Dear all,

I am quite new to Perl scripting and I am trying to solve the following:

Given a list of mutlifasta file (file.txt): 

>JJ57
MKIKLVTVGDAKEEYLIQGINEYLKRLNSYAKRETIEVPDEKAPEKLSDAEMLQVKEKEGEYVFVLAI
NGKQLSSEEFSKEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ22
MDQNGASGSHPNRASTRKGAHARERGATVSAMSANRSNIIDEMAKICEADRQTFAIARRTRNESQ
FFGFRTASNKAIEITEAMEKRGAMFLTQSKATDQLNGWQPSDEPDKTSAESEPWFRGKQLSSEEFS
KEIFQTGISGKSNLTFTTCFSLGLSDSVLQRIMKGEPYHKL
>JJ41
MWKTVAPIFAAIFAVGLCGTFRTNTRKGEPTTKCFVFVHDTKARIYQCTFKTWSCPWLNNIVSAQF
QFVTGANYKIVVKLVGELFTETALFNWSSPTTIFTGLGTLITADKTLDCDSNML

[download]

Given a user input (i.e. JJ22) as argument, I want to check if the input is present in the file.txt and count all the motifs MT.KA (M or T, any letter (.) followed by K or A) in the JJ22 sequence.

I tried (unsuccessfully) the following code: 

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

if(!open(MY_HANDLE, "file.txt")){
    die "Cannot open the file\n";
    }
@content = <MY_HANDLE>;
close(MY_HANDLE);

print("Type the input ID: ");    
my $id = <STDIN>;
chomp($id);
 
foreach $row(@content){
  chomp($row);
     if (@id=$row =~ /([MT].[KA]+)/g)  {
     $numID=scalar(@id);
     print(“@id,$numID\n”);
     }

[download]

Thank you a lot for your help

In reply to Find a sequence in a multifasta files and motifs by rebkirl

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