def testBaseCallInDel(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgaTtcg', '.........', 0, 0,
cigar='5M1I3M') # inserted T @6
bam.add_read('foo2', 'atcgacg', 'AAAAAAA', 0, 4,
cigar='5M1D2M') # deleted T @ 10
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam,
os.path.join(
os.path.dirname(__file__),
'test.fa'),
out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|1|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|2|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|3|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|4|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
test2|5|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0|
test2|6|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|1|T:1
test2|7|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0|
test2|8|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0|
test2|9|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|10|T|0|N||1.0|0|0|0|0|0|0|1|0|0|
test2|11|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|12|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallHetTest(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgaccg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgattg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgattg', '########', 0, 4, cigar='8M')
# ref: atcgatcgatcg
# atcgaccg
# atcgattg
# accgattg
# * *
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam,
os.path.join(
os.path.dirname(__file__),
'test.fa'),
variants=True,
hettest=True,
out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|alt. allele freq|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|6|T|3|C|T|1.0|0.333333333333|2.9097148334|0|2|0|1|0|0|0|0|
test2|11|C|2|T||1.0|0.0|4.24102241591|0|0|0|2|0|0|0|0|
'''.replace('|', '\t')
# print '---'
# print out.getvalue().replace('\t', '|')
# print '---'
# print valid.replace('\t', '|')
self.assertEqual(valid, out.getvalue())
def testBaseCallMinCount(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3',
'accgatcg',
'########',
0,
4,
cigar='8M',
tags=[('IH', 2), ('HI', 1)])
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam,
os.path.join(
os.path.dirname(__file__),
'test.fa'),
min_count=2,
out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|5|A|3|A||1.33333333333|1.65545182665|3|0|0|0|0|0|0|0|
test2|6|T|3|T|C|1.33333333333|2.9097148334|0|1|0|2|0|0|0|0|
test2|7|C|3|C||1.33333333333|4.85048518563|0|3|0|0|0|0|0|0|
test2|8|G|3|G||1.33333333333|1.65545182665|0|0|3|0|0|0|0|0|
test2|9|A|2|A||1.5|1.36179536943|2|0|0|0|0|0|0|0|
test2|10|T|2|T||1.5|4.24102241591|0|0|0|2|0|0|0|0|
test2|11|C|2|C||1.5|4.24102241591|0|2|0|0|0|0|0|0|
test2|12|G|2|G||1.5|1.36179536943|0|0|2|0|0|0|0|0|
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallMinQual(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgatcg', '########', 0, 4, cigar='8M', tags=[('IH', 2), ('HI', 1)])
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam, os.path.join(os.path.dirname(__file__), 'test.fa'), min_qual=10, out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|1|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|2|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|3|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|4|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
test2|5|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0|
test2|6|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0|
test2|7|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0|
