#!/usr/bin/perl

use strict;
use warnings;

# to modify cleangene
# an infile (to be read in)and an outfile (to write to)
# and both should be open
my $infile = "clean.txt"; #output of batch entrez gene cleaned
open (IN, $infile) or die "can't open file: $!";

my $outfile = "genetable.txt";
open (OUT, ">$outfile") or die "can't open file: $!";

my $kegg_found = 0;
# reading one line at a time using the FILE handle
while (<IN>) {
    if (/^\d+:\s\w.+/) { # disecting the first line into locus tag and
+ name
        my $name = $_;
        $name =~ s/\[\sArabidopsis\sthaliana\s\]|\[\sArabidopsis\s|\[/
+/;
        $name =~ s/^\d+:\s//;
        my @array = split /\s+/, $name;
        my $locus_tag = $array[0];
        print OUT "$locus_tag\n \n";
        $name =~ s/^AT\w+|\w+//;
        $name =~ s/^\s//;
        print OUT "$name\n";
    }

    if (/^Function\sEvidence/) {
        print OUT "Unknown\n\n" unless $kegg_found;
        $kegg_found = 0;
        
    }
    next if /^Function\sEvidence|^Process\sEvidence|^Component\sEviden
+ce|^\d+:\s\w.+/;
    
    if (/KEGG\spathway:|\w+\d{5}\s/){ #removing "KEGG pathway" from th
+e kegg description
        my $kegg = $_;
        $kegg =~ s/^KEGG\spathway:\s//;
        $kegg =~ s/KEGG/ KEGG/g;
        $kegg =~ s/KEGG\spathway:\s//g;
        print OUT "$kegg";
        $kegg_found = 1;
    }    
    else {
        print OUT $_;
    }
}        
close OUT;
close IN;
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