LWP::Simple problems

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks,
I am trying to use LWP::Simple to get sequences from a website. The web address for each sequence is always the same except for the sequence id at the end. I am only retrieving 537/603 sequences with the below code.
Obviously it seems that some of my sequences can't be found. However, if it can't find a sequence I am trying to print an error message to say so in the output - this is the part that i can't get to work.
I wondered if someone could suggest how I can print an error message if the sequence can't be found (e.g. web site is empty or doesn't exist). Thanks!

use strict;
use LWP::Simple;
my @fasta;
my $o;

# Note: @accession defined earlier has 603 elements

for (my $i=0; $i<@accession; $i++)      {
        if ($accession[$i] =~ /^(\w+)\_(\w+)\_(\w+)\;/) {
                #print "$accession[$i]\n";
        if ($1 eq $3)   {
                # USE $1 AS THE ACCESSION NUMBER
                my $seq = get "http://us.expasy.org/cgi-bin/get-sprot-
+fasta?$1";
                        #print "$seq\n";
                        push (@fasta, $seq);
                        push @fasta, "> COULDN'T FIND IT" unless defin
+ed $seq;
        }
        else {
#               # USE $3 AS THE ACCESSION NUMBER
                my $seq =  "http://us.expasy.org/cgi-bin/get-sprot-fas
+ta?$3";
                        push (@fasta, $seq);
                        push @fasta, "> COULDN'T FIND IT" unless defin
+ed $seq;
        }

        }
}
#print "$o\n";
# fasta only has 537 / 603 elements
print "@fasta\n";
[download]

Comment on LWP::Simple problems Download Code

Replies are listed 'Best First'.
Re: LWP::Simple problems by chromatic (Archbishop) on Jan 29, 2005 at 16:31 UTC
I think this code is shorter but still does what you want. `use strict; my @fasta; for my $acc (@accession) { next unless /_(\d+);/ my id = $1; my $seq = get( "http://us.expasy.org/cgi-bin/get-sprot-fasta?$id"; unless (defined $seq) { print "Couldn't find id $id\n"; next; } push @fasta, $seq; }` [download]	[reply] [d/l]
Re^2: LWP::Simple problems by davido (Cardinal) on Jan 29, 2005 at 16:34 UTC
Don't forget to sleep briefly between page hits. Dave	[reply]
Re^3: LWP::Simple problems by monkey_boy (Priest) on Jan 30, 2005 at 20:23 UTC
If its anything like the standard expasy site, sleep forever!, you should read the `robots.txt` file, as this aint allowed, that said, i cant check the us mirror at the moment , perhaps you've DOS'ed it! I should really do something about this apathy ... but i just cant be bothered	[reply] [d/l]
Re: LWP::Simple problems by ZlR (Chaplain) on Jan 29, 2005 at 13:16 UTC
Hello, i think this is not good : `push (@fasta, $seq); push @fasta, "> COULDN'T FIND IT" unless defined $seq;` [download] It will push $seq even if it's not defined. Use a full if/else statement : `if (defined $seq) { push @fasta, $seq } else { push @fasta, "> COULDN'T FIND IT" }` [download] Or you can use the short A?B:C construct which does the same thing : `defined $seq ? push @fasta, $seq : push @fasta, "> COULDN'T FIND IT" ;` [download] As a note i think the declaration for $seq should be up there with the other my variables. And also $o is not a very good name :) Hope this helps, ZlR.	[reply] [d/l] [select]
Re^2: LWP::Simple problems by saskaqueer (Friar) on Jan 29, 2005 at 17:38 UTC
`defined $seq ? push @fasta, $seq : push @fasta, "> COULDN'T FIND IT" ;` [download] You can save a few (meagre) keystrokes and make the statement more readable (IMO): `push( @fasta, defined($seq) ? $seq : "> COULDN'T FIND IT" );` [download]	[reply] [d/l] [select]
Re: LWP::Simple problems by foil (Sexton) on Jan 29, 2005 at 17:24 UTC
Error response codes are all built into the module . I quote " This module also exports the HTTP::Status constants and procedures. You can use them when you check the response code from getprint(), getstore() or mirror(). " Using this can give you more info if request failed ...	[reply]