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#!/usr/bin/perl
# Katharina J. Hoff, May 5th 2011
#
# PASA sometimes has problems with weird fasta headers.
# This script converts the headers of a fasta file to "simple headers" without any special characters or spaces
my $USAGE="simpleFastaHeaders.pl in.fa prefix out.fa mapping.txt\n\n in.fa - the file to be reformatted\n prefix - the prefix of every new header, e.g. contig\n out.fa - the reformatted fasta file\n mapping.txt - a tab-separated mapping table (newName \t oldName)\n\n";
if(@ARGV!=4){print STDERR $USAGE; exit -1}
my $inFile = $ARGV[0];
my $prefix = $ARGV[1];
my $outFa = $ARGV[2];
my $mapping = $ARGV[3];
my $preC = 1; # counter for prefix
open(INFILE, "<", $inFile) or die("Could not open file $inFile!\n");
open(OUTFA, ">", $outFa) or die ("Could not open file $outFa!\n");
open(MAP, ">", $mapping) or die ("Could not open file $mapping!\n");
while(<INFILE>){
if($_=~m/^>/){
chomp;
print MAP ">".$prefix.$preC."\t$_\n";
print OUTFA ">".$prefix.$preC."\n";
$preC = $preC+1;
}else{
print OUTFA $_;
}
}
close(INFILE) or die("Could not close file $inFile!\n");
close(OUTFA) or die("Could not close file $outFa!\n");
close(MAP) or die("Could not close file $mapping!\n");
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