Perl Script Modification

Can you post statistics.pl?

Hi Jesper,

Sorry, I thought I had attached it.
It should be attached to this reply.

Thanks again,
Stephen.
statistics.txt

I think that this might do it.  You need the "-final" file generated as input to your counters but I've added a line to remove it when it's done being used.


#!/usr/bin/perl -w
use strict;

my $counter_in = 0;
my $counter_out = 0;

open (COUNTERIN, "<$ENV{TMP}/$ENV{PARASITE}-in");
while (my $line = <COUNTERIN>) {
        if ($line =~ /^>/) {
                chomp $line;
                $counter_in++;
        }
}
close (COUNTERIN);

open (COUNTEROUT, "<$ENV{TMP}/$ENV{PARASITE}-out");
while (my $line = <COUNTEROUT>) {
        if ($line =~ /^>/) {
                chomp $line;
                $counter_out++;
        }
}
close (COUNTEROUT);

my $total_proteins = $counter_in + $counter_out;

open (STATISTICS, ">>$ENV{CANDIDATES}/Results");

my %whole_proteins;
my $mmcandidates = 0;
open (FINAL, "<$ENV{CANDIDATES}/$ENV{PARASITE}-$ENV{HOST}-final");
while (my $line = <FINAL>) {
        chomp $line;
        if ($line =~ /^(.+)-AA:\d+/) {
                $mmcandidates++;
                $whole_proteins{$1} = 1;
        }
}
close FINAL;
unlink("<$ENV{CANDIDATES}/$ENV{PARASITE}-$ENV{HOST}-final");

print STATISTICS "Molecular mimicry candidate 14-mers\t$mmcandidates\n";
close STATISTICS;

Hi Jesper,

Thanks for getting back to me.
You're almost there. I've run the script and it still produces three files:

1. Results
2. a "final" file (B_burgdorferi-H_sapiens-final)
3. a "endfile" file (B_burgdorferi-H_sapiens-endfile)

(see attached picture)

I only need the Results file, the other two files shouldn't be generated (I'm trying to save data space as I'll be running this script 1000 times).

The Results file is almost right.
The file contains:

"Molecular mimicry candidate 14-mers      23"

I wanted just the number "23" to be in the file, without the "Molecular mimicry candidate 14-mers" statement beforehand. Is this possible?

What I'm trying to achieve is so, that if I run the same script 1000 times, 1000 result numbers will append to the same results file.

Hope this makes sense.

Thanks,

Stephen.
Results.jpg

Those two files that are being left may be from another script.  

If all of the scripts are in the same directory,

     grep final *
     grep endfile *

Please post any other scripts that reference these file names.