Hello friends,
I have a simple program I've written that is going through and parsing some data for me....sort of. The way I've coded it, I'm pulling out a unique part of each line by which to classify a group of lines and therefore separate them (this will make a bit more sense as you check the code I hope). This unique portion-in this case the target name (ATH1121501:244901 in the input as you'll see)of 244901-is what I am pattern matching each of the next lines against. If a line comes up that does not match this, then I want the new target name to be extracted and become the value of $target_name. All the next lines of the input file will be matched against this, etc, until the end of the file. However, this isn't occuring; $target_name does not change in the program, even though the target name in the input data does. Help??
#! C:\Perl\bin\perl
#########################################################
# probe.pl- converts affy probe set files to excel files#
# by D. Newkirk on 9/9/03                               #
#########################################################
use strict;
use warnings;

print STDOUT 'Please state the file containing the probes: ';
chomp(my $input=<STDIN>);
open (INPUT, "$input")or die "Cannot open file: $!";

print STDOUT 'Please name the output file: ';
chomp(my $output=<STDIN>);
open (OUTPUT, ">$output")or die "Cannot open file: $!";

$_=<INPUT>;

my ($target_name, %probes);
$target_name=$1 if m[:(\d{6})_]x;
#print "$target_name\n";
do {
    if ($_=~ m/$target_name/) {
        chomp(my $probe=<INPUT>);
        if ($probe=~ /^(\w{20})/) {print "$probe\n";
            push @{$probes{$target_name}}, $probe;
        }
    }
    if ($_ !=~ [$target_name]) { 
        $_= m[:(\d{6})_]x;
        $target_name=$_;
        print "$target_name\n";
    }
}until eof INPUT;

for $target_name(sort{@{probes{$b}}<=>@{probes{a}}}keys %probes) {
    print OUTPUT "$target_name, ", join(", ", sort @{$probes{$target_n
+ame}}), "\n";
}

close (INPUT);
close (OUTPUT);
exit;

_input_
>probe:ATH1-121501:244901_at:594:703;Interrogation_Position=56;Antisen
+se;TTGCTGCTATTCTATCTATTTGTGC
Times 11
>probe:ATH1121501:244902_at:522:511;Interrogation_Position=153;Antisen
+se;
GGTATTTTCCGTTTCTTCGGATGAT
Times 11

_output_
244901, AACACTTACAAATGCCACTTCTTCC, AGCAATTTGCCTACTCTTGTATCTC, AGCTGTGA
+ATTCGAACTTTTTGGTA, ATATTCCTATTATGTCAATGCCAAT, CCAACGGTGGCAGCTGCGGAATC
+CG, GAAGAATCGCAGCAATTCCCCAATC, GAAGTAGTTCCTCCGGAATCCAATG, GACTTTCAAAG
+TGACTCTCGACGGG, GAGCCTCCAGGCTATTCAGGAAGAA, GAGTCCGAGGTACTATTGCTGTAGA,
+ GATGGGTCAAGTATTTGCTTCATTG, GCAAGCTTTGTTATGCCGAAACCTA, GCGGAATCCGCTAT
+TGGGTTAGCCA, GGTATTTTCCGTTTCTTCGGATGAT, GTATTCGGGGAATCCTCCTTAATAG, GT
+CGCATCCGTTTTCAGGACGATCT, TAACTTTCCGAGTCCGAGGTACTAT, TAGCCATTTTCGTTATA
+ACTTTCCG, TCAGCTTGCGAATTTGTGGCACCGT, TGCTTCATTGGTTCCAACGGTGGCA, TTACC
+AATGGCACGCTGTGCGCCTA, TTGCTGCTATTCTATCTATTTGTGC

[download]
Everything else about the output is fine.
Thanks!!!!!!!

Bioinformatics

In reply to Why is it matching?? by bioinformatics

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