def _wiggle_writers(self, lib_name, strands, no_of_aligned_reads,
min_no_of_aligned_reads):
"""Write the calculated coverages to wiggle files."""
coverage_writers_raw = dict([
(strand,
WiggleWriter(
"%s_%s" % (lib_name, strand),
open(self._paths.wiggle_file_raw_path(lib_name, strand),
"w"))) for strand in strands
])
coverage_writers_tnoar_min_norm = dict([
(strand,
WiggleWriter(
"%s_%s" % (lib_name, strand),
open(
self._paths.wiggle_file_tnoar_norm_min_path(
lib_name,
strand,
multi=min_no_of_aligned_reads,
div=no_of_aligned_reads), "w"))) for strand in strands
])
coverage_writers_tnoar_mil_norm = dict([
(strand,
WiggleWriter(
"%s_%s" % (lib_name, strand),
open(
self._paths.wiggle_file_tnoar_norm_mil_path(
lib_name,
strand,
multi=1000000,
div=no_of_aligned_reads), "w"))) for strand in strands
])
return (coverage_writers_raw, coverage_writers_tnoar_min_norm,
coverage_writers_tnoar_mil_norm)
def _wiggle_writers(self, strands, no_of_aligned_reads,
min_no_of_aligned_reads):
if self._args.output_coverage is None:
filename = self.get_filename(self._args.input_coverage)
if os.path.dirname(self._args.input_coverage) == "":
output_path = "."
else:
output_path = os.path.dirname(self._args.input_coverage)
else:
filename = self.get_filename(self._args.output_coverage)
if os.path.dirname(self._args.output_coverage) == "":
output_path = "."
else:
output_path = os.path.dirname(self._args.output_coverage)
if self._args.trackname is None:
trackname = filename
else:
trackname = self.get_filename(self._args.trackname)
coverage_writers_raw = dict([(
strand, WiggleWriter(
"%s_%s" % (trackname, strand),
open("%s/%s_%s-raw.wig" % (output_path, filename, strand),
"w"))) for strand in strands])
coverage_writers_tnoar_min_norm = dict([(
strand, WiggleWriter(
"%s_%s" % (trackname, strand),
open(
"%s/%s_%s-tnoar_mil_norm_multi_by_%.1f_div_by_%.1f.wig" % (
output_path, filename, strand,
min_no_of_aligned_reads, no_of_aligned_reads),
"w"))) for strand in strands])
coverage_writers_tnoar_mil_norm = dict([(
strand, WiggleWriter(
"%s_%s" % (trackname, strand),
open(
"%s/%s_%s-tnoar_mil_norm_multi_by_%.1f_div_by_%.1f.wig" % (
output_path, filename, strand, self._args.factor,
no_of_aligned_reads),
"w"))) for strand in strands])
return(coverage_writers_raw, coverage_writers_tnoar_min_norm,
coverage_writers_tnoar_mil_norm)