Thanks to those that helped. The code works great. Now I will practice
one honing it down to the bare essentials. Below is the final code you
all helped with.
-Thanks a million!
-Mike
>>> Begin PERL Code<<<
#! /usr/bin/perl -w
use strict;
use FileHandle;
my %organisms;
print "Enter in a list of files to be processed:\n";
# For example:
# CytB.fasta
# NADH1.fasta
# ....
chomp (my @infiles = <STDIN>);
# TODO we should make this nice later
#my @infiles = ('genetics.txt');
print "Enter in the name of the OUTFILE:\n";
chomp (my $outfile = <STDIN>);
open(OUTFILE, ">$outfile")
or die "Can't open OUTFILE: $!";
foreach my $infile (@infiles) {
my $FASTA = new FileHandle;
open ($FASTA, $infile)
or die "Can't open INFILE: $!";
# I moved this variable outside the while-loop
# in order to be able to assign the "data" in
# the nextline to the organism it belongs to
# (we're keeping track of the last start line
# that we came across here)
my $orgID;
while (defined($_ = <$FASTA>)) {
chomp;
print "\nWorking on >>$_<<\n";
# see if this line is the start of an
# organism; the thing we´re searching for
# looks like this:
# >dog
# so try to match something like
# \s* zero-to-many characters of
# optional whitespace
# > the bigger-than sign
# \w+ one-to-many (word) characters
# the parenthesis around the \w+ means that
# we want to access this value later using $1
if (/\s*>(\w+)/) {
$orgID = $1;
print "Found a new organism start line ('$orgID')\n";
}
# or just some data belonging to the last
# organism we found
else {
print "Sequence data found: $_\n";
print "Appending data to $orgID\n";
# let´s check if we´ve got data for this entry
if (exists ($organisms{$orgID})) {
# TODO append the data to the hash here
$organisms{$orgID} .= $_;
}
else {
# create a new hash entry for this data
$organisms{$orgID} = $_;
}
}
}
# do not forget to close the input file
close ($FASTA)
or die "could not close INFILE : $!";
}
# we've processed all input files...print the resulting hash
print "\n****************************************\n";
while (my ($orgID, $sequence) = each(%organisms)) {
print OUTFILE ">$orgID\n$sequence\n\n";
}
>>>END PERL CODE<<<
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