Help with Perl script to modify file

[kdejan]

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!

 

[feherke]

Hi

[ul]
[li]Please choose an Indent style and use it consistently.[/li]
[li]Next time please post your code between [tt][ignore]

[/ignore][/tt] and [tt][ignore]

[/ignore][/tt] TGML tags.[/li]
[/ul]

Possibly I misunderstood your task, but for now sounds like it could be reduced to :

perl -pe '[b]if[/b][teal]([/teal][b]length[/b][navy]$_[/navy][teal]>=[/teal][purple]1480[/purple][teal])[/teal][teal]{[/teal][navy]$e[/navy][teal]=[/teal][b]substr[/b][navy]$_[/navy][teal],[/teal][purple]1417[/purple][teal];[/teal][navy]$e[/navy][teal]=~[/teal][b]s[/b][fuchsia]/a/0/[/fuchsia][b]gi[/b][teal];[/teal][navy]$e[/navy][teal]=~[/teal][b]s[/b][fuchsia]/g/1/[/fuchsia][b]gi[/b][teal];[/teal][b]substr[/b][navy]$_[/navy][teal],[/teal][purple]1417[/purple][teal],-[/teal][purple]1[/purple][teal],[/teal][navy]$e[/navy][teal];[/teal][b]s[/b][fuchsia]/(.)\s/$1/[/fuchsia][b]g[/b][teal]}[/teal]' whatshappenin

Regarding your mistake, the [tt]==[/tt] operator does numeric comparison. Use [tt]eq[/tt] to compare strings. ( See Equality Operators in [tt]man perlop[/tt] for details. )

Feherke.
[link feherke.github.com/]

http://feherke.github.com/

[/url]