def test_indel_realigner(self,
bams=None,
output="realign.bam",
intervals="realign"):
"""
Test the indel_realigner method to determine whether the output
command matches the expected command.
"""
if bams is None:
bams = ["input.bam"]
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
self.assertTrue(hasattr(gatk, "indel_realigner"),
"indel_realigner() not found in gatk")
indel_realign_run = gatk.indel_realigner(bams=bams,
output=output,
intervals=intervals)
expected_realign_run_command = " ".join([
"/usr/bin/java -Xmx20g -Djava.io.tmpdir=./tmp",
"-jar GenomeAnalysisTK.jar", "-T IndelRealigner", "-I input.bam",
"-o PROCESSED_BAMS/realign.bam", "-targetIntervals realign",
"-R ref.fa"
])
self.assertEqual(indel_realign_run["command"],
expected_realign_run_command,
"command does not match expected indel realignment")
def test_print_reads(self,
bam="realign.bam",
output="recal.bam",
recaldata="recal.table"):
"""
Test whether the print_reads method provides the expected output.
"""
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
# check to see if command exists for object
self.assertTrue(hasattr(gatk, "print_reads"),
msg="print_reads() not found in gatk")
printreads_run = gatk.print_reads(bam=bam,
output=output,
recaldata=recaldata)
expected_printreads_command = " ".join([
"/usr/bin/java -Xmx20g -Djava.io.tmpdir=./tmp",
"-jar GenomeAnalysisTK.jar", "-T PrintReads", "-I realign.bam",
"-o PROCESSED_BAMS/recal.bam", "-R ref.fa", "-BQSR recal.table",
"-nct 4", "-rf BadCigar"
])
self.assertEqual(printreads_run["command"],
expected_printreads_command,
"PrintReads command does not match expected")
def test_depthofcoverage(self, bam="input.bam", output="depth.txt"):
"""
Test the depth_of_coverage command outputs the same as expected.
"""
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
self.assertTrue(hasattr(gatk, "depth_of_coverage"),
"depth_of_coverage() not found in gatk package")
depth_run = gatk.depth_of_coverage(
bam=bam,
output=output,
)
print(depth_run)
def test_realign_target_creator(self, bams=None, output="realign"):
"""
Test the realign_target_creator method to determine whether the output
command matches the expected command.
"""
if bams is None:
bams = ["input.bam"]
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
self.assertTrue(hasattr(gatk, "realigner_target_creator"),
"realigner_target_creator() not found in gatk")
realign_run = gatk.realigner_target_creator(bams=bams, output=output)
expected_realigner_command = " ".join([
"/usr/bin/java -Xmx20g -Djava.io.tmpdir=./tmp",
"-jar GenomeAnalysisTK.jar", "-T RealignerTargetCreator",
"-I input.bam", "-o PROCESSED_BAMS/realign", "-R ref.fa", "-nt 8",
"-l INFO"
])
self.assertEqual(realign_run["command"], expected_realigner_command)
def test_split_n_cigar_reads(self, bams=None, output="split.bam"):
"""
Test the split_n_cigar_reads function to ensure command remains consistent
with expected.
"""
if bams is None:
bams = ["input.bam"]
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
self.assertTrue(hasattr(gatk, "split_n_cigar_reads"),
"split_n_cigar_reads() not found in gatk")
split_run = gatk.split_n_cigar_reads(bams=bams, output=output)
expected_split_command = " ".join([
"/usr/bin/java -Xmx20g -Djava.io.tmpdir=./tmp",
"-jar GenomeAnalysisTK.jar", "-T SplitNCigarReads", "-I input.bam",
"-R ref.fa", "-o PROCESSED_BAMS/split.bam",
"-rf ReassignOneMappingQuality", "-rf UnmappedRead",
"--reassign_mapping_quality_from 255",
"--reassign_mapping_quality_to 60", "-U ALLOW_N_CIGAR_READS"
])
self.assertEqual(split_run["command"], expected_split_command,
"command does not match expected")
def test_base_quality_recalibration(self,
bams=None,
output="basequalrecal.table"):
"""
Test the base_quality_recalibration method to see if command matches
expected.
"""
if bams is None:
bams = ["indel_realign.bam"]
gatk = ngs.Gatk(output_dir="PROCESSED_BAMS")
self.assertTrue(hasattr(gatk, "base_quality_recalibration"),
"base_quality_recalibration() not found in gatk")
base_qual_recal_run = gatk.base_quality_recalibration(bams=bams,
output=output)
baserecal_command = " ".join([
"/usr/bin/java -Xmx20g -Djava.io.tmpdir=./tmp",
"-jar GenomeAnalysisTK.jar", "-T BaseRecalibrator",
"-I indel_realign.bam", "-o PROCESSED_BAMS/basequalrecal.table",
"-R ref.fa", "-U ALLOW_N_CIGAR_READS"
])
self.assertEqual(base_qual_recal_run["command"], baserecal_command,
"command does not match expected")