Hi, as was pointed out in a fashion by another monk, you have a great deal of duplication in your code. One of the great things about variables is that they are, um, variable. That is, they can hold variable values. Thus, you don't need a different variable for each piece of data you are processing. Then, once you are reusing variables, you will find that you can reuse code that processes them.

Another important technique is to use meaningful variable names, so that a reader of code, or you a week later, can understand what is going on.

So for example I might gently rewrite your code to contain something like:

...
my @infiles = @ARGV;    

for my $file ( @infiles ) {
    my ($descriptions, $sequences) = ParseFile( $file );
    
    ... # output the data here    
}

...

sub ParseFile {
    my $file = shift;

    my %descriptions = my %sequences = ();
    open (my $fh,  '<', $file)  or die "Cannot open input file $file: 
+$!\n";
    while ( my $line = <$fh> ) {
        chomp $line;
        if ( $line =~ m/^>(\S+)\s(.+)/ ) {
            $descriptions{$1} = $2;
        } else {
             $sequences{$1} = $.;
        }
    }

    return (\%descriptions, \%sequences);
}

...
[download]

Hope this helps!

for my $key (keys %File1) {
    print "Gene: $key\nDescription: $File1_D{$key}\nData: $File1{$key}
+\n";
}
[download]

Once you understand this you can trivially convert it into FASTA format using a Template or format or your own routine.

Hello FIJI42,

Regarding I want to print the hash information into two separate files in fasta format try sample of code below:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use YAML qw( DumpFile LoadFile );

my %hash = ( ';LCBO - Prolactin precursor - Bovine' => "a sample seque
+nce in FASTA format
         MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHD
+LSS
         EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPL
+YHL
         VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTK
+DED
         ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*" );

p %hash;

my $filename = 'test.txt';

DumpFile( $filename, \%hash );

my $reconstituted = LoadFile($filename);

# check it out in Data::Dumper style-
print Dumper $reconstituted;

__END__

$ perl test.pl
{
    ';LCBO - Prolactin precursor - Bovine'   "a sample sequence in FAS
+TA format
         MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHD
+LSS
         EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPL
+YHL
         VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTK
+DED
         ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*"
}
$VAR1 = {
          ';LCBO - Prolactin precursor - Bovine' => 'a sample sequence
+ in FASTA format
         MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHD
+LSS
         EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPL
+YHL
         VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTK
+DED
         ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*'
        };
$ cat test.txt 
---
';LCBO - Prolactin precursor - Bovine': |-
  a sample sequence in FASTA format
           MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYI
+HDLSS
           EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWND
+PLYHL
           VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQ
+TKDED
           ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
[download]

I do not have sample of your data to test but it should be ok.

Update: Adding sample of fasta data and output that I found here FASTA format. Play around with the hash and the data that you want to populate.

Hope this helps, BR.

Hi thanos1983,

What is p %hash;? Typo?

$ perl -c 1202669.pl

Operator or semicolon missing before %hash at 1202669.pl line 13.
Ambiguous use of % resolved as operator % at 1202669.pl line 13.
Bareword "p" not allowed while "strict subs" in use at 1202669.pl line
+ 13.
Bareword "hash" not allowed while "strict subs" in use at 1202669.pl l
+ine 13.
1202669.pl had compilation errors
[download]



The way forward always starts with a minimal test.

Hello 1nickt,

I was experimenting with Data::Printer as an alternative way.

You can use it for example like:

use Data::Printer;
p %hash;
[download]

This why you could see the printing part. Hope is more clear now. :)

Update: Sample of code that I was experimenting, see below:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Printer;

my %hash = ( ';LCBO - Prolactin precursor - Bovine' => "a sample seque
+nce in FASTA format
         MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHD
+LSS
         EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPL
+YHL
         VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTK
+DED
         ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*" );

my $filename = 'output.txt';

open(my $fh, '>', $filename)
    or die "Could not open file '$filename' $!";

p(%hash, output => $fh);

close $fh
    or warn "Could not open file '$filename' $!";

print "Done\n";

__END__

$ perl test.pl
Done
$ cat output.txt
{
    ';LCBO - Prolactin precursor - Bovine'   "a sample sequence in FAS
+TA format
         MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHD
+LSS
         EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPL
+YHL
         VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTK
+DED
         ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*"
}
[download]

BR / Thanos

Seeking for Perl wisdom...on the process of learning...not there...yet!