Nathan has found your problem, but see below for more suggestions on your code:
On 11/12/2013 02:15 AM, Alaba, Oluwafemi (IITA) wrote:
*Dear ALL,*
I created a file named NM021964fragment.pep (using text editor) but I
could not read that particular file.
*Here is the script I used:*
#!/usr/bin/perl -w
Remove the ' -w' above and add the following two lines to get extra error
checking that will lead you towards better Perl programming habits
#!/usr/bin/perl
use strict;
use warnings;
#Reading protein sequence from a file
The filename of the file containing the protein sequence data
$proteinfilename = "NM021964fragment.pep";
#First we have to 'open' the file and associate it a 'filehandle' with
it. We choose the filehandle
#PROTEINFILE for readability.
open(PROTEINFILE, $proteinfilename);
PROTEINFILE is known as a 'bareword filehandle' and it has some
limitations. Better to use a filehandle variable. The '<' indicates that
you are opening the file for reading. It is the default but using it tells
someone reading your code what your intentions are. You should also check
to see whether the open succeeded:
open my $PROTEINFILE, '<', $proteinfilename
or die "Failed to open protein file $proteinfilename. Reason: $!";
#now we do the actual reading of the protein sequence data from the file
by using angle bracket < and >
$protein = <PROTEINFILE>;
This will read the first line of the file including the trailing newline.
If that is what you want, fine. The 'strict' line you inserted above means
that you will have to declare variables on their first use. To remove the
trailing newline use chomp:
my $protein = <$PROTEINFILE>;
chomp $protein;
If what you wanted is to read all the lines of the file, it is customary to
use a while loop:
while ( my $protein = <$PROTEINFILE> ) {
chomp $protein;
# do something with $protein
}
close PROTEINFILE;
You should always check the return value of system calls such as close.
It's unlikely after reading but a big problem after writing:
close $PROTEINFILE
or warn "Problem closing protein file $proteinfilename. Reason: $!";
Cheers,
Michael
--
Michael Brader Senior Software Engineer and Perl Person
There's no such thing as a DevOps team Technology/Softdev/DevOps
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