| 1 |
#!/bin/tcsh -f |
| 2 |
if ("x"$1 == "x-h") then |
| 3 |
echo "Usage: gtfcount [-g][-c][-l] <gtfile>" |
| 4 |
echo " Show the count of distinct transcript names.\n Options:" |
| 5 |
echo " -g : report distinct gene names count (gene_id attribute)" |
| 6 |
echo " -c : report transcript counts per reference sequence" |
| 7 |
echo " -l : list transcripts" |
| 8 |
echo " -f : report transcript counts per gene_id" |
| 9 |
exit 1 |
| 10 |
endif |
| 11 |
if ("x"$1 == "x-g") then |
| 12 |
shift |
| 13 |
perl -ne 'print "$1\n" if m/gene_id "([^"]+)/' $1 | sort -u | wc -l |
| 14 |
exit |
| 15 |
endif |
| 16 |
if ("x"$1 == "x-l") then |
| 17 |
shift |
| 18 |
perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u |
| 19 |
exit |
| 20 |
endif |
| 21 |
if ("x"$1 == "x-c") then |
| 22 |
shift |
| 23 |
perl -ne '@t=split(/\t/);print "$t[0]\t$1\n" if $t[8]=~m/transcript_id "([^"]+)/' $1 | sort -u | cut -f1 | uniq -c |
| 24 |
exit |
| 25 |
endif |
| 26 |
if ("x"$1 == "x-f") then |
| 27 |
shift |
| 28 |
perl -ne '($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 |
| 29 |
exit |
| 30 |
endif |
| 31 |
perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u | wc -l |
