def combine_express(samples, combined): """Combine tpm, effective counts and fpkm from express results""" if not combined: return None to_combine = [ dd.get_express_counts(x) for x in dd.sample_data_iterator(samples) if dd.get_express_counts(x) ] gtf_file = dd.get_gtf_file(samples[0][0]) isoform_to_gene_file = os.path.join(os.path.dirname(combined), "isoform_to_gene.txt") isoform_to_gene_file = express.isoform_to_gene_name( gtf_file, isoform_to_gene_file, dd.sample_data_iterator(samples).next()) if len(to_combine) > 0: eff_counts_combined_file = os.path.splitext( combined)[0] + ".isoform.express_counts" eff_counts_combined = count.combine_count_files( to_combine, eff_counts_combined_file, ext=".counts") to_combine = [ dd.get_express_tpm(x) for x in dd.sample_data_iterator(samples) if dd.get_express_tpm(x) ] tpm_counts_combined_file = os.path.splitext( combined)[0] + ".isoform.express_tpm" tpm_counts_combined = count.combine_count_files( to_combine, tpm_counts_combined_file) to_combine = [ dd.get_express_fpkm(x) for x in dd.sample_data_iterator(samples) if dd.get_express_fpkm(x) ] fpkm_counts_combined_file = os.path.splitext( combined)[0] + ".isoform.express_fpkm" fpkm_counts_combined = count.combine_count_files( to_combine, fpkm_counts_combined_file, ext=".fpkm") return { 'counts': eff_counts_combined, 'tpm': tpm_counts_combined, 'fpkm': fpkm_counts_combined, 'isoform_to_gene': isoform_to_gene_file } return {}
def combine_express(samples, combined): """Combine tpm, effective counts and fpkm from express results""" to_combine = [dd.get_express_counts(x) for x in dd.sample_data_iterator(samples) if dd.get_express_counts(x)] gtf_file = dd.get_gtf_file(samples[0][0]) isoform_to_gene_file = os.path.join(os.path.dirname(combined), "isoform_to_gene.txt") isoform_to_gene_file = express.isoform_to_gene_name(gtf_file, isoform_to_gene_file) if len(to_combine) > 0: eff_counts_combined_file = os.path.splitext(combined)[0] + ".isoform.express_counts" eff_counts_combined = count.combine_count_files(to_combine, eff_counts_combined_file) to_combine = [dd.get_express_tpm(x) for x in dd.sample_data_iterator(samples) if dd.get_express_tpm(x)] tpm_counts_combined_file = os.path.splitext(combined)[0] + ".isoform.express_tpm" tpm_counts_combined = count.combine_count_files(to_combine, tpm_counts_combined_file) to_combine = [dd.get_express_fpkm(x) for x in dd.sample_data_iterator(samples) if dd.get_express_fpkm(x)] fpkm_counts_combined_file = os.path.splitext(combined)[0] + ".isoform.express_fpkm" fpkm_counts_combined = count.combine_count_files(to_combine, fpkm_counts_combined_file) return {'counts': eff_counts_combined, 'tpm': tpm_counts_combined, 'fpkm': fpkm_counts_combined, 'isoform_to_gene': isoform_to_gene_file} return {}