pick_columns_into_fasta

#!/usr/bin/perl

#This file is designed to pull specific columns from a spreadsheet and put them into a new file in fasta format which can be read by BLAT.
#import the Tie::File module which allows a file to be read one line at a time
use Tie::File;
use Fcntl;
use strict;
use warnings;

 
#define variables (an array and then all columns in the spreadsheet)
my (@primers,$primers);
my $Gene;
my $Exon;
my $Chromosomes;
my $Primername;
my $Newname;
my $Primerseq;
my $PCRcond;
my $Modification;
my $Ampsize;
my $Stock;
my $Tray;
my $Gridref;
my $SNPCheck;
my $datesnpcheck;
my $SNPdbbuild;
my $SNP;

# use tie to take each line of the file and enter it into the array primers 
tie @primers, 'Tie::File', "/home/aled/Documents/primerdb/ACTA.csv";
#specify the fasta file for the output
open (MYFILE, '>>/home/aled/Documents/primerdb/primersequences.fa');

# for each element ($primers) of the array (@primers) split it on the comma into these named elements. Then print selected columns into the file in a fasta format.
foreach $primers (@primers) {
	my @s = split(/,/, $primers);
	($Gene,$Exon,$Chromosomes,$Primername,$Newname,$Primerseq,$PCRcond,$Modification,$Ampsize,$Stock,$Tray,$Gridref,$SNPCheck,$datesnpcheck,$SNPdbbuild,$SNP) = @s;
	print MYFILE "> $Primername \n $Primerseq \n";
	} untie @primers;