HW3

ath_chr1.pl

#!bin/perl
use strict;

# number of 3'UTR
open(IN, "grep -c 'three_prime' ath_chr1.gff | ") || die $!;
while(my $count = <IN>) {
open(my $outfh => "UTR.txt") || die $!;
print $outfh "$count\n";
}

# number of introns
my $fh = "ath_chr1.gff";
open(my $fh => 'ath_chr1.gff') || die $!;
while (<$fh>) {
chomp;

my @cols = split("\t",$_), $fh;
    my ( $l, $r ) = ( 0, 0 );
    for ( $l = 0 ; $l <= $#cols ;) {
        for ( $r = 0 ; $r <= $#cols ;) {
open(my $outfh => "intron.txt") || die $!;        
 print $outfh "$cols[$l] - $cols[$r], "\n"";
}
}
}

# avg length of genes
#still working on this one

cat UTR.txt intron.txt length.txt > ath_chr1_stats.txt