Comment programmer en Bioperl

Bonjour Cloti,

J'ai écrit un petit programme faisant ce que tu demandes.
Tu dois utiliser Bio::DB::GenBank de bioperl.
http://search.cpan.org/~birney/biope.../DB/GenBank.pm

Code:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
#!/usr/local/bin/perl
 
 
use Bio::DB::GenBank;
use strict;
use warnings;
 
 
 
# Args    : -db       database ('protein' or 'nucleotide')
#           -query    query string
#           -mindate  minimum date to retrieve from
#           -maxdate  maximum date to retrieve from
#           -reldate  relative date to retrieve from (days)
#           -datetype date field to use ('edat' or 'mdat')
#           -ids      array ref of gids (overrides query)
#           -maxids   the maximum number of IDs you wish to collect (defaults to 100)
 
 
 
my $db ="nucleotide";
my $mindate ="";
my $maxdate ="";
my $reldate ="";
my $datetype ="";
my $ids ="";
my $maxids ="";
my $query_string = 'requete GenBank à effectuer'; # idem que ce que tu mettrais dans l'interface GenBank
 
 
my $query = Bio::DB::Query::GenBank->new(-db=>$db,
                                    -query=>$query_string,
				    -mindate => $mindate,
				    -maxdate => $maxdate,
                                    -reldate => $reldate,
                                    -datetype => $datetype,
                                    -ids => $ids,
                                    -maxids => $maxids
                                    );
my $count = $query->count;
print "Compte du nombre d'entrees = $count\n";
 
 
 
# get a genbank database handle
my $gb = new Bio::DB::GenBank;
my $stream = $gb->get_Stream_by_query($query);
 
while (my $seq = $stream->next_seq)
{
        my $Acc = $seq->display_id();
        print $Acc."\n";
}

N'hésite pas à me poser des questions.

Bon travail,

Jasmine,