def cufflinks_assemble(data):
bam_file = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
out_dir = os.path.join(dd.get_work_dir(data), "assembly")
num_cores = dd.get_num_cores(data)
assembled_gtf = cufflinks.assemble(bam_file, ref_file, num_cores, out_dir, data)
data = dd.set_assembled_gtf(data, assembled_gtf)
return [[data]]
def cufflinks_assemble(data):
bam_file = dd.get_work_bam(data)
ref_file = dd.get_sam_ref(data)
out_dir = os.path.join(dd.get_work_dir(data), "assembly")
num_cores = dd.get_num_cores(data)
assembled_gtf = cufflinks.assemble(bam_file, ref_file, num_cores, out_dir, data)
dd.get_assembled_gtf(data).append(assembled_gtf)
return [[data]]
def cufflinks_assemble(data):
config = data["config"]
dirs = data["dirs"]
bam_file = data["work_bam"]
ref_file = data["sam_ref"]
out_dir = os.path.join(dirs["work"], "assembly")
num_cores = config["algorithm"].get("num_cores", 1)
assembled_gtf = cufflinks.assemble(bam_file, ref_file, num_cores, out_dir)
data["assembled_gtf"] = assembled_gtf
return [[data]]
def cufflinks_assemble(data):
config = data["config"]
dirs = data["dirs"]
bam_file = data["work_bam"]
ref_file = data["sam_ref"]
out_dir = os.path.join(dirs["work"], "assembly")
num_cores = config["algorithm"].get("num_cores", 1)
assembled_gtf = cufflinks.assemble(bam_file, ref_file, num_cores, out_dir,
data)
data["assembled_gtf"] = assembled_gtf
return [[data]]
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
