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comparison getdata/get_gb_sp.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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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/perl
2 use strict;
3 no warnings; #genbank produces annoying warning if no sequence is found
4
5 #use FindBin;
6 #use lib "$FindBin::Bin/lib";
7 use Bio::DB::GenBank;
8 use Bio::SeqIO;
9 use Bio::Root::Exception;
10 use Error qw(:try);
11
12
13 my $datafile = $ARGV[0];
14 my $datatype = $ARGV[1];
15 my $outtype = $ARGV[2];
16 my $outfile = $ARGV[3];
17 my $nodata = $ARGV[4];
18
19 my $accessions;
20 my @accnums;
21
22 open (FILE,"<$datafile") or die "Cannot open file containing accession numbers\n";
23 open (OUT,">$outfile") or die "Cannot open outfile\n";
24 close OUT; #This overwrites old file if it exists
25 open (ND,">$nodata") or die "Cannot open file\n";
26 my $fh = Bio::SeqIO->newFh(-format=>$outtype, -file=>">>$outfile");
27
28
29 while (<FILE>)
30 {
31 chomp;
32 next unless ($_);
33 push(@accnums, $_);
34 }
35 close FILE;
36
37 my $countnames = 0;
38 foreach (@accnums){
39 #Should check input for one word per line and throw error if not, which is not done
40
41 $accessions = $_;
42 chomp;
43 if($accessions eq ""){
44 die "Put spaces between accession numbers. No Empty Lines allowed.\n";
45 }
46 my $qry_string .= $accessions."[organism]"." ";
47
48 # my $GBseq;
49 my $gb = new Bio::DB::GenBank;
50 my $query = Bio::DB::Query::GenBank->new
51 (-query =>$qry_string,
52 -db =>$datatype);
53
54 my $seqio;
55
56 if (eval {$gb->get_Stream_by_query($query)}){
57 $seqio = $gb->get_Stream_by_query($query);
58 while( my $GBseq = $seqio->next_seq ) {
59 my $sequence = $GBseq; # read a sequence object
60 print $fh $sequence; # write a sequence object
61 }
62 }else{
63 print ND "$accessions\n";
64 }
65 }
66 exit;
67
68