You dont explain very well what you want. What do you mean by gene for instance

I think this does most of what you are after. but it is a memory hog. 

use strict; use warnings; 

my @genes; 
my %genes_found; 
my $genesFn = "Genes_list.txt";
open my $genesFh, "<", $genesFn or die "could not open genes file hand
+le $!\n";
while (my $gene=<$genesFh>) {
    chomp $gene;
    push @genes, $gene;
    }

my $an_fn='annotation_files_path.txt'; 
open my $an,'<',$an_fn or die "cant open $an_fn $!"; 
while (my $annotationsFn =<$an>){ 
  chomp $annotationsFn ; 
  open my $gff,'<',$annotationsFn  or die "cant open $annotationsFn $!
+"; 
  while (my $gff_line =<$gff>){ 
    chomp $gff_line; 
    for my $gene (@genes) { 
      if (index($gff_line,$gene) != -1) { 
        $genes_found{$gene}{$annotationsFn}=[] unless (defined ($genes
+_found{$gene}{$annotationsFn})); 
        push @{$genes_found{$gene}{$annotationsFn}},$gff_line; 
        } # index 
      } # gene
    } # gff_line 
  close $gff; 
  } # my $annotationsFn

close $an; 

for my $gene (@genes) { 
  unless ($genes_found{$gene}) { print "gene $gene not found \n";} 
  else { 
    my $resultsFn='result-gene-'.$gene.'.txt'; 
    open my $resultsFh, ">", $resultsFn or die "could not open handle 
+to results file $!\n";
    for my $annotationsFn (sort keys (%{$genes_found{$gene}})) { 
      print $resultsFh 'from:'.$annotationsFn."\n"; 
      for my $found (@{$genes_found{$gene}{$annotationsFn}}){ 
        print $resultsFh 'line:'.$found."\n"; 
        } # found 
      } #$annotationsFn 
    close $resultsFh;
    } # else 
  } # gene

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In reply to Re: perl script for extracting gene information from gff file by huck
in thread perl script for extracting gene information from gff file by Anonymous Monk

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