def test_bam_compare_filter_blacklist():
"""
Test --samFlagInclude --samFlagExclude --minMappingQuality --ignoreDuplicates and --blackListFileName
"""
outfile = '/tmp/test_file_filter.bg'
args = "-b1 {} -b2 {} --normalizeTo1x 1400 -p 1 -o {} -of bedgraph --samFlagInclude 512 " \
"--samFlagExclude 256 --minMappingQuality 5 --ignoreDuplicates " \
"--blackListFileName {}".format(BAMFILE_FILTER1, BAMFILE_FILTER2, outfile, BEDFILE_FILTER)
args = args.split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = [
'3R\t0\t100\t0\n', '3R\t100\t150\t-0.220909\n',
'3R\t150\t200\t-0.159356\n', '3R\t200\t250\t-0.0718929\n',
'3R\t250\t300\t0.135883\n', '3R\t300\t350\t0.103093\n',
'3R\t350\t400\t-0.0895516\n', '3R\t400\t450\t0.0308374\n',
'3R\t450\t500\t0.0989418\n', '3R\t500\t550\t0.207044\n',
'3R\t550\t600\t0.0198996\n', '3R\t600\t650\t-0.0957241\n',
'3R\t650\t700\t0.00968255\n', '3R\t700\t750\t-0.040642\n',
'3R\t750\t800\t-0.123451\n', '3R\t900\t950\t0.212545\n',
'3R\t950\t1000\t0.199309\n', '3R\t1000\t1050\t0.167945\n',
'3R\t1050\t1500\t0\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_filter_blacklist():
"""
Test --samFlagInclude --samFlagExclude --minMappingQuality --ignoreDuplicates and --blackListFileName
"""
outfile = '/tmp/test_file_filter.bg'
args = "-b1 {} -b2 {} --normalizeTo1x 1400 -p 1 -o {} -of bedgraph --samFlagInclude 512 " \
"--samFlagExclude 256 --minMappingQuality 5 --ignoreDuplicates " \
"--blackListFileName {}".format(BAMFILE_FILTER1, BAMFILE_FILTER2, outfile, BEDFILE_FILTER)
args = args.split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t100\t0\n', '3R\t100\t150\t-0.220909\n',
'3R\t150\t200\t-0.159356\n', '3R\t200\t250\t-0.0718929\n',
'3R\t250\t300\t0.135883\n', '3R\t300\t350\t0.103093\n',
'3R\t350\t400\t-0.0895516\n', '3R\t400\t450\t0.0308374\n',
'3R\t450\t500\t0.0989418\n', '3R\t500\t550\t0.207044\n',
'3R\t550\t600\t0.0198996\n', '3R\t600\t650\t-0.0957241\n',
'3R\t650\t700\t0.00968255\n', '3R\t700\t750\t-0.040642\n',
'3R\t750\t800\t-0.123451\n', '3R\t900\t950\t0.212545\n',
'3R\t950\t1000\t0.199309\n', '3R\t1000\t1050\t0.167945\n',
'3R\t1050\t1500\t0\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files():
"""
Test with two different files
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --ratio subtract " \
"-o {} -p 1 --outFileFormat bedgraph".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
resp = open(outfile, 'r').readlines()
expected = ['3R\t0\t50\t0.00\n', '3R\t50\t100\t-1.00\n', '3R\t100\t150\t0.00\n', '3R\t150\t200\t-1.0\n']
assert resp == expected, "{} != {}".format(resp, expected)
unlink(outfile)
def test_bam_compare_ZoverZ():
"""
Ensure --skipZeroOverZero works in bamCompare
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --outFileFormat bedgraph --scaleFactors 1:1 -o {} " \
"--skipZeroOverZero".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t50\t100\t-1\n', '3R\t100\t150\t0\n', '3R\t150\t200\t-0.584963\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_pseudocounts():
"""
Test with different pseudocounts
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --outFileFormat bedgraph --scaleFactors 1:1 -o {} " \
"--pseudocount 1 0".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t50\tinf\n', '3R\t50\t100\t0\n', '3R\t100\t150\t1\n', '3R\t150\t200\t0\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files():
"""
Test with two different files
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --operation subtract " \
"-o {} -p 1 --outFileFormat bedgraph".format(A, B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t50\t0\n', '3R\t50\t100\t-1\n', '3R\t100\t150\t0\n', '3R\t150\t200\t-1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_extend():
"""
Test read extension
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --extend 100 --scaleFactors 1:1 --ratio subtract " \
"-o {} -p 1 --outFileFormat bedgraph".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t100\t-1\n', '3R\t100\t150\t1\n', '3R\t150\t200\t-1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_arguments():
"""
Test minimal command line args for bamCoverage. The ratio
between the same file is taken, therefore, the expected value
is 1.0 for all bins.
