reading file in Perl (input)

[mama12]

Hallo all,

Can anybody here tell me what I the problem of what I am messing to read in put file

I appreciate any help

regards

use strict;
use warnings;
use BeginPerlBioinfo; # sub get_file_data+for extract_sequence_from_fasta_data in 1
# Initialize variables
my @file_data = ( );
my $dna = '';
my $revcom = '';
my $protein = '';

print "name of the DNA file: ";

chomp (@file_data = <STDIN>);

# Read in the contents of the file "anything"
@file_data = get_file_data("file_data");

# Extract the sequence data from the contents of the file "file_data"
$dna = extract_sequence_from_fasta_data(@file_data);

# Translate the DNA to protein in six reading frames
# and print the protein in lines 70 characters long
print "\n -------Reading Frame 1--------\n\n";
$protein = translate_frame($dna, 1);
print_sequence($protein, 70);

print "\n -------Reading Frame 2--------\n\n";
$protein = translate_frame($dna, 2);
print_sequence($protein, 70);

print "\n -------Reading Frame 3--------\n\n";
$protein = translate_frame($dna, 3);
print_sequence($protein, 70);

# Calculate reverse complement
$revcom = revcom($dna);

print "\n -------Reading Frame 4--------\n\n";
$protein = translate_frame($revcom, 1);
print_sequence($protein, 70);

print "\n -------Reading Frame 5--------\n\n";
$protein = translate_frame($revcom, 2);
print_sequence($protein, 70);

print "\n -------Reading Frame 6--------\n\n";
$protein = translate_frame($revcom, 3);
print_sequence($protein, 70);##

 

[TrojanWarBlade]

Try changing

# Read in the contents of the file "anything"
@file_data = get_file_data("file_data");

to

# Read in the contents of the file "anything"
@file_data = get_file_data("[red]$[/red]file_data");

And next time, please use code tags, you have been asked to do that before. If you're not sure how, click on "Process TGML" at the bottom of your window.


Trojan.