def cufflinks_merge(*samples):
to_merge = filter_missing([dd.get_assembled_gtf(data) for data in
dd.sample_data_iterator(samples)])
data = samples[0][0]
bam_file = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
gtf_file = dd.get_gtf_file(data)
out_dir = os.path.join(dd.get_work_dir(data), "assembly")
num_cores = dd.get_num_cores(data)
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores, samples[0][0])
for data in dd.sample_data_iterator(samples):
dd.set_assembled_gtf(data, merged_gtf)
return samples
def cufflinks_merge(*samples):
to_merge = filter_missing(flatten([dd.get_assembled_gtf(data) for data in
dd.sample_data_iterator(samples)]))
data = samples[0][0]
ref_file = dd.get_sam_ref(data)
gtf_file = dd.get_gtf_file(data)
num_cores = dd.get_num_cores(data)
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores,
samples[0][0])
updated_samples = []
for data in dd.sample_data_iterator(samples):
data = dd.set_merged_gtf(data, merged_gtf)
updated_samples.append([data])
return updated_samples
def cufflinks_merge(*samples):
to_merge = filter_missing(flatten([dd.get_assembled_gtf(data) for data in
dd.sample_data_iterator(samples)]))
data = samples[0][0]
ref_file = dd.get_sam_ref(data)
gtf_file = dd.get_gtf_file(data)
num_cores = dd.get_num_cores(data)
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores,
samples[0][0])
updated_samples = []
for data in dd.sample_data_iterator(samples):
data = dd.set_merged_gtf(data, merged_gtf)
updated_samples.append([data])
return updated_samples
def cufflinks_merge(*samples):
rnaseq_resources = samples[0][0]["genome_resources"]["rnaseq"]
config = samples[0][0]["config"]
dirs = samples[0][0]["dirs"]
bam_file = samples[0][0]["work_bam"]
ref_file = samples[0][0]["sam_ref"]
gtf_file = rnaseq_resources.get("transcripts", None)
out_dir = os.path.join(dirs["work"], "assembly")
num_cores = config["algorithm"].get("num_cores", 1)
to_merge = [data[0]["assembled_gtf"] for data in samples if
"assembled_gtf" in data[0]]
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores)
for data in samples:
data[0]['assembled_gtf'] = merged_gtf
return samples
def cufflinks_merge(*samples):
to_merge = filter_missing([dd.get_assembled_gtf(data) for data in
dd.sample_data_iterator(samples)])
data = samples[0][0]
bam_file = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
gtf_file = dd.get_gtf_file(data)
out_dir = os.path.join(dd.get_work_dir(data), "assembly")
num_cores = dd.get_num_cores(data)
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores, samples[0][0])
updated_samples = []
for data in dd.sample_data_iterator(samples):
data = dd.set_assembled_gtf(data, merged_gtf)
updated_samples.append([data])
return updated_samples
def cufflinks_merge(*samples):
rnaseq_resources = samples[0][0]["genome_resources"]["rnaseq"]
config = samples[0][0]["config"]
dirs = samples[0][0]["dirs"]
bam_file = samples[0][0]["work_bam"]
ref_file = samples[0][0]["sam_ref"]
gtf_file = rnaseq_resources.get("transcripts", None)
out_dir = os.path.join(dirs["work"], "assembly")
num_cores = config["algorithm"].get("num_cores", 1)
to_merge = [
data[0]["assembled_gtf"] for data in samples
if "assembled_gtf" in data[0]
]
merged_gtf = cufflinks.merge(to_merge, ref_file, gtf_file, num_cores,
samples[0][0])
for data in samples:
data[0]['assembled_gtf'] = merged_gtf
return samples
def cufflinks_assemble(*samples):
rnaseq_resources = samples[0][0]["genome_resources"]["rnaseq"]
config = samples[0][0]["config"]
dirs = samples[0][0]["dirs"]
gtf_file = rnaseq_resources.get("transcripts", None)
ref_file = samples[0][0]["sam_ref"]
bam_files = [data[0]['work_bam'] for data in samples]
num_cores = config["algorithm"].get("num_cores", 1)
out_dir = os.path.join(dirs["work"], "assembly")
safe_makedir(out_dir)
merged_file = os.path.join(out_dir, "merged.bam")
merged_file = bam.merge(bam_files, merged_file, config)
assembly_dir = cufflinks.assemble(merged_file, ref_file, gtf_file,
num_cores, out_dir)
transcripts = [os.path.join(assembly_dir, "assembly", "transcripts.gtf")]
merged_gtf = cufflinks.merge(transcripts, ref_file, gtf_file, num_cores)
for data in samples:
data[0]['assembly'] = assembly_dir
return samples
