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 {}
