Creating a gene version of the Kallisto Gene Matrix: Perl

Question

[VenGeno]

Hi, I am getting the following error when I use the perl script available at rnabio.org tutorial

Could not identify gene id from trans id: Soltu.Cru.S183680.1

This is the relvent part of the script

#Build a map of transcript to gene IDs
my %trans;
my $gtf_fh = IO::File->new($gtf_file, 'r');
while (my $gtf_line = $gtf_fh->getline) {
  chomp($gtf_line);
  my @gtf_entry = split("\t", $gtf_line);
  next unless $gtf_entry[2] eq 'transcript';
  my $g_id = '';
  my $t_id = '';
  if ($gtf_entry[8] =~ /gene_id\s+\"(\w+)\"/){
    $g_id = $1;
  }
  if ($gtf_entry[8] =~ /transcript_id\s+\"(\w+)\"/){
    $t_id = $1;
  }
  die "\n\nCould not identify gene and transcript id in GTF transcript line:\n$gtf_line\n\n" unless ($g_id && $t_id);
  $trans{$t_id}{g_id} = $g_id;
}
$gtf_fh->close;

The related entry in my GTF file appears as follows;

scaffold11494   MSU_Castle_Russet_v2.0  mRNA    8589    9215    .   +   .   gene_id "Soltu.Cru.S183680"; transcript_id "Soltu.Cru.S183680.1"; ID "Soltu.Cru.S183680.1"; Name "Soltu.Cru.S183680.1"; Parent "Soltu.Cru.S183680";

Can someone help me with this?

Answer 1

[JC]

the problem is the RegEx used, as \wmatches only alfanumeric and "_", your gene ids contains ".", just change /gene_id\s+\"(\w+)\"/ as /gene_id\s+\"(.+?)\"/ and /transcript_id\s+\"(\w+)\"/ to /transcript_id\s+\"(.+?)\"/

[VenGeno]

Hi JC , Thank you for the answer.