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"""Benchmarking module for AlignmentFile functionality"""
import os
from TestUtils import BAM_DATADIR, force_str, flatten_nested_list
from PileupTestUtils import *
def test_build_pileup_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_pileup_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 2998
def test_build_pileup_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_pileup_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 2998
def test_build_pileup_from_bam_with_pysam(benchmark):
result = benchmark(build_pileup_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 2998
def test_build_depth_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_depth_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 107241
def test_build_depth_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_depth_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert sum(result) == 107241
def test_build_depth_from_bam_with_pysam(benchmark):
result = benchmark(build_depth_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
# different value, as samtools filters with a minimum
# base quality of 13
assert sum(result) == 110015
def test_build_depth_with_filter_from_bam_with_pysam(benchmark):
result = benchmark(build_depth_with_filter_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert sum(result) == 107241
def test_build_query_bases_from_bam_with_samtoolsshell(benchmark):
result = benchmark(build_query_bases_with_samtoolsshell,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert result == 116308
def test_build_query_bases_from_bam_with_samtoolspysam(benchmark):
result = benchmark(build_query_bases_with_samtoolspysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 116308
def test_build_query_bases_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_query_bases_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 116308
def test_build_query_bases_from_bam_with_pysam_pileups(benchmark):
# note that there is no overlap detection here
result = benchmark(build_query_bases_with_pysam_pileups,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 107241
def test_build_query_bases_from_bam_with_pysam(benchmark):
result = benchmark(build_query_bases_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(flatten_nested_list(result))) == 116308
# note that pileups with/without reference sequence will differ due to
# realignment.
def test_build_query_bases_with_reference_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_query_bases_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"),
"-f", os.path.join(BAM_DATADIR, "ex1.fa"))
assert len("".join(flatten_nested_list(result))) == 115924
def test_build_query_bases_with_reference_from_bam_with_pysam(benchmark):
with pysam.FastaFile(os.path.join(BAM_DATADIR, "ex1.fa")) as fasta:
result = benchmark(build_query_bases_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"),
fastafile=fasta)
assert len("".join(flatten_nested_list(result))) == 115924
def test_build_query_bases_with_reference_from_bam_with_samtoolspysam(benchmark):
result = benchmark(build_query_bases_with_samtoolspysam,
os.path.join(BAM_DATADIR, "ex2.bam"),
"-f", os.path.join(BAM_DATADIR, "ex1.fa"))
assert len("".join(flatten_nested_list(result))) == 115924
def test_build_query_qualities_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_query_qualities_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(result)) == 107241
def test_build_query_qualities_from_bam_with_pysam(benchmark):
result = benchmark(build_query_qualities_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert sum([len(x) for x in result]) == 107241
def test_build_query_names_from_bam_with_pysam(benchmark):
result = benchmark(build_query_names_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join([x for column in result for x in column])) == 2307343
def test_build_mapping_qualities_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_mapping_qualities_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert len("".join(result)) == 107241
def test_build_mapping_qualities_from_bam_with_pysam(benchmark):
result = benchmark(build_mapping_qualities_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert sum([len(x) for x in result]) == 107241
def test_build_query_positions_from_bam_with_samtoolspipe(benchmark):
result = benchmark(build_query_positions_with_samtoolspipe,
os.path.join(BAM_DATADIR, "ex2.bam"))
# positions output by samtools are 1-based
assert sum([sum(x) - len(x) for x in result]) == 1841699
def test_build_query_positions_from_bam_with_pysam(benchmark):
result = benchmark(build_query_positions_with_pysam,
os.path.join(BAM_DATADIR, "ex2.bam"))
assert sum([sum(x) for x in result]) == 1841699
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