test2|8|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0|
test2|9|A|1|A||1.0|0.91686730441|1|0|0|0|0|0|0|0|
test2|10|T|1|T||1.0|3.25488750216|0|0|0|1|0|0|0|0|
test2|11|C|1|C||1.0|3.25488750216|0|1|0|0|0|0|0|0|
test2|12|G|1|G||1.0|0.91686730441|0|0|1|0|0|0|0|0|
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallHetTest(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgaccg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgattg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgattg', '########', 0, 4, cigar='8M')
# ref: atcgatcgatcg
# atcgaccg
# atcgattg
# accgattg
# * *
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam, os.path.join(os.path.dirname(__file__), 'test.fa'), variants=True, hettest=True, out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|alt. allele freq|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|6|T|3|C|T|1.0|0.333333333333|2.9097148334|0|2|0|1|0|0|0|0|
test2|11|C|2|T||1.0|0.0|4.24102241591|0|0|0|2|0|0|0|0|
'''.replace('|', '\t')
# print '---'
# print out.getvalue().replace('\t', '|')
# print '---'
# print valid.replace('\t', '|')
self.assertEqual(valid, out.getvalue())
def testBaseCallMinCount(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgatcg', '########', 0, 4, cigar='8M', tags=[('IH', 2), ('HI', 1)])
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam, os.path.join(os.path.dirname(__file__), 'test.fa'), min_count=2, out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts
test2|5|A|3|A||1.33333333333|1.65545182665|3|0|0|0|0|0|0|0|
test2|6|T|3|T|C|1.33333333333|2.9097148334|0|1|0|2|0|0|0|0|
test2|7|C|3|C||1.33333333333|4.85048518563|0|3|0|0|0|0|0|0|
test2|8|G|3|G||1.33333333333|1.65545182665|0|0|3|0|0|0|0|0|
test2|9|A|2|A||1.5|1.36179536943|2|0|0|0|0|0|0|0|
test2|10|T|2|T||1.5|4.24102241591|0|0|0|2|0|0|0|0|
test2|11|C|2|C||1.5|4.24102241591|0|2|0|0|0|0|0|0|
test2|12|G|2|G||1.5|1.36179536943|0|0|2|0|0|0|0|0|
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallStrand(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgatcg', '########', 0, 4, cigar='8M', is_reverse=True)
bam.add_read('foo4', 'atcgactgatcg', '############', 0, 0, cigar='12M')
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam, os.path.join(os.path.dirname(__file__), 'test.fa'), showstrand=True, out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|1|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|2|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|3|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|4|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
test2|9|A|3|A||1.0|1.65545182665|3|0|0|0|0|0|0|0||0.666666666667|0.333333333333|0.0|0.0|0.0|0.0|0.0|0.0
test2|10|T|3|T||1.0|4.85048518563|0|0|0|3|0|0|0|0||0.666666666667|0.0|0.0|0.0|0.333333333333|0.0|0.0|0.0
test2|11|C|3|C||1.0|4.85048518563|0|3|0|0|0|0|0|0||0.666666666667|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|12|G|3|G||1.0|1.65545182665|0|0|3|0|0|0|0|0||0.666666666667|0.0|0.0|0.333333333333|0.0|0.0|0.0|0.0
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallRegionStrand(self):
# confirm that BED strand *isn't* used
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3', 'accgatcg', '########', 0, 4, cigar='8M', is_reverse=True)
bam.add_read('foo4', 'atcgactgatcg', '############', 0, 0, cigar='12M')
bed = BedFile(fileobj=StringIO.StringIO('''\
test2|4|7|foo|1|-
'''.replace('|', '\t')))
