def salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, data, index):
samplename = dd.get_sample_name(data)
quant_dir = salmon_dir
safe_makedir(salmon_dir)
out_file = os.path.join(quant_dir, "quant.sf")
if file_exists(out_file):
return out_file
num_cores = dd.get_num_cores(data)
strandedness = dd.get_strandedness(data).lower()
salmon = config_utils.get_program("salmon", dd.get_config(data))
libtype = sailfish._libtype_string(fq1, fq2, strandedness)
num_cores = dd.get_num_cores(data)
resources = config_utils.get_resources("salmon", dd.get_config(data))
params = ""
bias = True
if resources.get("options") is not None:
params = " ".join([str(x) for x in resources.get("options", [])])
if any("--noLengthCorrection" in x
for x in resources.get("options", [])):
bias = False
cmd = ("{salmon} quant {libtype} -i {index} -p {num_cores} "
" --validateMappings "
"-o {tx_out_dir} {params} ")
if bias:
cmd += " --seqBias "
fq1_cmd = "<(cat {fq1})" if not is_gzipped(fq1) else "<(gzip -cd {fq1})"
fq1_cmd = fq1_cmd.format(fq1=fq1)
if not fq2:
cmd += " -r {fq1_cmd} "
else:
if bias:
cmd += " --gcBias "
fq2_cmd = "<(cat {fq2})" if not is_gzipped(
fq2) else "<(gzip -cd {fq2})"
fq2_cmd = fq2_cmd.format(fq2=fq2)
cmd += " -1 {fq1_cmd} -2 {fq2_cmd} "
# skip --useVBOpt for now, it can cause segfaults
cmd += "--numBootstraps 30 "
with file_transaction(data, quant_dir) as tx_out_dir:
message = ("Quantifying transcripts in %s and %s with Salmon." %
(fq1, fq2))
do.run(cmd.format(**locals()), message, None)
sailfish.sleuthify_sailfish(tx_out_dir)
return out_file
def salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, ref_file, data):
samplename = dd.get_sample_name(data)
quant_dir = os.path.join(salmon_dir, "quant")
safe_makedir(salmon_dir)
out_file = os.path.join(quant_dir, "quant.sf")
if file_exists(out_file):
return out_file
num_cores = dd.get_num_cores(data)
strandedness = dd.get_strandedness(data).lower()
salmon = config_utils.get_program("salmon", dd.get_config(data))
libtype = sailfish._libtype_string(fq1, fq2, strandedness)
num_cores = dd.get_num_cores(data)
index = salmon_index(gtf_file, ref_file, data, os.path.dirname(salmon_dir))
resources = config_utils.get_resources("salmon", dd.get_config(data))
params = ""
if resources.get("options") is not None:
params = " ".join([str(x) for x in resources.get("options", [])])
cmd = ("{salmon} quant {libtype} -i {index} -p {num_cores} "
" --seqBias "
"-o {tx_out_dir} {params} ")
fq1_cmd = "<(cat {fq1})" if not is_gzipped(fq1) else "<(gzip -cd {fq1})"
fq1_cmd = fq1_cmd.format(fq1=fq1)
if not fq2:
cmd += " -r {fq1_cmd} "
else:
cmd += " --gcBias "
fq2_cmd = "<(cat {fq2})" if not is_gzipped(fq2) else "<(gzip -cd {fq2})"
fq2_cmd = fq2_cmd.format(fq2=fq2)
cmd += " -1 {fq1_cmd} -2 {fq2_cmd} "
# skip --useVBOpt for now, it can cause segfaults
cmd += "--numBootstraps 30 "
with file_transaction(data, quant_dir) as tx_out_dir:
message = ("Quantifying transcripts in %s and %s with Salmon."
%(fq1, fq2))
do.run(cmd.format(**locals()), message, None)
sailfish.sleuthify_sailfish(tx_out_dir)
return out_file
