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
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
#!/usr/bin/perl
=head1 NAME
bp_download_query_genbank - script to query Genbank and retrieve records
=head1 USAGE
bp_download_query_genbank --query "Neurospora[ORGN]" --db nucest -o Ncrassa_ESTs.fa --format fasta
bp_download_query_genbank --queryfile 'filewithquery' --db nucest -o Ncrassa_ESTs.fa --format fasta
=head2 Other options
Provide ONE of:
-q --query query string OR
--queryfile profile file with query OR
--gi --gis --gifile file with list of GIs to download
Database type:
-d --db database (nucleotide [default], nucest, protein, )
-o --out --outfile output file (results are displayed on screen otherwise)
-f --format sequence file output format (fasta by default)
-v --verbose debugging output
=head2 Query options
--maxids maximum number of IDs to retrieve in a set (100 at a time by default)
--reldate
--maxdate maxdate for a record
--mindate minimum date for record
--datetype edat or mdat (entered or modified)
=head1 AUTHOR Jason Stajich
Jason Stajich, jason-AT-bioperl.org
=cut
use strict;
use warnings;
use Bio::DB::GenBank;
use Bio::DB::GenPept;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Getopt::Long;
my ($queryfile,$outfile,$format,$debug,%options);
$format = 'fasta';
$options{'-maxids'} = '100';
$options{'-db'} = 'nucleotide'; # can be nucleotide, nucest, protein
my $gifile;
GetOptions(
'h|help' => sub { exec('perldoc', $0);
exit(0);
},
'v|verbose' => \$debug,
'f|format:s' => \$format,
'queryfile:s' => \$queryfile,
'o|out|outfile:s' => \$outfile,
'gi|gifile|gis:s' => \$gifile,
# DB::Query options
'd|db:s' => \$options{'-db'},
'mindate:s' => \$options{'-mindate'},
'maxdate:s' => \$options{'-maxdate'},
'reldate:s' => \$options{'-reldate'},
'datetype:s' => \$options{'-datetype'}, # edat or mdat
'maxids:i' => \$options{'-maxids'},
'q|query:s' => \$options{'-query'},
);
my $out;
if( $outfile ) {
$out = Bio::SeqIO->new(-format => $format,
-file => ">$outfile");
} else {
$out = Bio::SeqIO->new(-format => $format); # write to STDOUT
}
my $dbh;
if( $options{'-db'} eq 'protein' ) {
$dbh = Bio::DB::GenPept->new(-verbose => $debug);
} else {
$dbh = Bio::DB::GenBank->new(-verbose => $debug);
}
my $query;
if( $gifile ) {
my @ids;
open my $fh, '<', $gifile or die "Could not read file '$gifile': $!\n";
while(<$fh>) {
push @ids, split;
}
close $fh;
while( @ids ) {
my @mini_ids = splice(@ids, 0, $options{'-maxids'});
$query = Bio::DB::Query::GenBank->new(%options,
-verbose =>$debug,
-ids => \@mini_ids,
);
my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
$out->write_seq($seq);
}
}
exit;
} elsif( $options{'-query'}) {
$query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
} elsif( $queryfile ) {
open my $fh, '<', $queryfile or die "Could not read file '$queryfile': $!\n";
while(<$fh>) {
chomp;
$options{'-query'} .= $_;
}
$query = Bio::DB::Query::GenBank->new(%options,-verbose => $debug);
close $fh;
} else {
die("no query string or gifile\n");
}
my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
$out->write_seq($seq);
}
|
