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#!/usr/bin/env python
# Time-stamp: <2021-03-10 18:55:41 Tao Liu>
import unittest
from MACS3.IO.BAM import *
class Test_BAIFile ( unittest.TestCase ):
def setUp ( self ):
self.bamfile = "test/tiny.bam"
self.baifile = "test/tiny.bam.bai"
self.bai = BAIFile( self.baifile )
def test_load ( self ):
expected = {'ref_beg': 50724864, 'ref_end': 2709258240, 'n_mapped': 971, 'n_unmapped': 0}
meta = self.bai.get_metadata_by_refseq( 0 )
self.assertDictEqual( expected, meta )
def test_get_chunks_bin ( self ):
expected = [(2178362419, 2178363422)]
chunks = self.bai.get_chunks_by_bin( 0, 4728 )
self.assertListEqual( chunks, expected )
def test_get_chunks_list_bins ( self ):
expected = [(50741975, 50751615), (2178362419, 2178363422), (2178363422, 2709258240)]
chunks = self.bai.get_chunks_by_list_of_bins( 0, [ 591, 4694, 4728] )
self.assertListEqual( chunks, expected )
def test_get_chunks_region ( self ):
expected = [(1130775424, 1130820164), (1130820164, 1130822629), (1130822629, 2178352280), (2178352280, 2178353973), (2178353973, 2178356807), (2178356807, 2178358139), (2178358139, 2178359954), (2178359954, 2178362419), (2178362419, 2178363422), (2178363422, 2709258240)]
chunks = self.bai.get_chunks_by_region( 0, 557000, 851600 )
self.assertListEqual( chunks, expected )
def test_get_chunks_list_regions ( self ):
expected = [(1130770109, 1130772126), (1130772126, 1130775424), (1130775424, 1130820164), (2178363422, 2709258240)]
chunks = self.bai.get_chunks_by_list_of_regions( 0, [ (500000, 600000), (800000, 850000) ] )
self.assertListEqual( chunks, expected )
class Test_BAM_w_BAI ( unittest.TestCase ):
def setUp ( self ):
self.bamfile = "test/tiny.bam"
self.baifile = "test/tiny.bam.bai"
self.bam = BAMaccessor( self.bamfile )
def test_get_reads_large_dedup ( self ):
c = b"chr10"
s = 100
e = 900000
a = self.bam.get_reads_in_region( c, s, e, maxDuplicate = 1 )
self.assertEqual( len(a), 941 )
def test_get_reads_large ( self ):
c = b"chr10"
s = 100
e = 900000
a = self.bam.get_reads_in_region( c, s, e, maxDuplicate = 100 )
self.assertEqual( len(a), 971 )
def test_get_reads_mod ( self ):
c = b"chr10"
s = 100000
e = 550000
a = self.bam.get_reads_in_region( c, s, e, maxDuplicate = 100 )
self.assertEqual( len(a), 520 )
def test_get_reads_few( self ):
c = b"chr10"
s = 142999
e = 163000
expected = """chr10 145930 145966 MAGNUM:8:93:1052:1153#0 36 +
chr10 148133 148169 MAGNUM:8:108:19082:3782#0 36 -
chr10 148930 148966 MAGNUM:8:34:18198:13544#0 36 +
chr10 152575 152611 ROCKFORD:1:114:13238:15292#0 36 +
chr10 152927 152963 ROCKFORD:1:21:4055:6592#0 36 -
chr10 153995 154031 MAGNUM:8:44:12716:12267#0 36 +
chr10 156153 156189 MAGNUM:8:74:16381:18650#0 36 -
chr10 159259 159295 ROCKFORD:1:112:5095:4754#0 36 +"""
a = self.bam.get_reads_in_region( c, s, e, maxDuplicate = 100 )
result = "\n".join( map( str, a ) )
self.assertEqual( len(a), 8 )
self.assertEqual( result, expected )
def test_get_empty1 ( self ):
# region outside of bams
c = b"chr10"
s = 961000
e = 963000
a = self.bam.get_reads_in_region( c, s, e )
self.assertEqual( len(a), 0 )
def test_get_empty2 ( self ):
# small region missed in bam
c = b"chr10"
s = 70000
e = 90000
a = self.bam.get_reads_in_region( c, s, e )
self.assertEqual( len(a), 0 )
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