Erika at 02:24, 29 September 2009

2009-09-29T02:24:24Z

← Older revision		Revision as of 02:24, 29 September 2009
Line 72:		Line 72:

	#Calculate the percentage of hydrophobic a.a's in the chain		#Calculate the percentage of hydrophobic a.a's in the chain
			# $rounded = sprintf("%.3f", $number);

	$percentage_hydrophobic = ($count_hydrophobic/$count_other*100);		$percentage_hydrophobic = sprintf("%.1f",$count_hydrophobic/$count_other*100);

	#Print out the results		#Print out the results

Erika at 01:38, 29 September 2009

2009-09-29T01:38:30Z

← Older revision		Revision as of 01:38, 29 September 2009
Line 4:		Line 4:

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

			#Erika Phelps
			#28 Sept 2009
			#Exercise 5.5

			#Pseudocode:

			#Open a file, read it into a string, and close it again.
			#For each amino acid, check whether hydrophobic.
			#Keep a count of whether hydrophobic is true or false.
			#Calculate percentage of hydrophobic out of all a.a's read.
			#Exit program.

			#Define variables

			my $protein_filename = 0;
			my $protein_sequence = 0;
			my $count_hydrophobic = 0;
			my $count_other = 0;
			my $percentage_hydrophobic = 0;
			my @protein_string = 0;


			#Get the polypeptide information

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

			$protein_filename = <STDIN>;

			chomp $protein_filename;

			#Check to see if file exists.

			unless ( -e $protein_filename) {

			print "File \"$protein_filename \" does not seem to exist.\n";
			exit;
			}

			#Check to see if file can be opened.

			unless ( open(PROTEINFILE, $protein_filename) ) {

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

			@protein_string = <PROTEINFILE>;

			close PROTEINFILE;

			$protein_sequence = join( '', @protein_string);

			#Remove whitespace
			$protein_sequence =~ s/\s//g;

			#In a loop, check each amino acid to determine whether hydrophobic or other

			while ($protein_sequence =~ /A/ig) {$count_hydrophobic++}
			while ($protein_sequence =~ /I/ig) {$count_hydrophobic++}
			while ($protein_sequence =~ /L/ig) {$count_hydrophobic++}
			while ($protein_sequence =~ /V/ig) {$count_hydrophobic++}
			while ($protein_sequence =~ /[^AILV]/ig) {$count_other++}

			#Calculate the percentage of hydrophobic a.a's in the chain

			$percentage_hydrophobic = ($count_hydrophobic/$count_other*100);

			#Print out the results

			print "In the file \"$protein_filename\", $percentage_hydrophobic % are hydrophobic.\n";

			exit;

			#Could easily make more specific by reading AILV separately then adding
			#together for final calc, so that we can print out how many of each
			#specific hydrophobic a.a. there are.
	</pre>		</pre>

Erika: New page: Return to Week 2
Exercise 5.5 in Beginning Perl for Bioinformatics

2009-09-27T21:25:41Z

New page: Return to Week 2 Exercise 5.5 in Beginning Perl for Bioinformatics <pre> </pre>

New page

Return to [[Week 2]]
 
Exercise 5.5 in Beginning Perl for Bioinformatics

<pre>

</pre>

Exercise 5.5 - Revision history

Erika at 02:24, 29 September 2009

Erika at 01:38, 29 September 2009

Erika: New page: Return to Week 2
Exercise 5.5 in Beginning Perl for Bioinformatics

Exercise 5.5 - Revision history

Erika at 02:24, 29 September 2009

Erika at 01:38, 29 September 2009

Erika: New page: Return to Week 2 Exercise 5.5 in Beginning Perl for Bioinformatics

Erika: New page: Return to Week 2
Exercise 5.5 in Beginning Perl for Bioinformatics