def run_salmon_reads(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
salmon_dir = os.path.join(work_dir, "salmon", samplename)
gtf_file = dd.get_gtf_file(data)
files = dd.get_input_sequence_files(data)
if len(files) == 2:
fq1, fq2 = files
else:
fq1, fq2 = files[0], None
assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file
fasta_file = dd.get_ref_file(data)
assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file
out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data)
data = dd.set_sailfish(data, out_file)
data = dd.set_sailfish_dir(data, salmon_dir)
return [[data]]
def run_salmon_reads(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
salmon_dir = os.path.join(work_dir, "salmon", samplename)
gtf_file = dd.get_gtf_file(data)
files = dd.get_input_sequence_files(data)
if len(files) == 2:
fq1, fq2 = files
else:
fq1, fq2 = files[0], None
assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file
fasta_file = dd.get_ref_file(data)
assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file
out_file = salmon_quant_reads(fq1, fq2, salmon_dir, gtf_file, fasta_file, data)
data = dd.set_sailfish(data, out_file)
data = dd.set_sailfish_dir(data, salmon_dir)
return [[data]]
def run_sailfish(data):
samplename = dd.get_sample_name(data)
files = dd.get_input_sequence_files(data)
work_dir = dd.get_work_dir(data)
if len(files) == 2:
fq1, fq2 = files
else:
fq1, fq2 = files[0], None
if not fastq.is_fastq(fq1):
return [[data]]
sailfish_dir = os.path.join(work_dir, "sailfish", samplename)
gtf_file = dd.get_gtf_file(data)
assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file
fasta_file = dd.get_ref_file(data)
assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file
stranded = dd.get_strandedness(data).lower()
out_file = sailfish(fq1, fq2, sailfish_dir, gtf_file, fasta_file, stranded, data)
data = dd.set_sailfish(data, out_file)
data = dd.set_sailfish_dir(data, sailfish_dir)
return [[data]]
def run_sailfish(data):
samplename = dd.get_sample_name(data)
files = dd.get_input_sequence_files(data)
work_dir = dd.get_work_dir(data)
if len(files) == 2:
fq1, fq2 = files
else:
fq1, fq2 = files[0], None
if not fastq.is_fastq(fq1):
return [[data]]
sailfish_dir = os.path.join(work_dir, "sailfish", samplename)
gtf_file = dd.get_gtf_file(data)
assert file_exists(gtf_file), "%s was not found, exiting." % gtf_file
fasta_file = dd.get_ref_file(data)
assert file_exists(fasta_file), "%s was not found, exiting." % fasta_file
stranded = dd.get_strandedness(data).lower()
out_file = sailfish(fq1, fq2, sailfish_dir, gtf_file, fasta_file, stranded, data)
data = dd.set_sailfish(data, out_file)
data = dd.set_sailfish_dir(data, sailfish_dir)
return [[data]]