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): 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