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)
(_, sam_ref) = get_genome_ref(genome_build, config["algorithm"]["aligner"],
dirs["galaxy"])
fastq1, fastq2 = combine_fastq_files(fastq_files, dirs["work"])
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"]:
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):
tx_file = assemble_transcripts(sort_bam, sam_ref, config)
if sam_ref is not None:
log.info("Generating summary files: %s" % str(sample_name))
generate_align_summary(sort_bam, fastq2 is not None, sam_ref,
sample_name, config, dirs)
bam_to_wig(sort_bam, config, config_file)
return [sample_name, fastq_files, info, sort_bam, gatk_bam, vrn_file,
effects_file]
def recalibrate_sample(data):
"""Recalibrate quality values from aligned sample BAM file.
"""
logger.info("Recalibrating %s with GATK" % str(data["name"]))
if data["config"]["algorithm"]["recalibrate"]:
recal_bam = recalibrate_quality(
data["work_bam"], data["fastq1"], data["fastq2"], data["sam_ref"], data["dirs"], data["config"]
)
save_diskspace(data["work_bam"], "Recalibrated to %s" % recal_bam, data["config"])
data["work_bam"] = recal_bam
return [[data]]
def recalibrate_sample(data):
"""Recalibrate quality values from aligned sample BAM file.
"""
logger.info("Recalibrating %s with GATK" % str(data["name"]))
if data["config"]["algorithm"]["recalibrate"]:
recal_bam = recalibrate_quality(data["work_bam"], data["fastq1"],
data["fastq2"], data["sam_ref"],
data["dirs"], data["config"])
save_diskspace(data["work_bam"], "Recalibrated to %s" % recal_bam,
data["config"])
data["work_bam"] = recal_bam
return [[data]]
