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)
bam_to_wig(sort_bam, config, config_file)
if config["algorithm"]["recalibrate"]:
log.info("Recalibrating %s with GATK" % str(sample_name))
gatk_bam = recalibrate_quality(sort_bam, fastq1, fastq2, sam_ref, 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))
variation_effects(vrn_file, genome_build, 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,
config, sample_name, config_file)
def process_sample(data):
"""Finalize processing for a sample, potentially multiplexed.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"],
data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file, effects_file = variation_effects(data["vrn_file"],
data["sam_ref"],
data["genome_build"],
data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
data["effects_file"] = effects_file
if data["config"]["algorithm"].get("transcript_assemble", False):
data["tx_file"] = assemble_transcripts(data["work_bam"],
data["sam_ref"], data["config"])
if data["sam_ref"] is not None:
logger.info("Generating summary files: %s" % str(data["name"]))
generate_align_summary(data["work_bam"], data["fastq2"] is not None,
data["sam_ref"], data["name"], data["config"],
data["dirs"])
return [[data]]
def process_sample(data):
"""Finalize processing for a sample, potentially multiplexed.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"], data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file, effects_file = variation_effects(data["vrn_file"],
data["sam_ref"],
data["genome_build"],
data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
data["effects_file"] = effects_file
if data["config"]["algorithm"].get("transcript_assemble", False):
data["tx_file"] = assemble_transcripts(data["work_bam"],
data["sam_ref"],
data["config"])
if data["sam_ref"] is not None:
logger.info("Generating summary files: %s" % str(data["name"]))
generate_align_summary(data["work_bam"], data["fastq2"] is not None,
data["sam_ref"], data["name"],
data["config"], data["dirs"])
return [[data]]
def postprocess_variants(data):
"""Provide post-processing of variant calls.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"], data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file = variation_effects(data["vrn_file"], data["sam_ref"],
data["genome_build"], data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
return [[data]]
def postprocess_variants(data):
"""Provide post-processing of variant calls.
"""
if data["config"]["algorithm"]["snpcall"]:
logger.info("Finalizing variant calls: %s" % str(data["name"]))
data["vrn_file"] = finalize_genotyper(data["vrn_file"],
data["work_bam"],
data["sam_ref"], data["config"])
logger.info("Calculating variation effects for %s" % str(data["name"]))
ann_vrn_file = variation_effects(data["vrn_file"], data["sam_ref"],
data["genome_build"], data["config"])
if ann_vrn_file:
data["vrn_file"] = ann_vrn_file
return [[data]]
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]