bin/change_name_of_obsolete_stocks_matching_pattern.pl

   1 #!/usr/bin/env perl
   2
   3 =head1
   4
   5 change_name_of_obsolete_stocks_matching_pattern.pl
   6
   7 =head1 SYNOPSIS
   8
   9     change_name_of_obsolete_stocks_matching_pattern.pl -H [dbhost] -D [dbname] -f "Ug" -r "UG"
  10
  11 =head1 COMMAND-LINE OPTIONS
  12
  13  -H  host name
  14  -D  database name
  15  -f  string to find
  16  -r  replace string with this
  17
  18 =head2 DESCRIPTION
  19
  20
  21 =head2 AUTHOR
  22
  23 Jeremy D. Edwards (jde22@cornell.edu)
  24
  25 April 2014
  26
  27 =head2 TODO
  28
  29 Add support for other spreadsheet formats
  30
  31 =cut
  32
  33 use strict;
  34 use warnings;
  35
  36 use lib 'lib';
  37 use Getopt::Std;
  38 use Bio::Chado::Schema;
  39 use CXGN::DB::InsertDBH;
  40 use CXGN::DB::Connection;
  41
  42
  43
  44 our ($opt_H, $opt_D, $opt_f, $opt_r);
  45 getopts('H:D:f:r:');
  46
  47
  48 sub print_help {
  49   print STDERR "A script to rename obsolete stocks\nUsage: change_name_of_obsolete_stocks_matching_pattern.pl -D [database name] -H [database host, e.g., localhost] -f [find string] -r [replace string with this]\n";
  50 }
  51
  52
  53 if (!$opt_D || !$opt_H || !$opt_f ) {
  54   print_help();
  55   die("Exiting: options missing\n");
  56 }
  57
  58 my $dbh = CXGN::DB::InsertDBH
  59   ->new({
  60          dbname => $opt_D,
  61          dbhost => $opt_H,
  62          dbargs => {AutoCommit => 1,
  63                     RaiseError => 1},
  64         });
  65
  66 my $chado_schema = Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() } );
  67
  68 my $rs = $chado_schema->resultset('Stock::Stock')->search({'uniquename' => {like => $opt_f.'%'}});
  69
  70 my $count = 0;
  71 foreach my $stock ($rs->all()) {
  72   print STDERR "Original name: ".$stock->uniquename()."\n";
  73   $count++;
  74 }
  75 print STDERR "\nFound $count accessions\n";
  76
  77 if ($opt_r) {
  78   foreach my $stock ($rs->all()) {
  79     my $stockid = $stock->stock_id();
  80     my $uniquename = $stock->uniquename();
  81     my $newname = $uniquename."obsolete";
  82     print STDERR "new name: $newname\n";
  83     if ($stock->is_obsolete()) {
  84       print STDERR "$stockid changing name $uniquename to $newname\n";
  85       $stock->uniquename($newname);
  86       $stock->update();
  87     }
  88   }
  89 }