parse problem

[Anonymous Monk]

I want to get the number from a html source file, I want to parse the data like:

gi|12345678|ref|NP_001234.1|

and get 12345678, I did as below:

$data = gi|12345678|ref|NP_001234.1|;
@data = split ('gi|',$data);
@data1 = split ('|ref',$data[1]);
$number = $data1[0];

I got e, g,..., some weird letter, when I changed the code to below:

$data = gi|12345678|ref|NP_001234.1|;
@data = split ('gi',$data);
@data1 = split ('ref',$data[1]);
$number = $data1[0];

I got:|12345678|, I try use regular expression to remove the |:

$number =~ m/[0-9]*/;

I got the same thing which has |12345678|, What can I do? Please help and Thanks in advance! Please help and Thanks in advance!

[DrManhattan]

The first argument to split() needs to be a regular expression matching the string that delimits the fields in your data. In your case, the fields in your line are separated by a '|', so the code could look like this:

#!/usr/bin/perl

use strict;

my $data = 'gi|12345678|ref|NP_001234.1|';
my @data = split /\|/, $data;
my $number = $data[1];

Or more concisely:

#!/usr/bin/perl

use strict;

my $data = 'gi|12345678|ref|NP_001234.1|';
my $number = (split(/\|/, $data))[1];

-Matt

[dpuu]

Your problem may be that the first arg to split is a regular extression -- and the vertical bar is a pattern separator with an empty extression on its left -- which can always match. If you are only wanting the one number you show, then your could use:

  $data =~ /gi\|(\d+)\|ref/ and $number = $1;

Note that the vertical bar is escaped using the backslash. --Dave

[artist]

Hi
You have already received good solutions.
Your algorithm should be:
A. split the data with the pattern . (pipe symbol in your case)
B. get the second item from the result of the above split.
Learn more about split.

artist