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} " \
"-o {} -p 1 --outFileFormat bedgraph --ratio ratio".format(BAMFILE_B, BAMFILE_B, outfile).split()
bam_comp.main(args)
resp = open(outfile, 'r').readlines()
expected = ['3R\t0\t200\t1.0\n']
assert resp == expected, "{} != {}".format(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files_skipnas():
"""
Test skipnas
Compared to the previous tests, any region that do not have coverage (in either of the bam files)
is not included in the bedgraphfile.
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --ratio subtract " \
"-o {} -p 1 --outFileFormat bedgraph --skipNAs".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
resp = open(outfile, 'r').readlines()
expected = ['3R\t100\t150\t0.00\n', '3R\t150\t200\t-1.0\n']
assert resp == expected, "{} != {}".format(resp, expected)
unlink(outfile)
def test_bam_compare_extend():
"""
Test read extension
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --extend 100 --scaleFactors 1:1 --ratio subtract " \
"-o {} -p 1 --outFileFormat bedgraph".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t100\t-1\n', '3R\t100\t150\t1\n', '3R\t150\t200\t-1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_ZoverZ():
"""
Ensure --skipZeroOverZero works in bamCompare
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --outFileFormat bedgraph --scaleFactors 1:1 -o {} " \
"--skipZeroOverZero".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = [
'3R\t50\t100\t-1\n', '3R\t100\t150\t0\n', '3R\t150\t200\t-0.584963\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files_skipnas():
"""
Test skipnas
Compared to the previous tests, any region that do not have coverage (in either of the bam files)
is not included in the bedgraph file.
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --operation subtract " \
"-o {} -p 1 --outFileFormat bedgraph --skipNAs".format(A, B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t100\t150\t0\n', '3R\t150\t200\t-1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_pseudocounts():
"""
Test with different pseudocounts
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --outFileFormat bedgraph --scaleFactors 1:1 -o {} " \
"--pseudocount 1 0".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = [
'3R\t0\t50\tinf\n', '3R\t50\t100\t0\n', '3R\t100\t150\t1\n',
'3R\t150\t200\t0\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_arguments():
"""
Test minimal command line args for bamCoverage. The ratio
between the same file is taken, therefore, the expected value
is 1.0 for all bins.
"""
outfile = '/tmp/test_file.bg'
for fname in [BAMFILE_B, CRAMFILE_B]:
args = "--bamfile1 {} --bamfile2 {} " \
"-o {} -p 1 --outFileFormat bedgraph --operation ratio".format(fname, fname, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t200\t1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files_skipnas():
"""
Test skipnas
Compared to the previous tests, any region that do not have coverage (in either of the bam files)
is not included in the bedgraph file.
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --operation subtract " \
"-o {} -p 1 --outFileFormat bedgraph --skipNAs".format(A, B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t100\t150\t0\n', '3R\t150\t200\t-1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_arguments():
"""
Test minimal command line args for bamCoverage. The ratio
between the same file is taken, therefore, the expected value
is 1.0 for all bins.
