Exercise 5.5D

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Exercise 5.5 in Beginning Perl for Bioinformatics

#!/usr/bin/perl -w

use strict; 

#Damian Almiron



#write a program that reports the percentage of hydrophobic amino acids 
#in a protein sequence obtain from a file. 

#my variables (do we always have to make var equal to zero? If not always,when 

my @protein_original = 0;

my $protein_joint = 0; 

my $count_hydrophobic = 0;

my $count_other = 0;

my $percentage_hydrophobic = 0; 

#Open file. 


@protein_original = <PROTEINFILE>; 


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

#Removing whitespace

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

#Determine if each AA is hydrophobic or not (go over this code) 

while ($protein_sequence =~ /V/ig) {$count_hydrophobic++}

while ($protein_sequence =~ /I/ig) {$count_hydrophobic++}

while ($protein_sequence =~ /L/ig) {$count_hydrophobic++}

while ($protein_sequence =~ /A/ig) {$count_hydrophobic++}

while ($protein_sequence =~ /[^VILA]/ig) {$count_other++} 

#Calculate % hydrophobic aa (review code)

# $rounded = sprintf("%.3f", $number); 

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

#Print results 

print "The follwing percentage is hydrophobic:$percentage_hydrophobic.\n";