Hi dear all! I have a problem with using the flip-flop. First I need to show you the text file (gff.file) which contains the data I want to work with:

NC_014171.1 RefSeq gene 14311 14425 . + . ID=NC_014171.1:rrs_1;locus_t
+ag=BMB171_C5091;db_xref=GeneID:9190898
NC_014171.1 RefSeq exon 14311 14425 . + . ID=NC_014171.1:rrs_1:unknown
+_transcript_1;Parent=NC_014171.1:rrs_1;gbkey=rRNA;locus_tag=BMB171_C5
+091 ;product=5S ribosomal RNA;db_xref=GeneID:9190898;exon_number=1

NC_014171.1 RefSeq gene 14459 15460 . - . locus_tag=BMB171_C0007;db_xr
+ef=GeneID:9190899
NC_014171.1 RefSeq CDS 14462 15460 . - 0 locus_tag=BMB171_C0007;transl
+_table=11;product=hypothetical protein;protein_id=YP_003662545.1;db_x
+ref=GI:296500845;db_xref=GeneID:9190899;exon_number=1

[download]

The empty line above doesn't exist in the text file. I just wanted to show you which lines belong together. Now, here is my script:

# Task: Extract GeneID-Number and gene information

#!/usr/bin/perl
use strict;
use warnings;

my $in;
my $data;
my @array;
my $array;
my $GeneID;
my @BMB;
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 ($array [2] =~/gene/){ #if you find the word 'gene' a textbloxk fol
+lows which contains some information I want to extract and put in an 
+array)

$flag = 1;

@BMB = ($array[3], $array[4], $array[6]); #the array will be used as v
+alues for my hash later


}



if ($array[2] =~/CDS/){

push (@BMB, $array[2]);

#put more data in my array

} elsif ($array[2] =~/exon/){

push (@BMB, $array[2]);

}


if ($array[8] =~ /.*;db_xref=GeneID:(\d+)\n/) { #if you find the word 
+'GeneID' extract the following number and put it in my hash (as key),
+ then put the array in my hash

$GeneID = $1;

@{$hash {$GeneID}} = @BMB;

}



if ($array [8]=~ /.*;exon_number=1/){ #if you find the word 'exon numb
+er', then the textblock is over
$flag = 0;

}

}

close $in;

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

[download]

Okay, the script works but I do have more than one textblock I want to work with.For each time in the loop the new data which are putted in my array overwrite the data from the last time. So in the end, I only have information of the last textblock in my array. My supervisor told me what she wants me to do: I should think about something like a 'flag' which recognizes, that a new textblock appears which contains new data I want to store in the array. Interestingly I don't have a problem with the keys. I do have each key in my output (but each key has the same values). The problem is, I don't know how such a 'flag' could look like - so I don't know for what I have to search in literature etc. I hope you understand my problem, my english isn't the best. Has anybody an idea to help? Best wishes

In reply to problems with flip flop by bio25

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