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

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