[Bioperl-l] Reading protein from file - error

[Brian Osborne]

Teja,

I will be frank: this is not the right way to read sequence data from a file, if you intend to use Perl.

Please take a look at this documentation, it will get you started.

http://www.bioperl.org/w/index.php?title=HOWTO:Beginners

You also want to take a look at your NM_021964fragment.pep file - is it in RTF format?

Brian O.


On May 29, 2011, at 11:12 PM, sukeerthi teja Rallapalli wrote:

> 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\cocoasubrtf350
> 
> 
> I am not able to print the protein content on the screen.
> 
> Thank you
> Regards
> Teja
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l