def run_kallisto_singlecell(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", 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 = kallisto_singlecell(fq1, kallisto_dir, gtf_file, fasta_file, data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
def run_kallisto_singlecell(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", 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 = kallisto_singlecell(fq1, kallisto_dir, gtf_file, fasta_file, data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
def run_kallisto_rnaseq(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", 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
assert fq2, ("We don't support kallisto for single-end reads and fusion "
"calling with pizzly does not accept single end reads.")
out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file, data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
def run_kallisto_rnaseq(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", 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
assert fq2, ("bcbio doesn't support kallisto for single-end reads, we can "
"add support for this if you open up an issue about it here: "
"https://github.com/bcbio/bcbio-nextgen/issues")
out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file, data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
def run_kallisto_rnaseq(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", samplename)
gtf_file = dd.get_transcriptome_gtf(data, default=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
assert fq2, ("We don't support kallisto for single-end reads and fusion "
"calling with pizzly does not accept single end reads.")
out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file,
data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
def run_kallisto_rnaseq(data):
samplename = dd.get_sample_name(data)
work_dir = dd.get_work_dir(data)
kallisto_dir = os.path.join(work_dir, "kallisto", 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
assert fq2, ("bcbio doesn't support kallisto for single-end reads, we can "
"add support for this if you open up an issue about it here: "
"https://github.com/chapmanb/bcbio-nextgen/issues")
out_file = kallisto_rnaseq(fq1, fq2, kallisto_dir, gtf_file, fasta_file, data)
data = dd.set_kallisto_quant(data, out_file)
return [[data]]
