instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383 TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0 mm9_chr13_random.fa:1240R0')
out = StringIO()
- makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
- self.failUnlessEqual(out.getvalue(), 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
+ out = list(makebed.make_bed_from_multi_eland_generator(instream, 'name', 'description', 'mm9_chr', 1))
+ self.failUnlessEqual(out[1], 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
def test_multi_1_0_0_limit_255(self):
instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383 TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0 mm9_chr13_random.fa:1240R0')
out = StringIO()
- makebed.parse_multi_eland(instream, out, 'mm9_chr', 255)
- self.failUnlessEqual(out.getvalue(), 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
+ out = list(makebed.make_bed_from_multi_eland_generator(instream, 'name', 'desc', 'mm9_chr', 255))
+ self.failUnlessEqual(out[1], 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
def test_multi_2_0_0_limit_1(self):
instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:104:586 GTTCTCGCATAAACTNACTCTNAATAGATTCA 2:0:0 mm9_chr4.fa:42995432F0,mm9_chrX.fa:101541458F0')
out = StringIO()
- makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
- self.failUnlessEqual(out.len, 0)
+ out = list(makebed.make_bed_from_multi_eland_generator(instream, 'name', 'desc', 'mm9_chr', 1))
+ self.failUnlessEqual(len(out), 1)
def test_multi_2_0_0_limit_255(self):
instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:104:586 GTTCTCGCATAAACTNACTCTNAATAGATTCA 2:0:0 mm9_chr4.fa:42995432F0,mm9_chrX.fa:101541458F0')
out = StringIO()
- makebed.parse_multi_eland(instream, out, 'mm9_chr', 255)
- self.failUnlessEqual(out.len, 98)
+ out = list(makebed.make_bed_from_multi_eland_generator(instream, 'name', 'desc', 'mm9_chr', 255))
+ self.failUnlessEqual(len(out), 3)
+ self.failUnlessEqual(out[1],
+ 'mm9_chr4 42995432 42995464 read 0 + - - 0,0,255\n')
+ self.failUnlessEqual(out[2],
+ 'mm9_chrX 101541458 101541490 read 0 + - - 0,0,255\n')
def test_multi_0_2_0_limit_1(self):
instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:115:495 TCTCCCTGAAAAATANAAGTGNTGTTGGTGAG 0:2:1 mm9_chr14.fa:104434729F2,mm9_chr16.fa:63263818R1,mm9_chr2.fa:52265438R1')
out = StringIO()
- makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
- print out.getvalue()
- self.failUnlessEqual(out.len, 0)
+ out = list(makebed.make_bed_from_multi_eland_generator(instream, 'name', 'desc', 'mm9_chr', 1))
+ print out
+ self.failUnlessEqual(len(out), 1)
def suite():
return unittest.makeSuite(testMakeBed, 'test')