Python MockBam.add_read Examples

Example #1

File: test_basecall.py Project: xuwei684/ngsutils

    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())

Example #2

File: test_basecall.py Project: xuwei684/ngsutils

    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())

Example #3

File: test_basecall.py Project: xuwei684/ngsutils

    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())

Example #4

File: test_basecall.py Project: ZhangQiuxue/ngsutils

    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())

Example #5

File: test_basecall.py Project: ZhangQiuxue/ngsutils

    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())

Example #6

File: test_basecall.py Project: ZhangQiuxue/ngsutils

    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())

Example #7

File: test_basecall.py Project: ZhangQiuxue/ngsutils

    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())

Example #8

File: test_basecall.py Project: ZhangQiuxue/ngsutils

    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())

Example #9

File: test_basecall.py Project: xuwei684/ngsutils

    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())

Example #10

File: test_basecall.py Project: xuwei684/ngsutils

    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())

Example #11

File: test_count.py Project: ZhangQiuxue/ngsutils

#!/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):

Example #12

File: test_innerdist.py Project: ZhangQiuxue/ngsutils

#!/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')

Example #13

File: test_extract.py Project: ZhangQiuxue/ngsutils

#!/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:

Example #14

File: test_export.py Project: ZhangQiuxue/ngsutils

#!/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):

Example #15

#!/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,

Example #16

File: test_innerdist.py Project: xuwei684/ngsutils

#!/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')

Example #17

File: test_count.py Project: xuwei684/ngsutils

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')

Example #18

#!/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'