On 2012.01.26 12:59, Chris Stinemetz wrote:
Hello Tiago,
On Thu, Jan 26, 2012 at 11:08 AM, Tiago Hori<tiago.h...@gmail.com> wrote:
Hi All,
I need some help to get started on a script.
I have these huge data files 16K rows and several columns. I need to parse
the rows into a subset of these 16K rows. Each rows has a identifier made
up of 2 letters and 6 numbers and the ones I want have specific letter,
they start with either C or D. So I know I can use regex, but I have been
trying to figure out the rest and I don't know where to start. This is the
first time I am trying to do something from scratch so any suggestions
would be appreciated. I am not asking for the script but just some help on
how to go about it.
So, what I want to be able to do is retrieve all the rows that have
identifiers starting with C or D. Should I use arrays, can I store each row
as one item a (set of information separated by tabs) in an array?
Yes I would use an array to store the data and then use regex to
extract the rows based on your criteria.
I put together a little sample program using fictitious data. You
should be able to apply the same concept to your needs.
***tested***
#!/usr/bin/perl
use warnings;
use strict;
while (<DATA> ) {
chomp;
my @array = split;
my $GeneID = $array[6];
if ($GeneID =~ /^C|D/) {
print $_,"\n";
}
}
__DATA__
Line1 c 2 3 4 5 C 7 8 9
Line2 1 2 3 4 5 6 7 8 9
Line3 1 2 3 4 5 D 7 8 9
Line4 1 2 3 4 5 6 7 8 9
Line5 1 2 3 4 5 D 7 8 9
Line6 1 2 3 4 5 6 7 8 9
***output***
Line1 c 2 3 4 5 C 7 8 9
Line3 1 2 3 4 5 D 7 8 9
Line5 1 2 3 4 5 D 7 8 9
This code erases the contents of @array and creates a new instance on
each loop of while(). If I'm not mistaken, the OP needs to save the
subset outside of the loop. I've modified your code a bit:
#!/usr/bin/perl
use warnings;
use strict;
my @array;
while ( <DATA> ) {
chomp;
my $GeneID = ( split( /\s+/, $_ ))[6];
if ($GeneID =~ /^C|D/) {
push( @array, $_ );
}
}
print "$_\n" for @array;
__DATA__
Line1 c 2 3 4 5 C 7 8 9
Line2 1 2 3 4 5 6 7 8 9
Line3 1 2 3 4 5 D 7 8 9
Line4 1 2 3 4 5 6 7 8 9
Line5 1 2 3 4 5 D 7 8 9
Line6 1 2 3 4 5 6 7 8 9
Note that the shift() line does the same thing yours does, but
eliminates the step of having to assign to a temporary array variable.
All of the logic could technically be shortened to:
if ( ( split( /\s+/, $_ ))[6] =~ /^[CD]/) {
push( @array, $_ );
}
...but oftentimes brevity is not nice on the eyes, especially in a
program longer than five or six lines :)
Steve
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