Hello,
I was trying to run the script listed below and got some trouble... I have
the last version of Bioperl properly installed and working in my machine, but
that script asked me for IO/String.pm, I installed it then it asked me for
URI.pm (I downloaded it from Cpan then installed), then WWW/Search(libwww), then
HTML/Parser... I had all those last 3 modules installed in my machine (runing Fedora
Core 2 and kernel 2.6), however the sxript does not work and I also do not get any
error msg... any suggestions on how to fix this or even on hot to uninstall Perl
modules installed by make/make install downloaded from the Cpan website ?
Thanks in advance for any help you may offer.
Cheers, Alberto
davila AT ioc.fiocruz.br
[EMAIL PROTECTED] script]$ more genbank.pl
#!/usr/local/bin/perl -w
use lib "/usr/local/bioperl14";
use Bio::SearchIO;
#use strict;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Bio::DB::GenBank;
my $organismname = $ARGV[0];
my $genbankfile = "GenBank."."$organismname";
&download ($organismname);
sub download {
my $query_string = $organismname."[Organism] AND ribosomal gene[title] OR
mitochondrial gene[title] OR rDNA [title] OR rRNAgene[title]";
my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide',
-query=>$query_string,
-mindate => '1985',
-maxdate => '2004');
my $count = $query->count;
my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query);
#open a seqio handle for writing the outputfile in fasta
my $outfile = new Bio::SeqIO(-format=>'fasta',
-file=>">$genbankfile");
while (my $s = $seqio->next_seq) {
#print $query_string, "\n";
print $count, "\n";
#write the fasta
$outfile->write_seq($s);
}
}
