Mariano Loza Coll wrote:
Hello everyone,
Hello,
Here's what I need to do: I need to take each of the words in one
List1, search for their presence (or not) in a second List2 and make a
new list with all the words in both. These are lists of gene names,
which can often include numbers and symbols in addition to letters.
The very newbie code that I wrote performs well, but it's missing the
words that have parentheses in them (for instance "Su(var)2-5").
Below are examples of the lists that I'm working with, the code that
I'm using, and the output.
I realize that there may be a number of ways to do what I need to do
(most of them better, I bet), and I'd love to learn about them. But
now I'm mostly curious about why grep// cannot "see" words with
parentheses in either (or both lists). I suspect the trick may be
somehow escaping the (), but I tried a number of ways of doing that to
no avail.
Any help will be greatly appreciated! And as usual, if you ever have
questions about molecular biology and genetics, fire away - I'd love
to pay the favor back.
Thanks in advance,
Mariano
Example of List 1
numb
Dl
cad99C
ham
esg
Stat92E
Hh
l(2)Lg
neur
CG32150
sox15N
Su(var)2-5
E(spl)-m4
ci
brd
vvl
Example of List 2
Src42A
cad99C
ham
Hh
l(2)Lg
neur
sox15N
numb
ubx
Su(var)2-5
esg
E(spl)-m4
ci
ttk
egfr
brd
ocho
vvl
CG32150
############## SCRIPT BEGINS
#!usr/bin/perl
use warnings;
use strict;
print "\nEnter path to List 1\n\n";
$path1 =<STDIN>; chomp $path1;
print "\nEnter path to List 2\n\n";
$path2 =<STDIN>; chomp $path2;
open (INPUT1, "$path1"); open (INPUT2, "$path2"); open (INPUT3, "$path3");
You should *always* verify that a file opened correctly:
open INPUT1, '<', $path1 or die "Cannot open '$path1' because: $!";
open INPUT2, '<', $path2 or die "Cannot open '$path2' because: $!";
open INPUT3, '<', $path3 or die "Cannot open '$path3' because: $!";
@array1 =<INPUT1>;
@array2 =<INPUT2>;
my ($array1,$array2,$in1and2);
You never use those variables anywhere.
my $ctr1 = 0;
while ($ctr1< @array1){
if(grep(/^$array1[$ctr1]$/,@array2)){
Change that line to this to get your program to work correclty:
if ( grep $_ eq $array1[ $ctr1 ], @array2 ) {
push (@in1and2,$array1[$ctr1]);
}
$ctr1 +=1;
}
print "in 1= ".@array1."\nin 2= ".@array2."in 1 and 2= ".@in1and2."\n\nDone!";
exit;
######
The output is...
in 1= 16
in 2= 19
in 1 and 2= 11
Done!
...when it should have been...
in 1= 16
in 2= 19
in 1 and 2= 14
but it's not "seeing" l(2)Lg, Su(var)2-5, E(spl)-m4 in both lists...
(I know this based on troubleshooting)
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
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