def test_paired_end_file(self):
"""Test, paired end SAM file"""
# here is the example
# >ref
# 5p CGA AAA CGA 3p
# 3p GCT TTT GCT 5p
# >r001/1
# CGA
# >r001/2
# GCA
# The sam file looks like this
#@HD VN:1.5 SO:coordinate
#@SQ SN:ref LN:9
#r001 163 ref 1 30 3M = 7 9 CGA III MR:f:0 #the normal ones
#r001 83 ref 7 30 3M = 1 -9 TCG III MR:f:0
#r002 163 ref 1 30 3M = 7 9 TGA III MR:f:0.9 #With one dam subs
#r002 83 ref 7 30 3M = 1 -9 CAA III MR:f:0.009
#r003 83 ref 1 30 3M = 7 9 TGA III #The reverse complement, should not rescale (thus no flags)
#r003 163 ref 7 30 3M = 1 -9 CAA III
#
#hand calculated the correct rescaled sam file in pe_rescaled_correct.sam
options = mock_options("rescale_test/pe_test/pe.sam","rescale_test/pe_test/pe_rescaled.sam","rescale_test/pe_test/pe_output/")
ref = pysam.Fastafile("rescale_test/pe_test/ref.fa")
rescale.rescale_qual(ref,options,debug=True)
self.assertTrue(filecmp.cmp("rescale_test/pe_test/pe_rescaled.sam","rescale_test/pe_test/pe_rescaled_correct.sam"))
def test_paired_end_file(self):
"""Test, paired end SAM file"""
# here is the example
# >ref
# 5p CGA AAA CGA 3p
# 3p GCT TTT GCT 5p
# >r001/1
# CGA
# >r001/2
# GCA
# The sam file looks like this
#@HD VN:1.5 SO:coordinate
#@SQ SN:ref LN:9
#r001 163 ref 1 30 3M = 7 9 CGA III #the normal ones
#r001 83 ref 7 30 3M = 1 -9 TCG III
#r002 163 ref 1 30 3M = 7 9 TGA III #With one dam subs
#r002 83 ref 7 30 3M = 1 -9 CAA III
#r003 83 ref 1 30 3M = 7 9 TGA III #The reverse complement, should not rescale
#r003 163 ref 7 30 3M = 1 -9 CAA III
#
#hand calculated the correct rescaled sam file in pe_rescaled_correct.sam
options = mock_options("rescale_test/pe_test/pe.sam",
"rescale_test/pe_test/pe_rescaled.sam",
"rescale_test/pe_test/pe_output/")
ref = pysam.Fastafile("rescale_test/pe_test/ref.fa")
rescale.rescale_qual(ref, options, debug=True)
self.assertTrue(
filecmp.cmp("rescale_test/pe_test/pe_rescaled.sam",
"rescale_test/pe_test/pe_rescaled_correct.sam"))
def test_longalignshortread(self):
"""Check if fails on an aligment longer than the read"""
prefix = "rescale_test/long_align/"
options = mock_options(prefix + "pe.sam", prefix + "pe_out.sam",
prefix + "pe_output/")
ref = pysam.Fastafile("rescale_test/pe_test/ref.fa")
rescale.rescale_qual(ref, options, debug=True)
def test_longalignshortread(self):
"""Check if fails on an aligment longer than the read"""
prefix="rescale_test/long_align/"
options = mock_options(prefix+"pe.sam",prefix+"pe_out.sam",prefix+"pe_output/")
ref = pysam.Fastafile("rescale_test/pe_test/ref.fa")
rescale.rescale_qual(ref,options,debug=True)
#Should run without an error
self.assertTrue(True)
