| 1 |
#!/bin/tcsh -f |
| 2 |
if ("x"$1 == "x-h") then |
| 3 |
echo "Usage: gffcount [-g] <gff3_file>" |
| 4 |
echo " Show the count of distinct mRNA names." |
| 5 |
echo " use -g option to count distinct gene names only (Name attribute)" |
| 6 |
exit 1 |
| 7 |
endif |
| 8 |
if ("x"$1 == "x-g") then |
| 9 |
shift |
| 10 |
perl -ne 'chomp;@t=split(/\t/);print "$1\n" if $t[2]=~m/gene$/ && m/ID=([^;]+)/' $1 | sort -u | wc -l |
| 11 |
exit |
| 12 |
endif |
| 13 |
|
| 14 |
if ("x"$1 == "x-l") then |
| 15 |
shift |
| 16 |
perl -ne 'chomp;@t=split(/\t/);print "$1\n" if ($t[2]!~m/(?:exon|CDS|gene)$/) && m/ID=([^;]+)/' $1 | sort -u |
| 17 |
exit |
| 18 |
endif |
| 19 |
|
| 20 |
perl -ne 'chomp;@t=split(/\t/);print "$1\n" if ($t[2]!~m/(?:exon|CDS|gene)$/) && m/ID=([^;]+)/' $1 | sort -u | wc -l |
