[Bioperl-l] about error messages!

yaofx yaofx at xymu.net
Mon Aug 4 09:29:32 EDT 2003


Hello,

The following script is my first code using Bioperl module.
It works well, now I want to add some codes to get error messages and  
save as log file, such as :
" Could not connect internet", "ID does not exist", "verbose ID" , and 
so on.
But I can not find the information  about that, would you all like  help me?

Thanks in advance!

Fengxia


#!/usr/bin/perl -w
$idlist = $ARGV[0];

if (@ARGV != 1){
    print "USAGE: perl web_id2seq.pl <ID list file>\n";
    exit(1);
}

$faoutfile = $idlist."_fa.txt";
(unlink $faoutfile) if (-e $faoutfile);

open (INPUT,$idlist);

while ($line = <INPUT>){
    chomp ($line);
    $line =~ s/\r//;
    push (@querylist,$line);
}
$query = join ",", at querylist;
close INPUT;

use Bio::SeqIO;
use Bio::DB::GenBank;
my $gb = new Bio::DB::GenBank;

my $seqout = new Bio::SeqIO(-file => ">$faoutfile", -format => 'fasta');
my $seqio = $gb->get_Stream_by_id([$query]);
 
while($seq = $seqio->next_seq ) {
        $seqout->write_seq($seq);
}




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