Script for ChromoPainter

• Post by: EEPuckett
• December 8, 2014
• Comments off

I’m new to Perl so this may not be the most elegant script. The script converts fastPHASE output into a ChromoPainter input file. The for loop makes an input file for each scaffold for which my data maps to (in my case 284 scaffolds of the polar bear genome).

#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;
my($infile, $phasefile, $Chromofile, $constant, $i);
foreach my $chr (1..284){ #1 to 284 b/c my data maps to scaffolds that are named numerically and range from 1 to 284, non exclusive)
$constant = "0 0\n";
$infile="batch_1.scaffold".$chr.".phase.inp"; #Exported fastPHASE input file (.inp) for each scaffold from STACKS
$phasefile="Scaf".$chr."._hapguess_switch.out"; #_hapguess_switch.out is output from fastPHASE
$Chromofile="Scaf".$chr.".phase";
if (-e $infile && $phasefile) { #Using -e flag on infile and phasefile names to skip over any scaffold numbers (between 1-284) where my data does not map to; ex: no data on scaffold 100
open (INFILE, '+<', "$infile");
open (PHASEFILE, '+<', "$phasefile"); open (CHROMOFILE, '>>', "$Chromofile");
print CHROMOFILE ($constant); #Prints a 0 on the first line of the Chromofile, then moves to next line
my @infile = ;
my @phasefile = ;
print CHROMOFILE @infile[0..3]; #Prints first four lines of fastPHASE input file (num samples, num loci, loci bp position on scaffold, and a row of "S" * num loci)
print CHROMOFILE @phasefile[0..187]; #I have 94 samples (diploid); therefore, 188 haplotype lines when -Z flag used in fastPHASE. This prints all lines of the file fastPHASE output to ChromoPainter input file.
close INFILE;
close PHASEFILE;
close CHROMOFILE;
}
}