root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/align/maf_tests.py @ 3

リビジョン 3, 8.1 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html
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1"""
2Tests for `bx.align.maf`.
3"""
4
5import unittest
6import sys
7import bx.align as align
8import bx.align.maf as maf
9
10from StringIO import StringIO
11
12# A simple MAF from the rat paper days
13test_maf = """##maf version=1 scoring=humor.v4
14# humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
15# /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
16
17a score=0.128
18s human_hoxa 100  8 + 100257 ACA-TTACT
19s horse_hoxa 120  9 -  98892 ACAATTGCT
20s fugu_hoxa   88  7  + 90788 ACA--TGCT
21
22
23a score=0.071
24s human_unc 9077 8 + 10998 ACAGTATT
25# Comment
26s horse_unc 4555 6 -  5099 ACA--ATT
27s fugu_unc  4000 4 +  4038 AC----TT
28"""
29
30# A more complicated MAF with synteny annotation and such
31test_maf_2 = """##maf version=1 scoring=autoMZ.v1
32a score=3656.000000
33s hg17.chr1                   2005 34 + 245522847 TGTAACTTAATACCACAACCAGGCATAGGGG--AAA-------------
34s rheMac2.chr11            9625228 31 + 134511895 TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------
35i rheMac2.chr11           C 0 I 1678
36s panTro1.chr1                2014 34 + 229575298 TGTAACTTAATACCACAACCAGGCATGGGGG--AAA-------------
37i panTro1.chr1            C 0 C 0
38s bosTau2.chr5            64972365 47 +  76426644 TCCAGCCATGTGTTGTGATCAG--CCAGGGGCTAAAGCCATGGCGGTAG
39i bosTau2.chr5            C 0 I 1462
40s canFam2.chr27           45129665 31 +  48908698 TTTGACTCTGTGCTCTTATCAGGCCCAAGGG------------------
41i canFam2.chr27           C 0 I 1664
42e danRer3.chr18            2360867 428 +  50308305 I
43e oryCun1.scaffold_139397      643 1271 -      4771 I
44e loxAfr1.scaffold_5603      58454 1915 +     68791 I
45e echTel1.scaffold_212365     4641 1430 +      9822 I
46e echTel1.scaffold_212365     4641 1430 +      9822 I
47e rn3.chr4                29161032 1524 - 187371129 I
48e mm7.chr6                28091695 3290 - 149646834 I
49
50"""
51
52# A MAF to test slicing upon
53test_maf_3 = """##maf version=1 scoring=none
54a score=0
55s apple  34 64 + 110 AGGGA---GTTCGTCACT------GTCGTAAGGGTTCAGA--CTGTCTATGTATACACAAGTTGTGTTGCA--ACCG
56s orange 19 61 - 100 AGGGATGCGTT--TCACTGCTATCGTCGTA----TTCAGACTTCG-CTATCT------GAGTTGT---GCATTACCG
57
58"""
59
60def test_reader():
61
62    reader = maf.Reader( StringIO( test_maf ) )
63    assert reader.attributes["version"] == "1"
64    assert reader.attributes["scoring"] == "humor.v4"
65
66    a = reader.next()
67    assert a.score == 0.128
68    assert len( a.components ) == 3
69    check_component( a.components[0], "human_hoxa", 100, 8,  "+", 100257, "ACA-TTACT" )
70    check_component( a.components[1], "horse_hoxa", 120, 9, "-",  98892, "ACAATTGCT" )
71    check_component( a.components[2], "fugu_hoxa",    88, 7,  "+",  90788, "ACA--TGCT" )
72   
73    a = reader.next()
74    assert a.score == 0.071
75    assert len( a.components ) == 3
76    check_component( a.components[0], "human_unc", 9077, 8, "+", 10998, "ACAGTATT" )
77    check_component( a.components[1], "horse_unc", 4555, 6, "-",  5099, "ACA--ATT" )
78    check_component( a.components[2], "fugu_unc",   4000, 4, "+",  4038, "AC----TT" )
79
80    a = reader.next()
81    assert a is None
82
83    reader.close()
84
85def test_writer():
86
87    val = StringIO()
88    writer = maf.Writer( val, { 'scoring':'foobar' } )
89   
90    a = align.Alignment()
91    a.score = 7009
92
93    a.components.append( align.Component( src="human_hoxa", start=100, size=9,  strand="+", src_size=1000257, text="ACA-TTACT" ) )
94    a.components.append( align.Component( src="horse_hoxa", start=120, size=10, strand="-",   src_size=98892, text="ACAATTGCT" ) )
95
96    check_component( a.components[0], "human_hoxa", 100, 9,  "+", 1000257, "ACA-TTACT" )
97    check_component( a.components[1], "horse_hoxa", 120, 10, "-",   98892, "ACAATTGCT" )
98
99    writer.write( a )
100
101    assert val.getvalue() == """##maf version=1 scoring=foobar
102a score=7009
103s human_hoxa 100  9 + 1000257 ACA-TTACT
104s horse_hoxa 120 10 -   98892 ACAATTGCT
105
106"""
107
108
109
110def test_slice():
111
112    a = align.Alignment()
113    a.score = "7009"
114    a.components.append( align.Component( src="human_hoxa", start=100, size=9,  strand="+", src_size=100257, text="ACA-TTACT" ) )
115    a.components.append( align.Component( src="horse_hoxa", start=120, size=10, strand="-",   src_size=98892, text="ACAATTGCT" ) )
