Reading a protein sequence from file

tejaminnu's Avatar, Join Date: May 2011
Newbie Member
Hi,

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;

exit;



ERROR:

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

{\rtf1\ansi\ansicpg1252\cocoartf1038\cocoasubrtf35 0


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
Regards
Teja
0
sreek's Avatar, Join Date: Nov 2010
Go4Expert Member
Hi,

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.
0
sreek's Avatar, Join Date: Nov 2010
Go4Expert 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.