100,AGGGATG#GTT--TCACTGCTAT#GT##TA----TTCAGACTTCG-CTATCT------GAGTTGT---GCATTACCG"
22]
23
24cpg_restricted_result = [
25"##maf,version=1",
26"a,score=0",
27"s,apple,34,64,+,110,A##GA---#TT##TC#C#------#T##TA###GTTC#GA--C##TC#A#G#ATAC####GT#G#GT#GC#--AC#G",
28"s,orange,19,61,-,100,A##GA#G##TT--TC#C#GC#AT##T##TA----TTC#GAC#T##-C#A#C#------##GT#G#---GC#TTAC#G"                         
29]
30
31noncpg_result = [
32"##maf,version=1",
33"a,score=0",
34"s,apple,34,64,+,110,#GG##---G##CG##A#T------G#CG##AGG####A##--#TG##T#T#T####ACAA##T#T##T##A--##CG",
35"s,orange,19,61,-,100,#GG##T#CG##--##A#T##T##CG#CG##----###A###T#CG-#T#T#T------GA##T#T---##A####CG"
36]
37
38def test_cpg_inclusive():
39    reader = bx.align.maf.Reader( StringIO( test_maf_cpg ) )
40    out = tempfile.NamedTemporaryFile('w')
41    writer = bx.align.maf.Writer( out )
42    cpgfilter = cpg.Inclusive( mask='#' )
43    cpgfilter.run( reader, writer.write )
44    out.seek(0)
45    j=0
46    for line in file(out.name):
47        line = line.strip()
48        if not(line):
49            continue
50        assert cpg_inclusive_result[j] == ",".join(line.split())
51        j+=1
52   
53def test_cpg_restricted():
54    reader = bx.align.maf.Reader( StringIO( test_maf_cpg ) )
55    out = tempfile.NamedTemporaryFile('w')
56    writer = bx.align.maf.Writer( out )
57    cpgfilter = cpg.Restricted( mask='#' )
58    cpgfilter.run( reader, writer.write )
59    out.seek(0)
60    j=0
61    for line in file(out.name):
62        line = line.strip()
63        if not(line):
64            continue
65        assert cpg_restricted_result[j] == ",".join(line.split())
66        j+=1
67
68def test_non_cpg():
69    reader = bx.align.maf.Reader( StringIO( test_maf_cpg ) )
70    out = tempfile.NamedTemporaryFile('w')
71    writer = bx.align.maf.Writer( out )
72    cpgfilter = cpg.nonCpG( mask='#' )
73    cpgfilter.run( reader, writer.write )
74    out.seek(0)
75    j=0
76    for line in file(out.name):
77        line = line.strip()
78        if not(line):
79            continue
80        assert noncpg_result[j] == ",".join(line.split())
81        j+=1
82
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