"""
outfile = '/tmp/test_file.bg'
for fname in [BAMFILE_B, CRAMFILE_B]:
args = "--bamfile1 {} --bamfile2 {} " \
"-o {} -p 1 --outFileFormat bedgraph --operation ratio".format(fname, fname, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = ['3R\t0\t200\t1\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_subtract():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --ratio subtract --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph --normalizeTo1x 200".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
subtract: scale factors [1,0.5], after applying normalize to 1x, coverage of test_A is 0.5, thus
the factor to reach a coverate of 1 is x2. Thus, the final scale factors are [2,1]
after applying factors: 0 -1 1 0
"""
expected = [
'3R\t0\t50\t0\n', '3R\t50\t100\t-1\n', '3R\t100\t150\t1\n',
'3R\t150\t200\t0\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_diff_files():
"""
Test with two different files
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --scaleFactors 1:1 --operation subtract " \
"-o {} -p 1 --outFileFormat bedgraph".format(A, B, outfile).split()
bam_comp.main(args)
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
expected = [
'3R\t0\t50\t0\n', '3R\t50\t100\t-1\n', '3R\t100\t150\t0\n',
'3R\t150\t200\t-1\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_subtract():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --operation subtract --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph --scaleFactorsMethod None --normalizeUsing CPM".format(A, B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
subtract: After applying CPM normalization, the scale factors are [500000,250000]
after applying factors: 0 -25k 25k 0
"""
expected = [
'3R\t0\t50\t0\n', '3R\t50\t100\t-250000\n',
'3R\t100\t150\t250000\n', '3R\t150\t200\t0\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_subtract():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --ratio subtract --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph --normalizeTo1x 200".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
subtract: scale factors [1,0.5], after applying normalize to 1x, coverage of test_A is 0.5, thus
the factor to reach a coverate of 1 is x2. Thus, the final scale factors are [2,1]
after applying factors: 0 -1 1 0
"""
expected = ['3R\t0\t50\t0\n', '3R\t50\t100\t-1\n', '3R\t100\t150\t1\n', '3R\t150\t200\t0\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_ratio():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --ratio ratio --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
ratio: 0 (0+1)/(1*0.5+1)=0.67 (1+1)/(1+2*0.5)=1
(scale factors [1,0.5]) (1+1)/(1+1*0.5)=1.33
"""
expected = [
'3R\t0\t50\t1\n', '3R\t50\t100\t0.666667\n', '3R\t100\t150\t1.33333\n',
'3R\t150\t200\t1\n'
]
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_subtract():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
for A, B in [(BAMFILE_A, BAMFILE_B), (CRAMFILE_A, CRAMFILE_B)]:
args = "--bamfile1 {} --bamfile2 {} --operation subtract --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph --scaleFactorsMethod None --normalizeUsing CPM".format(A, B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
subtract: After applying CPM normalization, the scale factors are [500000,250000]
after applying factors: 0 -25k 25k 0
"""
expected = ['3R\t0\t50\t0\n', '3R\t50\t100\t-250000\n', '3R\t100\t150\t250000\n', '3R\t150\t200\t0\n']
assert_equal(resp, expected)
unlink(outfile)
def test_bam_compare_scale_factors_ratio():
"""
Test scale factor
"""
outfile = '/tmp/test_file.bg'
args = "--bamfile1 {} --bamfile2 {} --ratio ratio --ignoreForNormalization chr_cigar " \
"-o {} -p 1 --outFileFormat bedgraph".format(BAMFILE_A, BAMFILE_B, outfile).split()
bam_comp.main(args)
# The scale factors are [ 1. 0.5] because BAMFILE_B has dowble the amount of reads (4) compared to BAMFILE_A
_foo = open(outfile, 'r')
resp = _foo.readlines()
_foo.close()
"""
The distribution of reads for the bam file is:
0 100 200
|------------------------------------------------------------|
testA.bam 3R ==============>
<==============
testB.bam 3R <============== ==============>
==============>
==============>
------------------------------------------------------------------------------
ratio: 0 (0+1)/(1*0.5+1)=0.67 (1+1)/(1+2*0.5)=1
(scale factors [1,0.5]) (1+1)/(1+1*0.5)=1.33
"""
expected = ['3R\t0\t50\t1\n', '3R\t50\t100\t0.666667\n', '3R\t100\t150\t1.33333\n', '3R\t150\t200\t1\n']
assert_equal(resp, expected)
unlink(outfile)
