#! /usr/bin/perl

# Copyright 2013, 2015, 2019 Regents of The University of Michigan.

# This file is part of geo-omics-scripts.

# Geo-omics-scripts 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.

# Geo-omics-scripts 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 Geo-omics-scripts. If not, see <https://www.gnu.org/licenses/>.

# USAGE: perl getMyContigs.pl <CoverageOutputFromReadCoverage Script> <Your Contig Shortlist file> <OUTPUT.list>

use strict;

my $readCov=$ARGV[0];

my $list=$ARGV[1];

my $OUT=$ARGV[2];

die "Incorrect number of files input\nUSAGE: perl getMyContigs.pl <CoverageOutputFromReadCoverage Script> <Your Contig Shortlist file> <OUTPUT.list>" if (scalar(@ARGV) != 3);

open(LIST, $list)|| $!;

my %LIST;

while(my $line=<LIST>){

chomp;

next unless $line;

next if $line=~ /^#/;

# NODE_14_length_2679_cov_8.406121

my @headerParts=split(/\_/, $line);

$LIST{$headerParts[1]}++;

}

close LIST;

my %READS;

open(READ, $readCov)|| $!;

while(my $line=<READ>){

next if $line=~ /^#/;

chomp $line;

next unless $line;

my ($contigName, $size, @reads)=split(/\t/, $line);

next unless $LIST{$contigName};

foreach my $r(@reads){

$READS{$r}++;

}

}

close READ;

undef %LIST;

print "Total # Reads Mapped to this bin:".keys(%READS)."\n";

open(OUT, ">".$OUT)|| die $!;

foreach my $r(keys %READS){

print OUT $r."\n";

}

close OUT;