def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
lane_name = "%s_%s_%s" % (lane_items[0]['lane'], fc_date, fc_name)
logger.info("Preparing %s" % lane_name)
full_fastq1, full_fastq2 = get_fastq_files(
dirs["fastq"],
dirs["work"],
lane_items[0],
fc_name,
dirs=dirs,
config=shared.update_config_w_custom(config, lane_items[0]))
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items,
lane_name, dirs, config)
out = []
for item in lane_items:
config = shared.update_config_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if item["barcode_id"] in bc_files:
for fastq1, fastq2, lane_ext in _prep_fastq_files(
item, bc_files, dirs, config):
cur_lane_name = lane_name
cur_lane_desc = item["description"]
if item.get("name", "") and config["algorithm"].get(
"include_short_name", True):
cur_lane_desc = "%s : %s" % (item["name"], cur_lane_desc)
if item["barcode_id"] is not None:
cur_lane_name += "_%s" % (item["barcode_id"])
if lane_ext is not None:
cur_lane_name += "_s{0}".format(lane_ext)
out.append((fastq1, fastq2, item, cur_lane_name, cur_lane_desc,
dirs, config))
return out
def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
lane_name = "%s_%s_%s" % (lane_items[0]['lane'], fc_date, fc_name)
logger.info("Demulitplexing %s" % lane_name)
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"], dirs["work"],
lane_items[0], fc_name, config=config)
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items,
lane_name, dirs, config)
out = []
for item in lane_items:
config = _update_config_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if bc_files.has_key(item["barcode_id"]):
for fastq1, fastq2, lane_ext in _prep_fastq_files(item, bc_files, dirs, config):
cur_lane_name = lane_name
cur_lane_desc = item["description"]
if item.get("name", "") and config["algorithm"].get("include_short_name", True):
cur_lane_desc = "%s : %s" % (item["name"], cur_lane_desc)
if item["barcode_id"] is not None:
cur_lane_name += "_%s" % (item["barcode_id"])
if lane_ext is not None:
cur_lane_name += "_s{0}".format(lane_ext)
if config["algorithm"].get("trim_reads", False):
trim_info = brun_trim_fastq([x for x in [fastq1, fastq2] if x is not None],
dirs, config)
fastq1 = trim_info[0]
if fastq2 is not None:
fastq2 = trim_info[1]
out.append((fastq1, fastq2, item, cur_lane_name, cur_lane_desc,
dirs, config))
return out
def process_lane(info, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
config = _update_config_w_custom(config, info)
sample_name = info.get("description", "")
if (config["algorithm"].get("include_short_name", True) and
info.get("name", "")):
sample_name = "%s---%s" % (info.get("name", ""), sample_name)
genome_build = info.get("genome_build", None)
multiplex = info.get("multiplex", None)
log.info("Processing sample: %s; lane %s; reference genome %s; " \
"researcher %s; analysis method %s" %
(sample_name, info["lane"], genome_build,
info.get("researcher", ""), info.get("analysis", "")))
if multiplex:
log.debug("Sample %s multiplexed as: %s" % (sample_name, multiplex))
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"], info, fc_name)
lane_name = "%s_%s_%s" % (info['lane'], fc_date, fc_name)
lane_items = []
for mname, msample, fastq1, fastq2 in split_by_barcode(full_fastq1,
full_fastq2, multiplex, lane_name, dirs, config):
mlane_name = "%s_%s" % (lane_name, mname) if mname else lane_name
if msample is None:
msample = "%s---%s" % (sample_name, mname)
lane_items.append((fastq1, fastq2, genome_build, mlane_name, msample,
dirs, config))
return lane_items
def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
lane_name = "%s_%s_%s" % (lane_items[0]['lane'], fc_date, fc_name)
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"], dirs["work"],
lane_items[0], fc_name, config=config)
# Filter phiX
custom_config = _update_config_w_custom(config, lane_items[0])
if custom_config["algorithm"].get("filter_phix", False):
# If we are starting from demultiplexed material, we will skip a lane-wise screening
# Screening will be performed on a sample basis
if custom_config["algorithm"].get("demultiplexed", False):
logger.warn("Will not filter phix lane-wise on already demultiplexed files. " \
"You will have to specify genomes_filter_out option for each sample")
else:
logger.info("Filtering phiX from %s" % lane_name)
info = {"genomes_filter_out": "spiked_phix", "description": lane_name}
processed = remove_contaminants(full_fastq1, full_fastq2, info, lane_name, info["description"], dirs, custom_config)
(full_fastq1, full_fastq2, _, lane_name) = processed[0][0:4]
logger.info("Demultiplexing %s" % lane_name)
