Hello everyone, I am writing a script where I have to take multi fasta file as input if I am using open() then its giveing me correct result, but if file name is not given in open() function then ask for user input. Can anyone please help me with user input. I am attaching my code

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

my $FILE;

open (my $out, ">output.txt");
if (open $FILE, "<", 'chr.fa')
{
}
else
{
    print "Enter file name:\t";
    $FILE=<STDIN>;
}

local $/ = ">";
my $count = 0;


while (<$FILE>) 
{
    chomp;
    if ( $_ =~ /^(.*?)$(.*)$/ms) 
    {
        my $header = $1;
         my $seq = $2;
         $seq =~ s/\s//g; 
        while ( $seq  =~ /([AAGC)/g) 
        {
             print $out $1, "\n";
             $count = $count +1;
        }
    }
}
print $out "$count sequences were found\n";

[download]

In reply to if user provide input file use that in open() function istead by Uzma Shaikh

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.