appending ref_gene_id (or gene_name) info to MSTRG gene_ids in stringtie --merge output

mstrg_prep.py

#!/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)