***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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