gtfcount

#!/bin/bash
if [[ "x"$1 == "x-h" ]]; then
 echo "Usage: gtfcount [-g][-c][-l] <gtfile>"
 echo "  Show the count of distinct transcript names.\n  Options:"
 echo " -l  : list transcripts (unique transcript_ids)"
 echo " -g  : report distinct gene names count (gene_id attribute)"
 echo " -gl : list distinct gene names (gene_id attribute)"
 echo " -C  : list coding transcripts (=having CDS features)"
 echo " -r  : report transcript counts per reference sequence"
 echo " -rg : report transcript counts per reference sequence"
 echo " -f  : report transcript counts per gene_id"
 echo " -T  : list StringTie transcripts and their TPM"
 exit 1
fi

a=""
if [[ $1 =~ ^-.+ ]]; then
 a="${1:1}" #remove first character (the dash)
 shift
fi
if [[ -z "$a" ]]; then
  perl -ne 'if(m/transcript_id "([^"]+)/){ $_=$1;chomp;print "$_\n" if (++$n{$_})==1}' $1 | wc -l
  exit 0
fi

case $a in
 l)
   perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/ && (++$n{$1})==1' $1 
   ;;
 T)
   perl -ne 'next unless m/\ttranscript\t/;($t,$m)=((m/transcript_id\s+"([^"]+)/),(m/TPM\s+"([^"]+)/));print "$t\t$m\n"' $1
   ;;
 g)
   perl -ne 'print "$1\n" if m/gene_id "([^"]+)/ && (++$n{$1})==1' $1 | wc -l
   ;;
 gl)
   perl -ne 'print "$1\n" if m/gene_id "([^"]+)/ && (++$n{$1})==1' $1
   ;;
 C)
   perl -aF'\t' -ne 'if (($F[2] eq "CDS") && $F[8]=~m/\btranscript_id "([^"]+)/){$_=$1;chomp;print "$_\n" if(++$n{$_}==1) }' $1
   ;;
 r)
   perl -aF'\t' -ne 'print "$F[0]\t$1\n" if $F[8]=~m/transcript_id\s+"([^"]+)/' $1 | sort -u | cut -f1 | uniq -c
   ;;
 rg)
   perl -aF'\t' -ne 'print "$F[0]\t$1\n" if $F[8]=~m/gene_id\s+"([^"]+)/' $1 | sort -u | cut -f1 | uniq -c
   ;;
 f)
   perl -ne '($g)=(m/gene_id\s+"([^"]+)/); ($t)=(m/transcript_id\s+"([^"]+)/); print "$g\t$t\n" if $g && $t' $1 | sort -u | cut -f1 | uniq -c
   ;;
 *)
   show_usage
   echo "Error: -$a option not recognized!"
   exit 1
   ;;
esac