# remember: bed is 0-based, basecall is 1-based, so 4->7, corresponds to 5->8
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam, os.path.join(os.path.dirname(__file__), 'test.fa'), showstrand=True, regions=bed, out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallRegionStrand(self):
# confirm that BED strand *isn't* used
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3',
'accgatcg',
'########',
0,
4,
cigar='8M',
is_reverse=True)
bam.add_read('foo4', 'atcgactgatcg', '############', 0, 0, cigar='12M')
bed = BedFile(fileobj=StringIO.StringIO('''\
test2|4|7|foo|1|-
'''.replace('|', '\t')))
# remember: bed is 0-based, basecall is 1-based, so 4->7, corresponds to 5->8
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam,
os.path.join(
os.path.dirname(__file__),
'test.fa'),
showstrand=True,
regions=bed,
out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
def testBaseCallStrand(self):
bam = MockBam(['test2'])
bam.add_read('foo1', 'atcgatcg', '........', 0, 0, cigar='8M')
bam.add_read('foo2', 'atcgatcg', 'AAAAAAAA', 0, 4, cigar='8M')
bam.add_read('foo3',
'accgatcg',
'########',
0,
4,
cigar='8M',
is_reverse=True)
bam.add_read('foo4', 'atcgactgatcg', '############', 0, 0, cigar='12M')
out = StringIO.StringIO('')
ngsutils.bam.basecall.bam_basecall(bam,
os.path.join(
os.path.dirname(__file__),
'test.fa'),
showstrand=True,
out=out)
valid = '''chrom|pos|ref|count|consensus call|minor call|ave mappings|entropy|A|C|G|T|N|Deletions|Gaps|Insertions|Inserts|+ strand %|A minor %|C minor %|G minor %|T minor %|N minor %|Deletion minor %|Insertion minor %
test2|1|A|2|A||1.0|1.36179536943|2|0|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|2|T|2|T||1.0|4.24102241591|0|0|0|2|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|3|C|2|C||1.0|4.24102241591|0|2|0|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|4|G|2|G||1.0|1.36179536943|0|0|2|0|0|0|0|0||1.0|0.0|0.0|0.0|0.0|0.0|0.0|0.0
test2|5|A|4|A||1.0|1.87433193885|4|0|0|0|0|0|0|0||0.75|0.25|0.0|0.0|0.0|0.0|0.0|0.0
test2|6|T|4|T/C||1.0|2.94335833285|0|2|0|2|0|0|0|0||0.75|0.0|0.5|0.0|0.0|0.0|0.0|0.0
test2|7|C|4|C|T|1.0|3.45990045591|0|3|0|1|0|0|0|0||0.75|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|8|G|4|G||1.0|1.87433193885|0|0|4|0|0|0|0|0||0.75|0.0|0.0|0.25|0.0|0.0|0.0|0.0
test2|9|A|3|A||1.0|1.65545182665|3|0|0|0|0|0|0|0||0.666666666667|0.333333333333|0.0|0.0|0.0|0.0|0.0|0.0
test2|10|T|3|T||1.0|4.85048518563|0|0|0|3|0|0|0|0||0.666666666667|0.0|0.0|0.0|0.333333333333|0.0|0.0|0.0
test2|11|C|3|C||1.0|4.85048518563|0|3|0|0|0|0|0|0||0.666666666667|0.0|0.333333333333|0.0|0.0|0.0|0.0|0.0
test2|12|G|3|G||1.0|1.65545182665|0|0|3|0|0|0|0|0||0.666666666667|0.0|0.0|0.333333333333|0.0|0.0|0.0|0.0
'''.replace('|', '\t')
self.assertEqual(valid, out.getvalue())
#!/usr/bin/env python
'''
Tests for bamutils count
'''
import unittest
import StringIO
import ngsutils.bam
import ngsutils.bam.count
import ngsutils.bam.count.models
from ngsutils.bam.t import MockBam
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1', 'A' * 50, tid=0, pos=100, cigar='50M', tags=[('IH', 2)])
testbam1.add_read('foo1', 'A' * 50, tid=0, pos=1000, cigar='50M', tags=[('IH', 2)])
testbam1.add_read('foo2', 'A' * 50, tid=0, pos=101, cigar='50M')
testbam1.add_read('foo3', 'A' * 50, tid=0, pos=101, cigar='50M')
testbam1.add_read('foo4', 'A' * 50, tid=0, pos=103, cigar='50M')
testbam1.add_read('foo5', 'A' * 50, tid=0, pos=200, cigar='25M')
testbam1.add_read('foo6', 'A' * 50, tid=0, pos=200, cigar='25M')
