ssv2tsv

#!/usr/bin/perl

use warnings;
use strict;
use Getopt::Long;
use fralib;
use POSIX qw(ceil floor);
use File::Path;
use File::Basename;
use Pod::Usage;

=head1 NAME

ssv2tsv

=head1 SYNOPSIS

    usage: ssv2tsv <filename>	
	
    -h help : displays this help
    	
    example: ssv2tsv pscalare.txt
    
    Replaces the space delimiters to tab delimiters in a text file.
    This is equivalent to
    
    cat pscalare.txt | tr -s '\s' '\t'
    
    Output file is named as <filename>.txt
    Reads from STDIN too.  In this case, output is STDOUT.
    
    This is appropriate for plink output but please note that there 
    are spacings on the edge of each line.  A good way to handle this
    is by using trim.
    
    e.g. cat plink.assoc | trim | ssv2tsv > plink.assoc.txt

=head1 DESCRIPTION

=cut

#option variables
my $help;
my $columnNo;
my $currentColumnNo;
my $line;
my $ssvFile;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions ('h'=>\$help) || $help || scalar(@ARGV)>1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

#STDIN redirection
if (scalar(@ARGV)==1)
{
    $ssvFile = $ARGV[0];
	open(IN, $ssvFile) || die "Cannot open $ssvFile\n";
	my ($name, $dir, $ext) = fileparse($ssvFile, '\..*');
	open(OUT, ">$name.$ext.tsv") || die "Cannot open $ssvFile\n";
}
else
{
	*IN = *STDIN;
	*OUT = *STDOUT;
}

while(<IN>)
{
	s/\r?\n?$//;

   	#detects number of columns
   	$columnNo = s/\s+/\t/g + 1 if $.==1;
  
    $currentColumnNo = s/\s+/\t/g + 1;
	
	warn "Different number of columns detected in line $." if $columnNo != $currentColumnNo;
	
    print OUT "$_\n";
}

close(IN);