def _sam2bam2sorted_bam(self):
subprocess.getoutput("rm -f {}*".format(self._pk.samtools_sorted_file_name))
Utilities.batch_remove(self._pk.samtools_converted_log_file_name)
# SamTools details: http://www.htslib.org/doc/samtools.html
# Avoiding self._pk.samtools_converted_file_name
s = subprocess.getoutput("samtools view -bu -@ 1 {a} | \
samtools sort - -o -@ 1 {b}".format(a=self._pk.mapped_reads_file_name,
b=self._pk.samtools_sorted_file_name))
Utilities.dump_string(string=s, file=self._pk.samtools_converted_log_file_name)
logging.info("Sorted SAM file: '{}'".format(self._pk.samtools_sorted_file_name))
del s
def compile(input_file: str,
output_dir: str,
preserve_headers: bool = False,
chop: bool = False,
chunk_length: int = int(3.6 * 10**9)):
import json
from modules.FASTAArray import FASTAArray
from modules.RefDataLine import RefDataLine
output_dir = Utilities.ends_with_slash(output_dir)
os.makedirs(output_dir, exist_ok=True)
refdatas_dict = FASTAArray.prepare_nfasta_for_indexing(
input_file=input_file,
output_dir=output_dir,
preserve_headers=preserve_headers,
chop=chop,
chunk_length=chunk_length)
output_dict = {}
for sequence_id in refdatas_dict:
annotation_dict = refdatas_dict[sequence_id]
nfasta_file = annotation_dict.get("reference_nfasta")
if not nfasta_file:
continue
indexing_dict = {"alias": Utilities.filename_only(nfasta_file)}
indexing_dict.update(RefDataLine.fill_dict(nfasta_file))
indexing_dict.update(annotation_dict)
print("Processing nFASTA: '{}'".format(nfasta_file))
refdata = RefDataLine(indexing_dict)
refdata.index()
output_dict[sequence_id] = indexing_dict
output_file = "{a}{b}_refdata.json".format(
a=Utilities.ends_with_slash(output_dir),
b=Utilities.filename_only(input_file))
Utilities.dump_string(
string=json.dumps(output_dict, sort_keys=False, indent=4) + "\n",
file=output_file)
print("Created reference data linker: '{}'".format(output_file))
return output_file
def __samtools_faidx(self):
s = subprocess.getoutput("samtools faidx {}".format(self._nfasta))
Utilities.dump_string(string=s, file="{}_samtools_faidx.log".format(self._reference_mask))
os.rename("{}.fai".format(self._nfasta), self.samtools_index_file)
print("Created SAMTools FAI file: '{}'".format(self.samtools_index_file))
self.___fai2genome()
def __bowtie2_build(self):
s = subprocess.getoutput("bowtie2-build {a} {b}".format(a=self._nfasta, b=self.bowtie2_index_mask))
Utilities.dump_string(string=s, file="{}_bowtie2-build.log".format(self._reference_mask))
print("Created bowtie2 index with mask: '{}'".format(self.bowtie2_index_mask))
def _index_bam(self):
Utilities.batch_remove(self._pk.samtools_index_file_name, self._pk.samtools_index_log_file_name)
s = subprocess.getoutput("samtools index {}".format(self._pk.samtools_sorted_file_name))
Utilities.dump_string(string=s, file=self._pk.samtools_index_log_file_name)
logging.info("Indexed BAM file: '{}'".format(self._pk.samtools_index_file_name))
del s
