def remove_short_reads(fastq_files, dirs, lane_config):
"""
remove reads from a single or pair of fastq files which fall below
a length threshold (30 bases)
"""
min_length = int(lane_config["algorithm"].get("min_read_length", 20))
supplied_quality_format = _get_quality_format(lane_config)
if supplied_quality_format == "illumina":
quality_format = "fastq-illumina"
else:
quality_format = "fastq-sanger"
if is_pair(fastq_files):
fastq1, fastq2 = fastq_files
out_files = fastq.filter_reads_by_length(fastq1, fastq2, quality_format, min_length)
else:
out_files = [fastq.filter_single_reads_by_length(fastq_files[0],
quality_format, min_length)]
map(os.remove, fastq_files)
return out_files
def _remove_short_reads(fastq_files, dirs, lane_config):
"""
remove reads from a single or pair of fastq files which fall below
a length threshold (30 bases)
"""
MIN_LENGTH = 20
supplied_quality_format = _get_quality_format(lane_config)
if supplied_quality_format == "illumina":
quality_format = "fastq-illumina"
else:
quality_format = "fastq-sanger"
if is_pair(fastq_files):
fastq1, fastq2 = fastq_files
out_files = fastq.filter_reads_by_length(fastq1, fastq2,
quality_format, MIN_LENGTH)
else:
out_files = fastq.filter_single_reads_by_length(
fastq_files[0], quality_format, MIN_LENGTH)
return out_files
def _remove_short_reads(fastq_files, dirs, lane_config):
"""
remove reads from a single or pair of fastq files which fall below
a length threshold (30 bases)
"""
MIN_LENGTH = 20
supplied_quality_format = _get_quality_format(lane_config)
if supplied_quality_format == "illumina":
quality_format = "fastq-illumina"
else:
quality_format = "fastq-sanger"
if is_pair(fastq_files):
fastq1, fastq2 = fastq_files
out_files = fastq.filter_reads_by_length(fastq1, fastq2, quality_format,
MIN_LENGTH)
else:
out_files = [fastq.filter_single_reads_by_length(fastq_files[0],
quality_format,
MIN_LENGTH)]
return out_files
def remove_short_reads(fastq_files, dirs, lane_config):
"""
remove reads from a single or pair of fastq files which fall below
a length threshold (30 bases)
"""
min_length = int(lane_config["algorithm"].get("min_read_length", 20))
supplied_quality_format = _get_quality_format(lane_config)
if supplied_quality_format == "illumina":
quality_format = "fastq-illumina"
else:
quality_format = "fastq-sanger"
if is_pair(fastq_files):
fastq1, fastq2 = fastq_files
out_files = fastq.filter_reads_by_length(fastq1, fastq2,
quality_format, min_length)
else:
out_files = [
fastq.filter_single_reads_by_length(fastq_files[0], quality_format,
min_length)
]
map(os.remove, fastq_files)
return out_files