testbam1.add_read('foo7', 'A' * 50, tid=0, pos=225, cigar='25M')
testbam1.add_read('foo8', 'A' * 50, tid=0, pos=225, cigar='25M')
testbam1.add_read('foo9', 'A' * 50, tid=0, pos=300, cigar='50M')
testbam1.add_read('foo10', 'A' * 50, tid=0, pos=301, cigar='50M')
testbam1.add_read('foo11', 'A' * 50, tid=0, pos=302, cigar='50M', is_reverse=True)
testbam1.add_read('foo12', 'A' * 50, tid=0, pos=303, cigar='50M', is_reverse=True)
class CountTest(unittest.TestCase):
#!/usr/bin/env python
'''
Tests for bamutils extract
'''
import unittest
import os
import ngsutils.bam
from ngsutils.bam.innerdist import bam_innerdist
from ngsutils.bam.t import MockBam, _matches
testbam1 = MockBam(['chr1'], insert_order=True)
testbam1.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M')
testbam1.add_read('foo2', tid=0, pos=200, aend=250, cigar='50M')
testbam1.add_read('foo3', tid=0, pos=300, aend=350, cigar='50M')
testbam1.add_read('foo4', tid=0, pos=400, aend=450, cigar='50M')
testbam1.add_read('foo5', tid=0, pos=400, aend=450, cigar='50M')
testbam1.add_read('foo6', tid=-1)
testbam2 = MockBam(['chr1'], insert_order=True)
testbam2.add_read('foo1', tid=0, pos=200, aend=250, cigar='50M')
testbam2.add_read('foo2', tid=0, pos=300, aend=350, cigar='50M')
testbam2.add_read('foo3', tid=0, pos=450, aend=500, cigar='50M')
testbam2.add_read('foo4', tid=0, pos=550, aend=600, cigar='50M')
testbam2.add_read('foo5', tid=-1)
testbam2.add_read('foo6', tid=0, pos=500, aend=550, cigar='50M')
testbam3 = MockBam(['chr1'], insert_order=True)
testbam3.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M')
#!/usr/bin/env python
'''
Tests for bamutils extract
'''
import unittest
import os
import ngsutils.bam
import ngsutils.bam.extract
from ngsutils.bam.t import MockBam, _matches
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M') # too early
testbam1.add_read('foo2', tid=0, pos=200, aend=250, cigar='50M') # in range, + strand
testbam1.add_read('foo3', tid=0, pos=1000, aend=1050, cigar='50M') # too late
testbam1.add_read('foo4', tid=0, pos=200, aend=350, cigar='25M100N25M') # in range, start, + strand
testbam1.add_read('foo5', tid=0, pos=200, aend=250, cigar='50M', is_reverse=True) # in range, start, - strand
testbam1.add_read('foo6', tid=0, pos=2000, aend=3050, cigar='20M500N20M500M10M') # touches (2000,2020), (2520, 2540), (3040, 3050)
class ExtractTest(unittest.TestCase):
def setUp(self):
self.fname1 = os.path.join(os.path.dirname(__file__), 'testbam1')
with open(self.fname1, 'w') as f:
f.write('chr1\t200\t250\tfoo\t1\t+\n')
f.write('chr1\t125\t170\tfoo\t1\t+\n')
self.fname2 = os.path.join(os.path.dirname(__file__), 'testbam2')
with open(self.fname2, 'w') as f:
#!/usr/bin/env python
'''
Tests for bamutils export
'''
import StringIO
import unittest
import ngsutils.bam
import ngsutils.bam.export
from ngsutils.bam.t import MockBam
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1', 'atcgatcg', 'AAAAAAAA', 0, 0, 8, '8M')
testbam1.add_read('foo2', 'atcgtttt', 'AAAABBBB', 0, 4, 12, '8M', is_reverse=True)
testbam1.add_read('foo3', 'gggggggg', 'CCCCCCCC')
testbam2 = MockBam(['chr1'])
testbam2.add_read('bar1', 'atcgatcg', 'AAAAAAAA', 0, 0, 8, '8M', rnext=0, pnext=100, is_paired=True, is_read1=True)
testbam2.add_read('bar1', 'gctagcta', 'AAAAAAAA', 0, 100, 108, '8M', is_paired=True, is_read2=True)
testbam2.add_read('bar2', 'atcgatcg', 'AAAAAAAA', is_paired=True, is_read1=True)
testbam2.add_read('bar2', 'gctagcta', 'AAAAAAAA', is_paired=True, is_read2=True)
