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