in reply to Re^3: problems with flip flop
in thread problems with flip flop

Hi, thanks for your efforts! I see your point and I liked the changes of variable declarations and the stuff with the references. Unfortunately I can't use the readline Function because I got the specific task to use flags (only flags) to solve that problem. Do you have any idea for that, even when your script makes much more sense than using flags?

Replies are listed 'Best First'.
Re^5: problems with flip flop
by Neighbour (Friar) on Aug 17, 2011 at 14:58 UTC
    In that case, set the $flag-variable to 0 when you expect to read a 'gene'-line, and set it to 1 when you expect to read a 'CDS' or 'exon'-line.
    You will need to keep the @BMB-variable declared before going into the while-loop, since you need to keep the data you put in there (when $flag was 0) to be still there when you're going through the while-loop with $flag being 1.
    Note that the error-handling is not present in this version, but you can add that yourself.
    This results in the following: 
    #!/usr/bin/perl

# Task: Extract GeneID-Number and gene information

use strict;
use warnings;

my $in;
my $data;
my @array;
my $array;
my $GeneID;
my @BMB;
my $flag = 0;
my %hash;
my $hash;

# 1) open the .gff Inputfile and while reading line by line split $dat
+a at each tab and put them in the @array

open $in, '<', "Genomteil.gff" or die $!;
while ($data = <$in>) {
    @array = split (/\t/, $data);
    if ($flag == 0) {
        if ($array[2] =~ /gene/) {    #if you find the word 'gene' a t
+extbloxk follows which contains some information I want to extract an
+d put in an array)
            $flag = 1; # Set the flag. We will be expecting a 'CDS' or
+ 'exon'-line next
            @BMB = ($array[3], $array[4], $array[6]);    #the array wi
+ll be used as values for my hash later
        } ## end if ($array[2] =~ /gene/)
        if ($array[8] =~ /.*;db_xref=GeneID:(\d+)\n/) {    #if you fin
+d the word 'GeneID' extract the following number and put it in my has
+h (as key), then put the array in my hash
            $GeneID = $1;
        } ## end if ($array[8] =~ /.*;db_xref=GeneID:(\d+)\n/)
    } elsif ($flag == 1) {
        if ($array[2] =~ /CDS/) {
            push (@BMB, $array[2]);
            #put more data in my array
        } elsif ($array[2] =~ /exon/) {
            push (@BMB, $array[2]);
        }
        @{$hash{$GeneID}} = @BMB;
        $flag = 0; # Reset the flag. We will be expecting a 'gene'-lin
+e next
    }
} ## end while ($data = <$in>)

close $in;

my $BMB;
while (($GeneID, $BMB) = each %hash) {
    print "$GeneID => $BMB[0]\n";
}

    [download]
[reply]
[d/l]

      hi, thanks for that. unfortunately I have an appointment now, so I can't try your script today. But I'm looking forward to run it tomorrow morning. Thanks again, have a nice evening

[reply]

        HI, still the same problem with your script. If I print, for example,

         while (($GeneID, $BMB) = each %hash) {
    print "$GeneID => $BMB[0]\n";}

        [download]

        I still get this output: 

         
9190899 => 15576
9190898 => 15576
9191049 => 15576
9190897 => 15576
9191048 => 15576

        [download]

        all keys but the same values. I'm trying to figure it out!

        Okay, I have no idea where the problem is!

[reply]
[d/l]
[select]

In Section Seekers of Perl Wisdom