***Philipp wrote:***
- open the first file
- search for the beginning of an "organism" (say: ">cat"), read everything
after this point
- search in your hash if you already stored data of this organism
- if yes, append your new sequence to the already existing data
- if no, create a new key in the hash
- repeat this until you run out of "organisms"
- repeat the whole procedure until you run out of files
***end***
#!/usr/bin/perl # This script will take separate FASTA files and combine the "like" # data into one FASTA file. #
use warnings; use strict;
my %organisms (
"$orgID" => "$orgSeq",
);print "Enter in a list of files to be processed:\n";
# For example: # CytB.fasta # NADH1.fasta # ....
chomp (my @infiles = <STDIN>);
foreach $infile (@infiles) {
open (FASTA, $infile)
or die "Can't open INFILE: $!";$/='>'; #Set input operator
while (FASTA) {
chomp; # Some regular expression match here?
# something that will set, say... ">cat"
# as the key "$orgID", something similar
# to below?
# and then set the sequence as the value
# "$orgSeq" like below? # Do not know if or where to put the following,
# but something like: if (exists $organisms{$orgID}) {
# somehow concatenate "like" data
# from the different files
}# print the final Hash to an outfile?
}
.... yeah, I'm lost. :-)
-Mike
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