post-processing of StringTie merge output to append ref_gene_id info to the MSTRG gene_id

mstrg_prep.pl

#!/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)=($t[8]=~m/gene_id "(MSTRG\.\d+)"/);
 if ($gid) {
   push(@prep, [$_, $gid]);
   my ($rn)=($t[8]=~m/ref_gene_id "([^"]+)/);
   #or for gene_name:
   #my ($rn)=($t[8]=~m/gene_name "([^"]+)/);
   if ($rn) {
     my $h=$g{$gid};
     if ($h) { $h->{$rn}=1 }
     else { $g{$gid}= { $rn=>1 } }
   }
 }
 else { print $_ }
}
my ($prevgid, $gadd);
foreach my $d (@prep) {
 my ($line, $gid)=@$d;
 if ($prevgid ne $gid) {
    $prevgid=$gid;
    $gadd='';
    if (my $gd=$g{$gid}) {
      $gadd='|'.join('|', (sort(keys(%$gd))))
    }
 }
 $line=~s/gene_id "MSTRG\.\d+/gene_id "$gid$gadd/ if $gadd;
 print $line;
}

I might be missing something but won't the last if statement always fail because the $gd hash reference hasn't been created yet?

You mean the one at line 30? if (my $gd=$g{$gid})? (even though that's not the last if statement ;)). If so, no. In that test expression the reference is being created, assigned to $g{$gid} and then it is actually tested.

Oh I gotcha. I read that as a double ==. Mark L. Farman Professor, Department of Plant Pathology 225 Plant Science Building<x-apple-data-detectors://1/1> 1405 Veteran's Dr.<x-apple-data-detectors://1/1> University of Kentucky<x-apple-data-detectors://1/1> Lexington, KY 40546 USA<x-apple-data-detectors://1/1> tel: (859) 218-0728<tel:(859)%20218-0728> fax: (859) 323-1961<tel:(859)%20323-1961> Sent from my iPhone On Aug 2, 2021, at 9:53 AM, Geo Pertea ***@***.***> wrote:  CAUTION: External Sender @gpertea commented on this gist.

…

________________________________ You mean the one at line 30? if (my $gd=$g{$gid})? (even though that's not the last if statement ;)). If so, no. In that test expression the reference is being created, assigned to $g{$gid} and then it is actually tested. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgist.github.com%2Fb83f1b32435e166afa92a2d388527f4b%23gistcomment-3840249&data=04%7C01%7Cmark.farman%40uky.edu%7C5b5a9d7ee355429a3fee08d955bce092%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637635091974156230%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=l%2BFyjr6xSeDKF7dnRafavhh6DR95UdG8p8X9mJECEf0%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAYUUDOA6AW2DVLAESHADKTT22PMXANCNFSM5BI5RBRQ&data=04%7C01%7Cmark.farman%40uky.edu%7C5b5a9d7ee355429a3fee08d955bce092%7C2b30530b69b64457b818481cb53d42ae%7C0%7C0%7C637635091974166236%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=DOb30Lw%2Btbe1wE9WXLYotZ36KsL%2BDmJMkCU84TqvqOs%3D&reserved=0>.