def screen_sample_contaminants(data):
"""Screen the sample fastq files for contaminants
"""
if data["config"]["algorithm"]["screen_contaminants"]:
logger.info("Screening for contaminants on sample %s with genome %s" \
% (str(data["name"]), str(data["genome_build"])))
screen_for_contamination(data["fastq1"], data["fastq2"],
data["config"])
def screen_sample_contaminants(data):
"""Screen the sample fastq files for contaminants
"""
if data["config"]["algorithm"]["screen_contaminants"]:
logger.info("Screening for contaminants on sample %s with genome %s" \
% (str(data["name"]), str(data["genome_build"])))
screen_for_contamination(data["fastq1"],
data["fastq2"],
data["config"])
def process_sample(sample_name, fastq_files, info, bam_files, dirs, config, config_file):
"""Finalize processing for a sample, potentially multiplexed.
"""
config = _update_config_w_custom(config, info)
genome_build = info.get("genome_build", None)
fastq1, fastq2 = combine_fastq_files(fastq_files, dirs["work"])
if config["algorithm"]["screen_contaminants"]:
log.info("Screening for contaminants on sample %s with genome %s" % (str(sample_name), str(genome_build)))
screen_for_contamination(fastq1, fastq2, config)
# _filter_out_genomes(data)
(_, sam_ref) = get_genome_ref(genome_build, config["algorithm"]["aligner"], dirs["galaxy"])
log.info("Combining and preparing wig file %s" % str(sample_name))
sort_bam = merge_bam_files(bam_files, dirs["work"], config)
(gatk_bam, vrn_file, effects_file) = ("", "", "")
if config["algorithm"]["recalibrate"] and os.path.exists(sort_bam):
log.info("Recalibrating %s with GATK" % str(sample_name))
gatk_bam = recalibrate_quality(sort_bam, fastq1, fastq2, sam_ref, dirs, config)
if config["algorithm"]["snpcall"]:
log.info("SNP genotyping %s with GATK" % str(sample_name))
vrn_file = run_genotyper(gatk_bam, sam_ref, config)
log.info("Calculating variation effects for %s" % str(sample_name))
effects_file = variation_effects(vrn_file, genome_build, config)
if config["algorithm"].get("transcript_assemble", False) and os.path.exists(sort_bam):
tx_file = assemble_transcripts(sort_bam, sam_ref, config)
if sam_ref is not None and os.path.exists(sort_bam):
log.info("Generating summary files: %s" % str(sample_name))
generate_align_summary(sort_bam, fastq2 is not None, sam_ref, sample_name, config, dirs)
if os.path.exists(sort_bam):
bam_to_wig(sort_bam, config, config_file)
return [sample_name, fastq_files, info, sort_bam, gatk_bam, vrn_file, effects_file]