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Reading a protein sequence from file

Discussion in 'Perl' started by tejaminnu, May 30, 2011.

  1. tejaminnu

    tejaminnu New Member


    I have been trying to execute this program and i am getting an error. Kindly help me.

    #!usr/bin/perl -w

    # The filename of the file which contains the protein sequence
    $proteinfilename = '/users/sukeerthiteja/desktop/perl/NM_021964fragment.pep';

    # First open the file and associate a filehandle with it. for readability purpose lets use the filehandle PROTEINFILE.
    open(PROTEINFILE, $proteinfilename);

    # Now we do the actual reading of the protein sequence data from the file,by using < > to get
    # input from the filehandle. We store the data into variable $protein
    $protein = <PROTEINFILE>;

    #now that we got our data we can close the file
    close PROTEINFILE;

    #Print the protein onto the screen
    print "Here is the protein:\n\n";

    print $protein;



    sukeerthi-tejas-macbook-pro:desktop sukeerthiteja$ perl 1.pl
    Here is the protein:


    I am not able to print the protein content on the screen.
    Is this a problem with me of first properly putting things in my directory.

    Email: tejaminnu@gmail.com

    Thank you
  2. sreek

    sreek New Member


    Your file "/users/sukeerthiteja/desktop/perl/NM_021964fragment.pep" contains only one value or line? Because if it contains more than one line of information , your assigning of

    "$protein = <PROTEINFILE>;"

    will not work. It will only he last line of your file. IF thats the case you have to read the filehandle through a while loop.
  3. sreek

    sreek New Member

    Sorry for a spelling mistake. My last sentence should be read like this :

    It will only print the last line of your file. If that is the case you have to read the filehandle through a while loop.

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