def _create_coverage_files_for_lib(self, lib_name, bam_path,
no_of_aligned_reads,
min_no_of_aligned_reads):
"""Perform the coverage calculation for a given library."""
if not self._args.non_strand_specific:
strands = ["forward", "reverse"]
else:
strands = ["forward_and_reverse"]
if self._all_coverage_file_exist(lib_name, strands,
no_of_aligned_reads,
min_no_of_aligned_reads):
return
read_count_splitting = True
if self._args.skip_read_count_splitting:
read_count_splitting = False
coverage_calculator = CoverageCalculator(
read_count_splitting=read_count_splitting,
uniquely_aligned_only=self._args.unique_only,
coverage_style=self._args.coverage_style,
clip_length=self._args.clip_length,
non_strand_specific=self._args.non_strand_specific,
)
(
coverage_writers_raw,
coverage_writers_tnoar_min_norm,
coverage_writers_tnoar_mil_norm,
) = self._wiggle_writers(lib_name, strands, no_of_aligned_reads,
min_no_of_aligned_reads)
for ref_seq, coverages in coverage_calculator.ref_seq_and_coverages(
bam_path):
for strand in strands:
coverage_writers_raw[strand].write_replicons_coverages(
ref_seq, coverages[strand])
coverage_writers_tnoar_min_norm[
strand].write_replicons_coverages(
ref_seq,
coverages[strand],
factor=min_no_of_aligned_reads / no_of_aligned_reads,
)
coverage_writers_tnoar_mil_norm[
strand].write_replicons_coverages(
ref_seq,
coverages[strand],
factor=1000000 / no_of_aligned_reads,
)
for strand in strands:
coverage_writers_raw[strand].close_file()
def _create_coverage_files_for_lib(
self, lib_name, bam_path, no_of_aligned_reads,
min_no_of_aligned_reads):
"""Perform the coverage calculation for a given library."""
if not self._args.non_strand_specific:
strands = ["forward", "reverse"]
else:
strands = ["forward_and_reverse"]
if self._all_coverage_file_exist(
lib_name, strands, no_of_aligned_reads,
min_no_of_aligned_reads):
return
read_count_splitting = True
if self._args.skip_read_count_splitting:
read_count_splitting = False
coverage_calculator = CoverageCalculator(
read_count_splitting=read_count_splitting,
uniquely_aligned_only=self._args.unique_only,
coverage_style=self._args.coverage_style,
clip_length=self._args.clip_length,
non_strand_specific=self._args.non_strand_specific)
(coverage_writers_raw, coverage_writers_tnoar_min_norm,
coverage_writers_tnoar_mil_norm) = self._wiggle_writers(
lib_name, strands, no_of_aligned_reads, min_no_of_aligned_reads)
for ref_seq, coverages in coverage_calculator.ref_seq_and_coverages(
bam_path):
for strand in strands:
coverage_writers_raw[strand].write_replicons_coverages(
ref_seq, coverages[strand])
coverage_writers_tnoar_min_norm[
strand].write_replicons_coverages(
ref_seq, coverages[strand],
factor=min_no_of_aligned_reads/no_of_aligned_reads)
coverage_writers_tnoar_mil_norm[
strand].write_replicons_coverages(
ref_seq, coverages[strand],
factor=1000000/no_of_aligned_reads)
for strand in strands:
coverage_writers_raw[strand].close_file()
def create_coverage_files_TK(
self, no_of_aligned_reads, min_no_of_aligned_reads):
if not self._args.non_strand_specific:
strands = ["forward", "reverse"]
else:
strands = ["forward_and_reverse"]
if self._args.skip_read_count_splitting:
read_count_splitting = False
else:
read_count_splitting = True
from reademptionlib.coveragecalculator import CoverageCalculator
coverage_calculator = CoverageCalculator(
read_count_splitting=read_count_splitting,
uniquely_aligned_only=self._args.unique_only,
coverage_style=self._args.coverage_style,
clip_length=self._args.clip_length,
non_strand_specific=self._args.non_strand_specific)
(coverage_writers_raw, coverage_writers_tnoar_min_norm,
coverage_writers_tnoar_mil_norm) = self._wiggle_writers(
strands, no_of_aligned_reads, min_no_of_aligned_reads)
for ref_seq, coverages in coverage_calculator.ref_seq_and_coverages(
self._args.input_coverage):
for strand in strands:
coverage_writers_raw[strand].write_replicons_coverages(
ref_seq, coverages[strand])
for strand in strands:
coverage_writers_tnoar_min_norm[
strand].write_replicons_coverages(
ref_seq, coverages[strand],
factor=min_no_of_aligned_reads/no_of_aligned_reads)
for strand in strands:
coverage_writers_tnoar_mil_norm[
strand].write_replicons_coverages(
ref_seq, coverages[strand],
factor=self._args.factor/no_of_aligned_reads)
for strand in strands:
coverage_writers_raw[strand].close_file()
