#!/usr/bin/perl

use strict; use warnings;

my $PATH = "/Users/MCN/Documents/UConn/Genomes/Yersinia/Submission_Preparation/ENA_Validate/";

my $log = $PATH . "Log.txt";

# Pre-execution safety checking

if ( ! @ARGV) {

die "Script aborted: Must supply an input fasta as a script variable!";

}

open (INFILE, "$ARGV[0]") or die "Cannot open input file\n";

my $thisline; # The current line that we're at in the file

my $line_number = 0; # Lets us know what line we're at

my $badlines = 0;

while ($thisline = <INFILE>) { # Begin reading in the input file, line by line

$thisline =~ s/\s+$//; # Remove any trailing whitespaces and end of line characters

$line_number++; # Increment line number by 1

my $length = length($thisline);

if ($thisline =~ /[A-Z]+[0-9]+/) {

if ($thisline =~ /locus_tag=/) {

next;

}

elsif ($thisline =~ /note=/) {

next;

}

$badlines++;

print "$line_number: $thisline\n";

}

}

print "\nThere are $badlines line left still to fix :(\n"