def mapReadsAgainstSpadesContigs(infiles, outfile):
'''
map reads against spades contigs
'''
inf = infiles[0]
to_cluster = True
index_dir = os.path.dirname(outfile)
if "agg" not in infiles[1]:
genome = re.search(
".*R[0-9]*", infiles[0]).group(0) + ".filtered.contigs.fa"
else:
genome = "agg-agg-agg.filtered.contigs.fa"
if infiles[1].endswith(".bt2") or infiles[1].endswith(".ebwt"):
infile, reffile = infiles[0], os.path.join(index_dir, genome) + ".fa"
m = PipelineMapping.Bowtie(
executable=P.substituteParameters(**locals())["bowtie_executable"])
elif infiles[1].endswith("bwt"):
genome = genome
job_options = " -l mem_free=%s" % (PARAMS["bwa_memory"])
bwa_index_dir = index_dir
bwa_mem_options = PARAMS["bwa_mem_options"]
bwa_threads = PARAMS["bwa_threads"]
m = PipelineMapping.BWAMEM(remove_non_unique=True)
statement = m.build((inf,), outfile)
P.run()
def mapReads(infile, outfile):
'''Map reads to the genome using BWA, sort and index BAM file,
generate alignment statistics and deduplicate using Picard'''
job_threads = PARAMS["bwa_threads"]
job_memory = PARAMS["bwa_memory"]
if PARAMS["bwa_algorithm"] == "aln":
m = PipelineMapping.BWA(
remove_non_unique=PARAMS["bwa_remove_non_unique"],
strip_sequence=False)
elif PARAMS["bwa_algorithm"] == "mem":
m = PipelineMapping.BWAMEM(
remove_non_unique=PARAMS["bwa_remove_non_unique"],
strip_sequence=False)
else:
raise ValueError("bwa algorithm '%s' not known" % algorithm)
statement = m.build((infile, ), outfile)
print(statement)
P.run()