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items,
lane_name, dirs, config)
out = []
for item in lane_items:
config = _update_config_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if item["barcode_id"] in bc_files:
fastq1, fastq2 = bc_files[item["barcode_id"]]
cur_lane_name = lane_name
cur_lane_desc = item["description"]
if item.get("name", "") and config["algorithm"].get("include_short_name", True):
cur_lane_desc = "%s : %s" % (item["name"], cur_lane_desc)
if item["barcode_id"] is not None:
cur_lane_name += "_%s" % (item["barcode_id"])
if config["algorithm"].get("trim_reads", False):
trim_info = brun_trim_fastq([x for x in [fastq1, fastq2] if x is not None],
dirs, config)
fastq1 = trim_info[0]
if fastq2 is not None:
fastq2 = trim_info[1]
out.append((fastq1, fastq2, item, cur_lane_name, cur_lane_desc,
dirs, config))
return out
def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
lane_name = "%s_%s_%s" % (lane_items[0]["lane"], fc_date, fc_name)
log.debug("Demulitplexing %s" % lane_name)
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"], lane_items[0], fc_name)
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items, lane_name, dirs, config)
out = []
for item in lane_items:
config = _update_config_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if bc_files.has_key(item["barcode_id"]):
fastq1, fastq2 = bc_files[item["barcode_id"]]
cur_lane_name = lane_name
cur_lane_desc = item["description"]
if item.get("name", ""):
cur_lane_desc = "%s : %s" % (item["name"], cur_lane_desc)
if item["barcode_id"] is not None:
cur_lane_name += "_%s" % (item["barcode_id"])
out.append((fastq1, fastq2, item, cur_lane_name, cur_lane_desc, dirs, config))
return out
def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"],
dirs["work"], lane_items[0], fc_name, dirs=dirs,
config=config_utils.update_w_custom(config, lane_items[0]))
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items,
lane_items[0]["rgnames"]["lane"], dirs, config)
out = []
for item in lane_items:
logger.debug("Preparing %s" % item["rgnames"]["lane"])
config = config_utils.update_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if item["barcode_id"] in bc_files:
for fastq1, fastq2, lane_ext in _prep_fastq_files(item, bc_files, dirs, config):
if item["barcode_id"] is not None:
item["rgnames"]["lane"] += "_%s" % (item["barcode_id"])
if lane_ext is not None:
item["rgnames"]["lane"] += "_s{0}".format(lane_ext)
out.append((fastq1, fastq2, item, dirs, config))
return out
def process_lane(lane_items, fc_name, fc_date, dirs, config):
"""Prepare lanes, potentially splitting based on barcodes.
"""
lane_name = "%s_%s_%s" % (lane_items[0]['lane'], fc_date, fc_name)
full_fastq1, full_fastq2 = get_fastq_files(dirs["fastq"],
dirs["work"],
lane_items[0],
fc_name,
config=config)
# Filter phiX
custom_config = _update_config_w_custom(config, lane_items[0])
if custom_config["algorithm"].get("filter_phix", False):
# If we are starting from demultiplexed material, we will skip a lane-wise screening
# Screening will be performed on a sample basis
if custom_config["algorithm"].get("demultiplexed", False):
logger.warn("Will not filter phix lane-wise on already demultiplexed files. " \
"You will have to specify genomes_filter_out option for each sample")
else:
logger.info("Filtering phiX from %s" % lane_name)
info = {
"genomes_filter_out": "spiked_phix",
"description": lane_name
}
processed = remove_contaminants(full_fastq1, full_fastq2, info,
lane_name, info["description"],
dirs, custom_config)
(full_fastq1, full_fastq2, _, lane_name) = processed[0][0:4]
logger.info("Demultiplexing %s" % lane_name)
bc_files = split_by_barcode(full_fastq1, full_fastq2, lane_items,
lane_name, dirs, config)
out = []
for item in lane_items:
config = _update_config_w_custom(config, item)
# Can specify all barcodes but might not have actual sequences
# Would be nice to have a good way to check this is okay here.
if item["barcode_id"] in bc_files:
fastq1, fastq2 = bc_files[item["barcode_id"]]
cur_lane_name = lane_name
cur_lane_desc = item["description"]
if item.get("name", "") and config["algorithm"].get(
"include_short_name", True):
cur_lane_desc = "%s : %s" % (item["name"], cur_lane_desc)
if item["barcode_id"] is not None:
cur_lane_name += "_%s" % (item["barcode_id"])
if config["algorithm"].get("trim_reads", False):
trim_info = brun_trim_fastq(
[x for x in [fastq1, fastq2] if x is not None], dirs,
config)
fastq1 = trim_info[0]
if fastq2 is not None:
fastq2 = trim_info[1]
out.append((fastq1, fastq2, item, cur_lane_name, cur_lane_desc,
dirs, config))
return out
