#!/usr/bin/perl -w -i.orig

################################################

# ReplaceMany.pl
# Version 1

# Son Nguyen
# UCSC Programming for Bioinformatics II
# October 10, 2003

################################################

# ReplaceMany will replace abc with xyz in all .fasta files
#
# Robert D. Cormia
# October 10, 2003
#
# After working on replace_many.pl on my own, I received
# substantial help from Son Nguyen on this program.
#
# Write a Perl program called 'ReplaceMany' that will replace
# all occurrences # of 'abc' to 'xyz' in all the data files
# whose names end in '.fasta'.
#

use strict;


# read file

my $updateFileName = 'tempfasta';
my $line;

#
# open file, if open fails call die
#

foreach my $fileToRead (<*.fasta>)
{
  #get the filename and start replacing its content
  print "$fileToRead\n";

  open(INFILE, "$fileToRead") or
        die("open() failed for 'fname'\nReason: $!\n\n");
  open(OUTFILE, ">$updateFileName") or
        die("open() failed for 'fname'\nReason: $!\n\n");

  while ($line = <INFILE>)
  {
    $line =~ s/abc/xyz/g;
    print OUTFILE $line;
  }

  close(INFILE);
  close(OUTFILE);

  rename("$updateFileName","$fileToRead") || die "can't rename file";

}


print "Replaced abc by xyz.  Content of all .fasta files within the current running directory has been changed!";

__END__

Replaced abc by xyz.  Content of all .fasta files within the current running directory has been changed!