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comparison getdata/get_1_gb.pl @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/perl -w
2 use strict;
3
4 #use FindBin;
5 #use lib "$FindBin::Bin/lib";
6 use Bio::DB::GenBank;
7 use Bio::SeqIO;
8
9 my $accession = $ARGV[0];
10 my $datatype = $ARGV[1];
11 my $outtype = $ARGV[2];
12 my $outfile = $ARGV[3];
13
14
15 my $qry_string .= $accession."[accession]";
16 my $fh = Bio::SeqIO->newFh(-format=>$outtype, -file=>">$outfile");
17
18 my $GBseq;
19 my $gb = new Bio::DB::GenBank;
20 my $query = Bio::DB::Query::GenBank->new
21 (-query =>$qry_string,
22 -db =>$datatype);
23
24 my $count;
25 my $species;
26 my $seqio = $gb->get_Stream_by_query($query);
27 while( defined ($GBseq = $seqio->next_seq )) {
28 my $sequence = $GBseq; # read a sequence object
29 print $fh $sequence; # write a sequence object
30 }
31
32 exit;