Week2 #5-7

Week2 #5-7

#!/usr/bin/perl
use strict;
use warnings;

my @seqnames = ("AAC35278", "AnCSMA", "AfCHSF", "AAF19257", "P30573-1");
my @seqs = ("LLIAITYYNEDKVLTARTLHGVMQNPAWQKIVVCLVFDGIDPVLATIGV-VMKKDVDGKE","AMCLVTCYSEGEEGIRTTLDSIALTPN-SHKSIVVICDGIIKVLRMMRD-TGSKRHNMAK", "ALCLVTCYSEGEEGIRTTLDSIAMTPN$

for ( my $i = 0; $i <= 4 ; $i++) {
print "Sequence name is $seqnames[$i]\n";
my @residues = split('-',$seqs[$i]);
my $len = join (/\s/, @residues);
my $length = length $len;
print "And residue length is $length\n";
}

my %columns;

for ( my $i = 0; $i <= 4; $i++) {
my $index = index($seqs[$i],"-");
while( $index >= 0) {
#print "Gaps at position(s) $index\n";
$columns{$index} = "1";
$index = index($seqs[$i],"-",$index+=2);
}
}

my $hash = keys %columns;
print "Unique gapped columns $hash\n";

my $identity = 0;

for ( my $i = 0; $i < 60; $i++) {
 my $AfC = substr($seqs[2], $i, 1);
 my $AAF = substr($seqs[3], $i, 1);
 if( $AfC eq $AAF) {
  $identity++;
}
}

print "Number of identical residues between AfCHSF and AAF19527 is $identity\n"