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sort2candi.pl
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sort2candi.pl
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#!/usr/bin/env perl
##################################
# Classify tags from sort files
##################################
use warnings;
use strict;
sub help{
print STDERR <<EOF;
Usage: perl sort2candi_v1.pl infile
Note: the rules to select sRNA
1. at IGR or AS.
2. >=100 bp from 5' ORF and >=60 bp from 3' ORF.
EOF
}
my $infile = shift;
if(!defined $infile){
&help();
exit(1);
}
open F,$infile or die;
my ($total_input, $total_sRNA, $total_AS, $candi_AS, $total_IGR, $candi_IGR, $total_UTR, $total_IM, $total_PM, $total_other) = (0,0,0,0,0,0,0,0,0,0);
my ($print_sRNA, $print_UTR, $print_IM, $print_other) = ("", "", "", "");
while(<F>){
$total_input ++;
my $line = $_;
chomp;
my @lines = split /\t/;
my ($gap_1, $gap_2, $dir, $des) = ($lines[7], $lines[9], $lines[10], $lines[11]);
if($des =~ /AS|AM/i){
$total_AS ++;
if(($dir eq '/+/+/+/' && $gap_1 >= 100 && $gap_2 >= 60) ||
($dir eq '/-/-/-/' && $gap_1 >= 60 && $gap_2 >= 100) ||
($dir eq '/+/+/-/' && $gap_1 >= 100) ||
($dir eq '/-/-/+/' && $gap_1 >= 60) ||
($dir eq '/-/+/+/' && $gap_2 >= 60) ||
($dir eq '/+/-/-/' && $gap_2 >= 100) ||
($dir eq '/+/-/+/') ||
($dir eq '/-/+/-/')){
$print_sRNA .= $line;
$candi_AS ++;
}else{
$print_UTR .= $line;
$total_UTR ++;
}
}elsif($des =~ /IGR/i){
$total_IGR ++;
if(($dir eq '/+/+/+/' && $gap_1 >= 100 && $gap_2 >= 60) ||
($dir eq '/-/-/-/' && $gap_1 >= 60 && $gap_2 >= 100) ||
($dir eq '/+/+/-/' && $gap_1 >= 100) ||
($dir eq '/-/-/+/' && $gap_1 >= 60) ||
($dir eq '/-/+/+/' && $gap_2 >= 60) ||
($dir eq '/+/-/-/' && $gap_2 >= 100) ||
($dir eq '/+/-/+/') ||
($dir eq '/-/+/-/')){
$print_sRNA .= $line;
$candi_IGR ++;
}else{
$print_UTR .= $line;
$total_UTR ++;
}
}elsif($des =~ /IM/i){
$print_IM .= $line;
$total_IM ++;
}elsif($des =~ /PM|CM/i){
$print_UTR .= $line;
$total_PM ++;
}else{
$print_other .= $line;
$total_other ++;
}
}
close F;
$infile =~ /(.*)\.txt/;
my $head_name = (defined $1)?$1:"out";
open OUT,">$head_name\_sRNA\.txt" or die; print OUT $print_sRNA; close OUT;
open OUT,">$head_name\_UTR\.txt" or die; print OUT $print_UTR; close OUT;
open OUT,">$head_name\_IM\.txt" or die; print OUT $print_IM; close OUT;
open OUT,">$head_name\_OTR\.txt" or die; print OUT $print_other; close OUT;
$total_sRNA = $candi_AS + $candi_IGR;
my $stat = "Stat the total sRNAs:
ID\tTotal\tOutput
AS\:\t$total_AS\t$candi_AS
IGR\:\t$total_IGR\t$candi_IGR
PM\:\t$total_PM\t0
IM\:\t$total_IM\t0
Other\:\t$total_other\t0
Sum\:\t$total_input\t$total_sRNA
UTR\:\t$total_UTR\t0";
open OUT,">$head_name\.stat" or die;
print OUT $stat . "\n";
close OUT;