testbam3 = MockBam(['chr1'])
testbam3.add_read('baz1', 'atcgatcg', 'AAAAAAAA', 0, 0, 8, '8M', mapq=10, isize=100, tlen=120, tags=[('ZZ', 'foo'), ('ZY', 100), ('ZX', 1.0), ('ZW', 'a'), ])
class ExportTest(unittest.TestCase):
def testExport1(self):
#!/usr/bin/env python
'''
Tests for bamutils export
'''
import StringIO
import unittest
import ngsutils.bam
import ngsutils.bam.export
from ngsutils.bam.t import MockBam
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1', 'atcgatcg', 'AAAAAAAA', 0, 0, 8, '8M')
testbam1.add_read('foo2',
'atcgtttt',
'AAAABBBB',
0,
4,
12,
'8M',
is_reverse=True)
testbam1.add_read('foo3', 'gggggggg', 'CCCCCCCC')
testbam2 = MockBam(['chr1'])
testbam2.add_read('bar1',
'atcgatcg',
'AAAAAAAA',
0,
0,
#!/usr/bin/env python
'''
Tests for bamutils extract
'''
import unittest
import os
import ngsutils.bam
from ngsutils.bam.innerdist import bam_innerdist
from ngsutils.bam.t import MockBam, _matches
testbam1 = MockBam(['chr1'], insert_order=True)
testbam1.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M')
testbam1.add_read('foo2', tid=0, pos=200, aend=250, cigar='50M')
testbam1.add_read('foo3', tid=0, pos=300, aend=350, cigar='50M')
testbam1.add_read('foo4', tid=0, pos=400, aend=450, cigar='50M')
testbam1.add_read('foo5', tid=0, pos=400, aend=450, cigar='50M')
testbam1.add_read('foo6', tid=-1)
testbam2 = MockBam(['chr1'], insert_order=True)
testbam2.add_read('foo1', tid=0, pos=200, aend=250, cigar='50M')
testbam2.add_read('foo2', tid=0, pos=300, aend=350, cigar='50M')
testbam2.add_read('foo3', tid=0, pos=450, aend=500, cigar='50M')
testbam2.add_read('foo4', tid=0, pos=550, aend=600, cigar='50M')
testbam2.add_read('foo5', tid=-1)
testbam2.add_read('foo6', tid=0, pos=500, aend=550, cigar='50M')
testbam3 = MockBam(['chr1'], insert_order=True)
testbam3.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M')
Tests for bamutils count
'''
import unittest
import StringIO
import ngsutils.bam
import ngsutils.bam.count
import ngsutils.bam.count.models
from ngsutils.bam.t import MockBam
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1',
'A' * 50,
tid=0,
pos=100,
cigar='50M',
tags=[('IH', 2)])
testbam1.add_read('foo1',
'A' * 50,
tid=0,
pos=1000,
cigar='50M',
tags=[('IH', 2)])
testbam1.add_read('foo2', 'A' * 50, tid=0, pos=101, cigar='50M')
testbam1.add_read('foo3', 'A' * 50, tid=0, pos=101, cigar='50M')
testbam1.add_read('foo4', 'A' * 50, tid=0, pos=103, cigar='50M')
testbam1.add_read('foo5', 'A' * 50, tid=0, pos=200, cigar='25M')
testbam1.add_read('foo6', 'A' * 50, tid=0, pos=200, cigar='25M')
testbam1.add_read('foo7', 'A' * 50, tid=0, pos=225, cigar='25M')
testbam1.add_read('foo8', 'A' * 50, tid=0, pos=225, cigar='25M')
#!/usr/bin/env python
'''
Tests for bamutils extract
'''
import unittest
import os
import ngsutils.bam
import ngsutils.bam.extract
from ngsutils.bam.t import MockBam, _matches
testbam1 = MockBam(['chr1'])
testbam1.add_read('foo1', tid=0, pos=100, aend=150, cigar='50M') # too early
testbam1.add_read('foo2', tid=0, pos=200, aend=250,
cigar='50M') # in range, + strand
testbam1.add_read('foo3', tid=0, pos=1000, aend=1050, cigar='50M') # too late
testbam1.add_read('foo4', tid=0, pos=200, aend=350,
cigar='25M100N25M') # in range, start, + strand
testbam1.add_read('foo5',
tid=0,
pos=200,
aend=250,
cigar='50M',
is_reverse=True) # in range, start, - strand
testbam1.add_read('foo6',
tid=0,
pos=2000,
aend=3050,
cigar='20M500N20M500M10M'