def test_7_calculate_snp_distances(self):
"""Run calculate_snp_distances and verify snp_distance_matrix.tsv contains expected contents.
"""
command_line = "distance -f " + os.path.join(self.__class__.directory_run_result, 'snpma.fasta') + ' ' + \
"--matrix " + os.path.join(self.__class__.directory_run_result, 'snp_distance_matrix.tsv')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snp_distance_matrix.tsv')
def test_3_call_consensus(self):
"""Run call_consensus and verify consensus.fasta and consensus.vcf contain expected contents for each sample.
"""
command_line = "call_consensus -f -l " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + \
" --vcfRefName lambda_virus.fasta" + \
" --vcfFailedSnpGt 1" + \
" dummyAllPileupFile"
args = cfsan_snp_pipeline.parse_command_line(command_line)
ignore_lines = ["##fileDate", "##source"]
for dir in [
'samples/sample1', 'samples/sample2', 'samples/sample3',
'samples/sample4'
]:
args.allPileupFile = os.path.join(
self.__class__.directory_run_result, dir, 'reads.all.pileup')
args.consensusFile = os.path.join(
self.__class__.directory_run_result, dir, 'consensus.fasta')
args.vcfFileName = None
self.run_function_test(cfsan_snp_pipeline.run_command_from_args,
args, os.path.join(dir, 'consensus.fasta'))
args.vcfFileName = 'consensus.vcf'
self.run_function_test(cfsan_snp_pipeline.run_command_from_args,
args, os.path.join(dir, 'consensus.vcf'),
ignore_lines)
def test_4_create_snp_matrix(self):
"""Run snp_matrix and verify snpma.fasta contains expected contents.
"""
command_line = "snp_matrix -f -o " + os.path.join(self.__class__.directory_run_result, 'snpma.fasta') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snpma.fasta')
def test_7_calculate_snp_distances(self):
"""Run calculate_snp_distances and verify snp_distance_matrix.tsv contains expected contents.
"""
command_line = "distance -f " + os.path.join(self.__class__.directory_run_result, 'snpma.fasta') + ' ' + \
"--matrix " + os.path.join(self.__class__.directory_run_result, 'snp_distance_matrix.tsv')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args,
'snp_distance_matrix.tsv')
def test_4_create_snp_matrix(self):
"""Run snp_matrix and verify snpma.fasta contains expected contents.
"""
command_line = "snp_matrix -f -o " + os.path.join(self.__class__.directory_run_result, 'snpma.fasta') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args,
'snpma.fasta')
def test_5_create_snp_reference_seq(self):
"""Run create_snp_reference_seq and verify referenceSNP.fasta contains expected contents.
"""
command_line = "snp_reference -f -l " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + \
" -o " + os.path.join(self.__class__.directory_run_result, 'referenceSNP.fasta') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'reference/lambda_virus.fasta')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'referenceSNP.fasta')
def test_2_merge_sites(self):
"""Run merge_sites and verify snplist.txt contains expected contents.
"""
command_line = "merge_sites -f -o " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'filteredSampleDirectories.txt')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snplist.txt')
def test_5_create_snp_reference_seq(self):
"""Run create_snp_reference_seq and verify referenceSNP.fasta contains expected contents.
"""
command_line = "snp_reference -f -l " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + \
" -o " + os.path.join(self.__class__.directory_run_result, 'referenceSNP.fasta') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'reference/lambda_virus.fasta')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args,
'referenceSNP.fasta')
def test_2_merge_sites(self):
"""Run merge_sites and verify snplist.txt contains expected contents.
"""
command_line = "merge_sites -f -o " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, 'filteredSampleDirectories.txt')
args = cfsan_snp_pipeline.parse_command_line(command_line)
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args,
'snplist.txt')
def test_1_filter_regions(self):
"""Run filter_regions and verify var.flt_preserved.vcf and var.flt_removed.vcf contains expected contents for each sample.
"""
command_line = "filter_regions -f " + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, "reference", "lambda_virus.fasta")
args = cfsan_snp_pipeline.parse_command_line(command_line)
for dir in ['samples/sample1', 'samples/sample2','samples/sample3','samples/sample4']:
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, os.path.join(dir, 'var.flt_preserved.vcf'))
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, os.path.join(dir, 'var.flt_removed.vcf'))
def test_1_filter_regions(self):
"""Run filter_regions and verify var.flt_preserved.vcf and var.flt_removed.vcf contains expected contents for each sample.
"""
command_line = "filter_regions -f " + \
os.path.join(self.__class__.directory_run_result, 'sampleDirectories.txt') + ' ' + \
os.path.join(self.__class__.directory_run_result, "reference", "lambda_virus.fasta")
args = cfsan_snp_pipeline.parse_command_line(command_line)
for dir in [
'samples/sample1', 'samples/sample2', 'samples/sample3',
'samples/sample4'
]:
self.run_function_test(cfsan_snp_pipeline.run_command_from_args,
args,
os.path.join(dir, 'var.flt_preserved.vcf'))
self.run_function_test(cfsan_snp_pipeline.run_command_from_args,
args,
os.path.join(dir, 'var.flt_removed.vcf'))
def test_3_call_consensus(self):
"""Run call_consensus and verify consensus.fasta and consensus.vcf contain expected contents for each sample.
"""
command_line = "call_consensus -f -l " + os.path.join(self.__class__.directory_run_result, 'snplist.txt') + \
" --vcfRefName lambda_virus.fasta" + \
" --vcfFailedSnpGt 1" + \
" dummyAllPileupFile"
args = cfsan_snp_pipeline.parse_command_line(command_line)
ignore_lines = ["##fileDate", "##source"]
for dir in ['samples/sample1', 'samples/sample2','samples/sample3','samples/sample4']:
args.allPileupFile = os.path.join(self.__class__.directory_run_result, dir, 'reads.all.pileup')
args.consensusFile = os.path.join(self.__class__.directory_run_result, dir, 'consensus.fasta')
args.vcfFileName = None
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, os.path.join(dir, 'consensus.fasta'))
args.vcfFileName = 'consensus.vcf'
self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, os.path.join(dir, 'consensus.vcf'), ignore_lines)