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appending ref_gene_id (or gene_name) info to MSTRG gene_ids in stringtie --merge output
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#!/bin/env python3 | |
#Usage: mstrg_prep.py merged.gtf > merged_prep.gtf | |
import re, fileinput | |
g={} #gene_id => {ref_gene_ids} | |
prep=[] #array of [line, mstrg_id] | |
for line in fileinput.input(): | |
line=line.rstrip() | |
t=line.split('\t') | |
if len(t)<9: | |
print(line) | |
continue | |
mgid=re.search('gene_id "(MSTRG\.\d+)"', t[8]) | |
if mgid: | |
gid=mgid.group(1) | |
prep.append([line, gid]) | |
mrn = re.search('ref_gene_id "([^"]+)', t[8]) | |
#or if you want gene_name: | |
#mrn = re.search('gene_name "([^"]+)', t[8]) | |
if mrn: | |
rn = mrn.group(1) | |
h=g.get(gid) | |
if h: h.add(rn) | |
else: g[gid]={ rn } | |
else: | |
print(line) | |
prevgid, gadd='', '' | |
for [line, gid] in prep: | |
if prevgid!=gid: | |
gadd='' | |
h=g.get(gid) | |
if h: | |
gadd='|'+'|'.join(sorted(g[gid])) | |
if len(gadd)>0: | |
line=re.sub('gene_id "MSTRG\.\d+', | |
'gene_id "'+gid+gadd, line) | |
print(line) |
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