cfarkas

#!/usr/bin/env python

# Copyright (c) 2020, Michael Boyle
#
# MIT License
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

cfarkas

#!/bin/env perl
#Usage: mstrg_prep.pl merged.gtf > merged_prep.gtf
use strict;
my %g; # gene_id => \%ref_gene_ids (or gene_names)
my @prep; # array of [line, original_id]
while (<>) {
 s/ +$//;
 my @t=split(/\t/);
 unless (@t>8) { print $_; next }
 my ($gid)=($t[8]=~m/gene_id "(MSTRG\.\d+)"/);