check_methyl.pl

#!/usr/bin/env perl
# ___UNDOCUMENTED___

use warnings;
use strict;
use Data::Dumper;
use Carp;
use Getopt::Long;
use Pod::Usage;
use version; our $VERSION = qv('0.0.1');
use feature qw( :5.10 );

use FindBin;
use lib "$FindBin::Bin/DZLab-Tools/lib";
use DZLab::Tools::RunUtils;

GetOptions(
    \%ARGV,
    'input|i=s', 'output|o=s', 'error|e=s',
    'fasta|f=s',
    _meta_options( \%ARGV ),
) and (@ARGV or $ARGV{input}) or pod2usage( -verbose => 1 );

my ( $INH, $OUTH, $ERRH ) = _prepare_io( \%ARGV, \@ARGV );

my $fasta = index_fasta( $ARGV{fasta} );

while ( <$INH> ) {

    my ($chr, $start) = (split /\t/, $_)[0, 3];

    my $nucleotide = substr $fasta->{$chr}, $start - 1, 1;

    die $nucleotide unless $nucleotide eq 'C' or $nucleotide eq 'G';
}

sub index_fasta {
    my ($fasta_file) = @_;

    my %fasta;
    my $header;

    open my $FASTA, '<', $fasta_file or die "Can't open $fasta_file: $!";
    while (<$FASTA>) {
        chomp;

        if (/^\s*>(\S+)/) {
            $header = lc $1;
        }
        else {
            $fasta{$header} .= $_;
        }

    }
    close $FASTA or die "Can't close $fasta_file: $!";

    return \%fasta;
}

__DATA__


__END__

=head1 NAME

 APerlyName.pl - Short description

=head1 SYNOPSIS

 APerlyName.pl [OPTION]... [[-i] FILE]...

=head1 DESCRIPTION

 Long description

=head1 OPTIONS

 -i, --input       <string>     input filename                           (STDIN)
 -o, --output      <string>     output filename                          (STDOUT)
 -e, --error       <string>     output error filename                    (STDERR)
     --verbose     [integer]    print increasingly verbose error messages
     --quiet                    print no diagnostic or warning messages
     --version                  print current version
     --license                  print author's contact and copyright information
     --help                     print this information
     --manual                   print the plain old documentation page

=head1 VERSION

 0.0.1

=head1 REVISION

 $Rev: $:
 $Author: $:
 $Date: $:
 $HeadURL: $:
 $Id: $:

=head1 AUTHOR

 Pedro Silva <pedros@berkeley.edu/>
 Zilberman Lab <http://dzlab.pmb.berkeley.edu/>
 Plant and Microbial Biology Department
 College of Natural Resources
 University of California, Berkeley

=head1 COPYRIGHT

 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with this program. If not, see <http://www.gnu.org/licenses/>.

=cut