So, I am not sure which part you need help with. Here is how you break each line into 'parts' 
foreach my $line (@lines){
  @lineFields = split( ' ', $line );
}

[download]
that gives us an array of the words in the line, so it has the following parts:

$lineFields[0] is the Operon name
$lineFields[1] is 1 2 3...
$lineFields[2] is forward or reverse
$lineFileds[3] is the 'genes'

Then we parse the 'genes' in a similar manner 

#get the comman separated list of genes
my @geneItems = split( ',', $lineFileds[3] );
#now look at each one in turn
foreach my @item ( @geneItems ){
   #just continue processing and store in hash
}

[download]
That is not the complete answer, but it will get you where you want to go.
"Never take yourself too seriously, because everyone knows that fat birds dont fly" -FLC

In reply to Re: Getting data from a file (Operons and Genes). by scmason
in thread Getting data from a file (Operons and Genes). by chrisantha

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