bin/load_locus_publications.pl

   1
   2 =head1 NAME
   3  load_locus_publications.pl - a script to associate publications (pubmed IDs) with locus
   4
   5 =head1 SYNOPSYS
   6
   7 load_locus_publications.pl -p [person_id] -H [hostname] -D [database name] file
   8
   9 where file contains a column with locus names and a column with associated pubmed_ids.
  10
  11 =head1 AUTHOR
  12
  13 Lukas Mueller <lam87@cornell.edu>
  14
  15 =cut
  16
  17 use strict;
  18 use warnings;
  19
  20 use Getopt::Std;
  21 use File::Slurp qw | slurp |;
  22 use CXGN::DB::InsertDBH;
  23 use CXGN::Phenome::Locus;
  24 use CXGN::Chado::Dbxref;
  25
  26 our %opts;
  27 getopts('p:H:D:', \%opts);
  28
  29 my $file = shift;
  30
  31 my @lines = slurp($file);
  32 chomp(@lines);
  33
  34 my $dbh = CXGN::DB::InsertDBH->new( { dbname => $opts{D},
  35                                       dbhost => $opts{H},
  36                                     });
  37
  38
  39
  40 foreach my $l (@lines) {
  41     my ($locus_name, $pubmed_id) = split /\t/, $l;
  42     my $sth = $dbh->prepare("SELECT locus_id FROM phenome.locus WHERE locus_name = ?");
  43     $sth->execute($locus_name);
  44     my ($locus_id) = $sth->fetchrow_array();
  45     my $locus = CXGN::Phenome::Locus->new($dbh, $locus_id);
  46
  47     my $pub = CXGN::Chado::Publication->get_pub_by_accession($dbh, $pubmed_id);
  48
  49     my ($dbxref, @more_dbxrefs) = $pub->get_dbxrefs();
  50     print STDERR "Adding dbxref ".($dbxref->get_dbxref_id())."...\n";
  51     my $dbxref = CXGN::Chado::Dbxref->new($dbh, $dbxref->get_dbxref_id);
  52
  53     $locus->add_locus_dbxref($dbxref, undef, $opts{p});
  54
  55 }
  56 $dbh->commit();
  57
  58
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  63