Erika at 01:53, 29 September 2009

2009-09-29T01:53:37Z

← Older revision		Revision as of 01:53, 29 September 2009
Line 4:		Line 4:

	<pre>		<pre>
			#!/usr/bin/perl
			use warnings;
			use strict;

			#Erika Phelps
			#28 Sept 2009
			#Exercise 5.8 (nodification of example5-3.pl)

			#Ask the user for the filename of the file containing
			#the protein sequence data, and collect it from the keyboard

			print "Please type the filename of the protein sequence data: ";

			my $proteinfilename = <STDIN>;
			my $motif;

			#Remove the newline from the protein filename

			chomp $proteinfilename;

			#Open the file, or exit

			unless ( open (PROTEINFILE, $proteinfilename) ) {

			print "Cannot open file \"$proteinfilename\"\n\n";
			exit;
			}

			#Read the protein sequence data from the file, and store it
			#into the array variable @protein

			my @protein = <PROTEINFILE>;

			#Close the file - we've read all the data into @protein now.

			#Put the sequence data into a single string, as it's easier to search
			#for a motif in a string than in an array of lines

			my $protein = join( '' , @protein);

			#Remove white space

			$protein =~ s/\s//g;

			#In a loop, ask the user for a motif, search for the motif, and report
			#if it was found. Exit if no motif is entered.

			do {
			print "Enter a motif to search for: ";

			$motif = <STDIN>;

			#Remove the newline at the end of $motif

			chomp $motif;

			#Look for the motif

			if ( $protein =~ /$motif/, $& ) {

			print "I found the motif:\n$&\n";

			} else {

			print "I couldn\'t find it.\n\n";
			}

			#Exit on an empty user input

			} until ( $motif =~ /^\s*$/ );

			#Exit the program

			exit;
	</pre>		</pre>

Erika: New page: Return to Week 2
Exercise 5.8 in Beginning Perl for Bioinformatics

2009-09-27T21:25:51Z

New page: Return to Week 2 Exercise 5.8 in Beginning Perl for Bioinformatics <pre> </pre>

New page

Return to [[Week 2]]
 
Exercise 5.8 in Beginning Perl for Bioinformatics

<pre>

</pre>

Exercise 5.8 - Revision history