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
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
|
#!/usr/bin/perl
#
# Fetch sequence data via OBDA registry system
#
# usage: rfetch -i <file_with_accession_list> -a -v -d embl -s start -e end
#
use Bio::DB::Registry;
use Bio::SeqIO;
use Getopt::Long;
use strict;
my $database = 'embl_biosql';
my $start = undef;
my $end = undef;
my $format = 'fasta';
my $file = undef;
my $acc = undef;
my $verbose = undef;
&GetOptions(
'd|database:s' => \$database,
's|start:i' => \$start,
'e|end:i' => \$end,
'f|format:s' => \$format,
'i|input:s' => \$file,
'a|acc' => \$acc,
'v|verbose' => \$verbose,
);
my $registry = Bio::DB::Registry->new();
my $db = $registry->get_database($database);
my $seqout = Bio::SeqIO->new( '-format' => $format, '-fh' => \*STDOUT);
my @ids;
if( defined $file ) {
open my $F, '<', $file or die "Could not read file '$file': $!\n";
while( <$F> ) {
my ($id) = split;
push(@ids,$id);
}
close $F;
} else {
@ids = @ARGV;
}
foreach my $id ( @ids ) {
my $seq;
if( $verbose ){
print STDERR "fetching $id\n";
}
if( $acc ) {
$seq = $db->get_Seq_by_acc($id);
} else {
$seq = $db->get_Seq_by_id($id);
}
if( defined $start && defined $end ) {
$seq = $seq->trunc($start,$end);
}
$seqout->write_seq($seq);
}
|
