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geriksongerikson
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Added pytests for bamCoverage and bamCompare
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‎pydeeptools/deeptools/test/test_r_bamCompare.py‎

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import pytest
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from deeptools.bamCompare2 import r_bamcompare
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import os.path
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import filecmp
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from os import unlink
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ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
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BAMFILE_A = ROOT + "test1.bam"
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BAMFILE_B = ROOT + "test2.bam"
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def test_r_bamcompare():
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bamifile1 = BAMFILE_A
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bamifile2 = BAMFILE_B
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ofile = ROOT + "r_bamcompare_output.bedgraph"
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ofiletype = "bedgraph"
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norm = "None"
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effective_genome_size = 0
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scalefactorsmethod = "None"
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operation = "ratio"
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pseudocount = 0
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# filtering options
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ignoreduplicates = False
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minmappingquality = 0
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samflaginclude = 0
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samflagexclude = 0
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minfraglen = 0
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maxfraglen = 0
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nproc = 1
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_ignorechr = []
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binsize = 500
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regions = []
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verbose = False
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# Call the Rust function
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r_bamcompare(
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bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation,
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pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc,
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_ignorechr, binsize, regions, verbose
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)
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# Add assertions to verify the expected behavior
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expected = ['3R\t0\t500\t0.6213592\n',
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'3R\t500\t1000\t0.8252427\n',
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'3R\t1000\t1500\t0.2\n',]
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_foo = open(ofile, 'r')
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resp = _foo.readlines()
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_foo.close()
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assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
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unlink(ofile)
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def test_r_bamcompare_RPKM():
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bamifile1 = BAMFILE_A
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bamifile2 = BAMFILE_B
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ofile = ROOT + "r_bamcompare_output.bedgraph"
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ofiletype = "bedgraph"
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norm = "RPKM"
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effective_genome_size = 0
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scalefactorsmethod = "None"
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operation = "ratio"
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pseudocount = 0
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# filtering options
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ignoreduplicates = False
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minmappingquality = 0
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samflaginclude = 0
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samflagexclude = 0
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minfraglen = 0
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maxfraglen = 0
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nproc = 1
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_ignorechr = []
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binsize = 500
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regions = []
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verbose = False
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# Call the Rust function
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r_bamcompare(
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bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation,
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pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc,
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_ignorechr, binsize, regions, verbose
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)
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# Add assertions to verify the expected behavior
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expected = ['3R\t0\t500\t0.6213592\n',
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'3R\t500\t1000\t0.8252427\n',
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'3R\t1000\t1500\t0.2\n',]
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_foo = open(ofile, 'r')
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resp = _foo.readlines()
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_foo.close()
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assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
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unlink(ofile)

‎pydeeptools/deeptools/test/test_r_bamCoverage.py‎

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import pytest
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from deeptools.bamCompare2 import r_bamcompare
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import os.path
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import filecmp
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from os import unlink
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ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
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BAMFILE_A = ROOT + "test1.bam"
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BAMFILE_B = ROOT + "test2.bam"
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def test_r_bamcompare():
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bamifile1 = BAMFILE_A
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bamifile2 = BAMFILE_B
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ofile = ROOT + "r_bamcompare_output.bedgraph"
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ofiletype = "bedgraph"
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norm = "None"
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effective_genome_size = 0
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scalefactorsmethod = "None"
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operation = "ratio"
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pseudocount = 0
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# filtering options
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ignoreduplicates = False
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minmappingquality = 0
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samflaginclude = 0
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samflagexclude = 0
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minfraglen = 0
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maxfraglen = 0
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nproc = 1
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_ignorechr = []
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binsize = 500
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regions = []
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verbose = False
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# Call the Rust function
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r_bamcompare(
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bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation,
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pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc,
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_ignorechr, binsize, regions, verbose
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)
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# Add assertions to verify the expected behavior
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expected = ['3R\t0\t500\t0.6213592\n',
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'3R\t500\t1000\t0.8252427\n',
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'3R\t1000\t1500\t0.2\n',]
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_foo = open(ofile, 'r')
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resp = _foo.readlines()
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_foo.close()
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assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
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unlink(ofile)
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def test_r_bamcompare_RPKM():
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bamifile1 = BAMFILE_A
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bamifile2 = BAMFILE_B
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ofile = ROOT + "r_bamcompare_output.bedgraph"
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ofiletype = "bedgraph"
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norm = "RPKM"
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effective_genome_size = 0
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scalefactorsmethod = "None"
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operation = "ratio"
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pseudocount = 0
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# filtering options
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ignoreduplicates = False
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minmappingquality = 0
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samflaginclude = 0
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samflagexclude = 0
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minfraglen = 0
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maxfraglen = 0
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nproc = 1
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_ignorechr = []
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binsize = 500
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regions = []
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verbose = False
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# Call the Rust function
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r_bamcompare(
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bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation,
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pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc,
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_ignorechr, binsize, regions, verbose
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)
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# Add assertions to verify the expected behavior
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expected = ['3R\t0\t500\t0.6213592\n',
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'3R\t500\t1000\t0.8252427\n',
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'3R\t1000\t1500\t0.2\n',]
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_foo = open(ofile, 'r')
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resp = _foo.readlines()
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_foo.close()
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assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
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unlink(ofile)

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