def run(options):
assert len(options.reads_files) % 2 == 0
reads1_list = [
filename for i, filename in enumerate(options.reads_files)
if i % 2 == 0
]
reads2_list = [
filename for i, filename in enumerate(options.reads_files)
if i % 2 != 0
]
assert len(reads1_list) == len(reads2_list)
read_map.map_reads_set(
options.ref_fasta,
reads1_list,
reads2_list,
options.outfile,
rmdup=not options.unsorted_sam,
read_group=("1", options.sample_name),
)
def test_map_reads_set(self):
"""test map_reads_set"""
reads1 = [
os.path.join(data_dir, "reads_set_" + str(i) + ".1.fq")
for i in range(1, 4, 1)
]
reads2 = [
os.path.join(data_dir, "reads_set_" + str(i) + ".2.fq")
for i in range(1, 4, 1)
]
ref_fasta = os.path.join(data_dir, "ref.fa")
try:
os.unlink(tmp_bam)
except:
pass
tmp_bam = "tmp.read_map.map_reads_set.bam"
def reads_in_bam(bam_file):
return len(
list(pysam.Samfile(bam_file, "rb").fetch(until_eof=True)))
# check works when list length is 1. Should have 12 read pairs in the bam
read_map.map_reads_set(ref_fasta, [reads1[0]], [reads2[0]],
tmp_bam,
rmdup=True)
self.assertTrue(os.path.exists(tmp_bam))
self.assertEqual(24, reads_in_bam(tmp_bam))
os.unlink(tmp_bam)
# check works when list length > 1, Should have 35 read pairs in the bam
read_map.map_reads_set(
ref_fasta,
reads1,
reads2,
tmp_bam,
rmdup=True,
read_group=("1", "GROUP_NAME"),
)
self.assertEqual(70, reads_in_bam(tmp_bam))
os.unlink(tmp_bam)
def test_map_reads_set(self):
'''test map_reads_set'''
reads1 = [
os.path.join(data_dir, 'reads_set_' + str(i) + '.1.fq')
for i in range(1, 4, 1)
]
reads2 = [
os.path.join(data_dir, 'reads_set_' + str(i) + '.2.fq')
for i in range(1, 4, 1)
]
ref_fasta = os.path.join(data_dir, 'ref.fa')
try:
os.unlink(tmp_bam)
except:
pass
tmp_bam = 'tmp.read_map.map_reads_set.bam'
def reads_in_bam(bam_file):
return len(
list(pysam.Samfile(bam_file, 'rb').fetch(until_eof=True)))
# check works when list length is 1. Should have 12 read pairs in the bam
read_map.map_reads_set(ref_fasta, [reads1[0]], [reads2[0]],
tmp_bam,
rmdup=True)
self.assertTrue(os.path.exists(tmp_bam))
self.assertEqual(24, reads_in_bam(tmp_bam))
os.unlink(tmp_bam)
# check works when list length > 1, Should have 35 read pairs in the bam
read_map.map_reads_set(ref_fasta,
reads1,
reads2,
tmp_bam,
rmdup=True,
read_group=('1', 'GROUP_NAME'))
self.assertEqual(70, reads_in_bam(tmp_bam))
os.unlink(tmp_bam)
def run(
reads1_list,
reads2_list,
ref_dir,
outdir,
sample_name="sample",
cortex_mem_height=22,
debug=False,
keep_bam=False,
):
if len(reads1_list) != len(reads2_list):
raise Exception(
"Must give same number of forward and reverse reads files. Got:\nForward:{reads1_list}\nReverse:{reads2_list}"
)
os.mkdir(outdir)
trimmed_reads_1 = []
trimmed_reads_2 = []
for i in range(len(reads1_list)):
trimmed_reads_1.append(
os.path.join(outdir, f"trimmed_reads.{i}.1.fq.gz"))
trimmed_reads_2.append(
os.path.join(outdir, f"trimmed_reads.{i}.2.fq.gz"))
read_trim.run_trimmomatic(
reads1_list[i],
reads2_list[i],
trimmed_reads_1[-1],
trimmed_reads_2[-1],
)
refdir = reference_dir.ReferenceDir(directory=ref_dir)
rmdup_bam = os.path.join(outdir, "map.bam")
read_map.map_reads_set(
refdir.ref_fasta,
trimmed_reads_1,
trimmed_reads_2,
rmdup_bam,
rmdup=True,
read_group=("1", sample_name),
)
utils.syscall(f"samtools index {rmdup_bam}")
if not debug:
for filename in trimmed_reads_1 + trimmed_reads_2:
os.unlink(filename)
samtools_vcf = os.path.join(outdir, "samtools.vcf")
cmd = f"bcftools mpileup --output-type u -f {refdir.ref_fasta} {rmdup_bam} | bcftools call -vm -O v -o {samtools_vcf}"
utils.syscall(cmd)
cortex_dir = os.path.join(outdir, "cortex")
ctx = cortex.CortexRunCalls(
refdir.directory,
rmdup_bam,
cortex_dir,
sample_name,
mem_height=cortex_mem_height,
)
ctx.run(run_mccortex_view_kmers=False)
ctx_vcf_dir = os.path.join(cortex_dir, "cortex.out", "vcfs")
cortex_vcfs = [
os.path.join(ctx_vcf_dir, x) for x in os.listdir(ctx_vcf_dir)
if x.endswith("raw.vcf")
]
if len(cortex_vcfs) != 1:
raise Exception("Error running cortex. Could not find output VCF file")
cortex_vcf = os.path.join(outdir, "cortex.vcf")
os.rename(cortex_vcfs[0], cortex_vcf)
if not debug:
utils.syscall(f"rm -rf {cortex_dir}")
minos_dir = os.path.join(outdir, "minos")
cmd = f"minos adjudicate --reads {rmdup_bam} {minos_dir} {refdir.ref_fasta} {samtools_vcf} {cortex_vcf}"
utils.syscall(cmd)
os.rename(os.path.join(minos_dir, "final.vcf"),
os.path.join(outdir, "final.vcf"))
if not debug:
utils.syscall(f"rm -rf {minos_dir}")
if not (keep_bam or debug):
os.unlink(rmdup_bam)
os.unlink(rmdup_bam + ".bai")
final_vcf = os.path.join(outdir, "final.vcf")
if not os.path.exists(final_vcf):
raise Exception(f"Error. Final VCF file not found: {final_vcf}")
logging.info(f"Finished variant calling. Final VCF file: {final_vcf}")