116
117    b = a.slice_by_component( 0, 101, 105 )
118
119    check_component( b.components[0], src="human_hoxa", start=101, size=4, strand="+", src_size=100257, text="CA-TT" )
120    check_component( b.components[1], src="horse_hoxa", start=121, size=5, strand="-", src_size=98892, text ="CAATT" )
121
122        # test slicing with + strand src
123    reader = maf.Reader( StringIO( test_maf_3 ) )
124    a = reader.next()
125    b = a.slice_by_component( 0, 40, 62 )
126    check_component( b.components[0], src="apple",  start=40, size=22, strand="+", src_size=110, text="TTCGTCACT------GTCGTAAGGGTTC" )
127    check_component( b.components[1], src="orange", start=28, size=22, strand="-", src_size=100, text="TT--TCACTGCTATCGTCGTA----TTC" )
128
129        # test slicing with - strand src
130    b = a.slice_by_component( 1, 30, 68 )
131    check_component( b.components[0], src="apple",  start=46, size=41, strand="+", src_size=110, text="ACT------GTCGTAAGGGTTCAGA--CTGTCTATGTATACACAAGTTG" )
132    check_component( b.components[1], src="orange", start=32, size=38, strand="-", src_size=100, text="ACTGCTATCGTCGTA----TTCAGACTTCG-CTATCT------GAGTTG" )
133
134    a = reader.next()
135    assert a is None
136
137
138def test_with_synteny():
139    reader = maf.Reader( StringIO( test_maf_2 ), parse_e_rows=True )
140   
141    a = reader.next()
142    check_component( a.components[0], "hg17.chr1", 2005, 34, "+", 245522847, "TGTAACTTAATACCACAACCAGGCATAGGGG--AAA-------------")
143    check_component( a.components[1], "rheMac2.chr11", 9625228, 31, "+", 134511895, "TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------")
144    print a.components[1].synteny_left
145    assert a.components[1].synteny_left == ( maf.MAF_CONTIG_STATUS, 0 )
146    assert a.components[1].synteny_right == ( maf.MAF_INSERT_STATUS, 1678 )
147
148    rat = a.get_component_by_src_start( "rn3." )
149    check_component( rat, "rn3.chr4", 29161032, 1524, "-", 187371129, None )
150    assert rat.synteny_empty == maf.MAF_INSERT_STATUS
151   
152def test_write_with_synteny():
153    reader = maf.Reader( StringIO( test_maf_2 ), parse_e_rows=True )
154    a = reader.next()
155    val = StringIO()
156    writer = maf.Writer( val, { 'scoring':'foobar' } )
157    writer.write( a )
158    actual = val.getvalue()
159    expected = """##maf version=1 scoring=foobar
160a score=3656.0
161s hg17.chr1                   2005   34 + 245522847 TGTAACTTAATACCACAACCAGGCATAGGGG--AAA-------------
162s rheMac2.chr11            9625228   31 + 134511895 TGTAACCTCTTACTGCAACAAGGCACAGGGG------------------
163i rheMac2.chr11                                     C 0 I 1678                                       
164s panTro1.chr1                2014   34 + 229575298 TGTAACTTAATACCACAACCAGGCATGGGGG--AAA-------------
165i panTro1.chr1                                      C 0 C 0                                           
166s bosTau2.chr5            64972365   47 +  76426644 TCCAGCCATGTGTTGTGATCAG--CCAGGGGCTAAAGCCATGGCGGTAG
167i bosTau2.chr5                                      C 0 I 1462                                       
168s canFam2.chr27           45129665   31 +  48908698 TTTGACTCTGTGCTCTTATCAGGCCCAAGGG------------------
169i canFam2.chr27                                     C 0 I 1664                                       
170e danRer3.chr18            2360867  428 +  50308305 I                                                 
171e oryCun1.scaffold_139397      643 1271 -      4771 I                                                 
172e loxAfr1.scaffold_5603      58454 1915 +     68791 I                                                 
173e echTel1.scaffold_212365     4641 1430 +      9822 I                                                 
174e echTel1.scaffold_212365     4641 1430 +      9822 I                                                 
175e rn3.chr4                29161032 1524 - 187371129 I                                                 
176e mm7.chr6                28091695 3290 - 149646834 I                                                 
177
178"""
179    print actual
180    print "---"
181    print expected
182    assert actual == expected
183
184def check_component( c, src, start, size, strand, src_size, text ):
185    assert c.src == src
186    assert c.start == start
187    assert c.size == size
188    assert c.strand == strand
189    assert c.src_size == src_size
190    assert c.text == text
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