0_get_cp_reads.pl

#!/usr/bin/perl 

# Script that fishes chloroplast reads from whole-genome read sets

#Carlos P Cantalapiedra (1), Ruben Sancho (1,2), Bruno Contreras Moreira (1,3)
#1) Estacion Experimental de Aula Dei-CSIC, Zaragoza, Spain
#2) Escuela Politecnica Superior de Huesca, U.Zaragoza, Spain
#3) Fundacion ARAID, Zaragoza, Spain

use strict;
use FindBin '$Bin';

my $DUKEXE = "'$Bin'".'/bin/duk/duk';

#my $refcpFASTA = $Bin.'/poaceae.fna';
# contains several cps from Poaceae species:
#>NC_015820 Acidosasa purpurea
#>NC_008591 Agrostis stolonifera
#...


if(!$ARGV[0] || !-d $ARGV[0] || !$ARGV[2])
{ 
  die "# usage: $_ <folder with all-read files> <output folder with cp-read files> <FASTA file with related cp genomes>\n"; 
}

my ($inpDIR,$outDIR,$refcpFASTA) = (@ARGV);

mkdir($outDIR) if(!-d $outDIR);

opendir(READS,$inpDIR);
my @readfiles = grep {!/^\./} grep {/.fastq/ || /.fq/} readdir(READS);
closedir(READS); 

foreach my $readf (@readfiles)
{ 
  print "# fishing cp reads from $inpDIR/$readf ...\n";
  system("$DUKEXE -k 24 -c 2 -m $outDIR/cp-$readf -o $outDIR/cp-$readf.duk.log $refcpFASTA $inpDIR/$readf");
  system("gzip $outDIR/cp-$readf");
}