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if else equality question

kdejan
New User

Feb 11, 2013, 4:27 PM

Post #1 of 3 (193 views)

if else equality question	Can't Post

Hi all,

I'm writing a program to replace A's and G's in a text file I have. This is the code I have:

#!usr/bin/perl

open(FILE, "whatshappenin") or die $!;

#QUICKEST WAY OF READING A LINE BY LINE INTO AN ARRAY
foreach $line (<FILE>)
{
chomp($line);

my @array_of_chars = split(//,$line);
my $array_of_charsSize = $#array_of_chars + 1;
if($array_of_charsSize < 1480)
{
#THIS PRINTS THE SEQUENCE TITLES
print"$line\n";
}else{
#LOOP THROUGH SEQUENCE DATA ONE CHARACTER AT A TIME
for($i=0;$i<$array_of_charsSize;$i++)
{
#ONLY EDIT ONCE YOU REACH GAP PARTITION (1416 FOR TRN)
if($i>1416)
{
#CHANGE PRESENCE OF DATA 'A' TO 1
if($array_of_chars[$i] == "A" || $array_of_chars[$i] == "a")
{
$array_of_chars[$i] = 0;
#CHANCE PRESENCE OF GAP 'G' TO 0
}elsif($array_of_chars[$i] == "G" || $array_of_chars[$i] == "g")
{
$array_of_chars[$i] = 1;
}
}
}
#PRINT EDITED SEQUENCE
$str = "@array_of_chars";
$str =~ s/(.)\s/$1/seg;
print"$str\n";

}
}

Unfortunately it does not recognize any G's and just changes all the characters to 0's once $i>1416. I have a feeling it has to do with the equality statement inside my ifelseif statements, but I can't figure it out. Do I need to use ASCII values or something?

Any help is much appreciated!

BillKSmith
Veteran

Feb 11, 2013, 8:53 PM

Post #2 of 3 (187 views)

Re: [kdejan] if else equality question [In reply to]	Can't Post

The operator '==' is for comparing numbers. Use the operator 'eq' to compare strings.

I have several other recommendations.

Always use strict and warnings.

Always use the three argument form of open.

Always use lexical (my) file handles.

Always explicitly close all open files.

Process each line of this file as a string. There is no reason to split it into a character array.

Update: Added sample code (Untested due to lack of data)

Code

use strict; 
use warnings; 
use Readonly; 
Readonly::Scalar my $GAP_PARTITION => 1417; 
Readonly::Scalar my $MAX_TITLE_SIZE => 1480; 
open( my $FILE, '<', "whatshappenin" ) or die $!; 
foreach my $line (<FILE>) { 
    chomp $line; 
    if (  length $line < $MAX_TITLE_SIZE ) { print $line ; next; } 
    (my $temp = substr( $line, $GAP_PARTITION )) =~ tr /AaGg/0011/; 
    substr($line, $GAP_PARTITION, length $temp, $temp); 
    $line =~ s/(.)\s/$1/seg; 
    print "$line\n"; 
} 
close $FILE;

Good Luck,
Bill

(This post was edited by BillKSmith on Feb 12, 2013, 7:48 AM)

Kenosis
User

Feb 24, 2013, 6:11 PM

Post #3 of 3 (125 views)

Re: [kdejan] if else equality question [In reply to]	Can't Post

Here's another option:

Code

use strict; 
use warnings; 
 
while (<>) { 
	chomp; 
 
	if ( length $_ < 1480 ) { 
		print "$_\n"; 
		next; 
	} 
 
	s/(.{1415})//; 
	tr/AaGg/0011/; 
 
	print "$1$_\n"; 
}

Usage: perl script.pl inFile [>outFile]

The substitution matches and captures the first 1415 characters of the read line (contained in the default scalar $_), then removes them. The variable $1 now contains the pre-gap string, and $_ contains the post-gap string. A transliteration (implicitly) operates on $_, and then the pre-gap and post-gap strings are printed.

The optional command-line parameter, if used, redirects output to a file.

(This post was edited by Kenosis on Feb 24, 2013, 6:19 PM)

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