bin/find_stock_uniquename.pl

   1 #!/usr/bin/perl
   2
   3 use strict;
   4 use warnings;
   5 use Bio::Chado::Schema;
   6 use Getopt::Std;
   7 use SGN::Model::Cvterm;
   8 use CXGN::DB::InsertDBH;
   9
  10
  11 our ($opt_H, $opt_D);
  12 getopts("H:D:");
  13 my $dbhost = $opt_H;
  14 my $dbname = $opt_D;
  15 my $file = shift;
  16
  17
  18
  19 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
  20                                       dbname=>$dbname,
  21                                       dbargs => {AutoCommit => 1,
  22                                                  RaiseError => 1,
  23                                       }
  24
  25                                     } );
  26
  27
  28 my $schema= Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() });
  29
  30 print STDERR "Getting genotype names... ";
  31 my %g2s;
  32
  33 my $q = "SELECT genotype.uniquename, stock.uniquename FROM genotype join nd_experiment_genotype using(genotype_id) JOIN nd_experiment_stock using(nd_experiment_id) join stock using(stock_id)";
  34
  35 my $h = $dbh->prepare($q);
  36 $h->execute();
  37
  38 while (my ($gt, $stock) = $h->fetchrow_array()) {
  39     $g2s{uc($gt)} = $stock;#uc($stock);
  40     if ($gt =~ m/(.*?)\|(.*)/) {
  41         $g2s{uc($1)} = $stock; #uc($stock);
  42     }
  43 }
  44
  45 print STDERR "Done.\n";
  46
  47 my %stock_types;
  48 print STDERR "Getting stock type ids... ";
  49 my $rs = $schema->resultset("Cv::Cvterm")->search( { 'cv.name' => 'stock_type'}, { join => 'cv' } );
  50
  51 while (my $r = $rs->next()) {
  52     $stock_types{$r->cvterm_id()} = $r->name();
  53 }
  54
  55 print STDERR "Done.\n";
  56
  57 open (my $file_fh, "<", $file ) || die ("\nERROR: the file $file could not be found\n" );
  58
  59 my $synonym_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id();
  60 my $accession_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'stock_synonym', 'stock_property')->cvterm_id();
  61
  62 my %stats;
  63 my $line_count = 0;
  64
  65 while (my $line = <$file_fh>) {
  66     chomp($line);
  67
  68     $line_count++;
  69
  70     $line = uc($line);
  71
  72     my $id = $line;
  73     if ($line =~ m/(.*?)\:(.*)$/) {
  74         $id = $1;
  75     }
  76
  77 #    if ($line =~ /^(TMS.*)\_A\d{5}$/) {
  78 #       $id = $1;
  79 #    }
  80
  81     my $uniquename = "";
  82     my $match_type = "";
  83     my $stock_type = "";
  84
  85     if ($g2s{$line}) {
  86         $uniquename = $g2s{$line};
  87         $match_type = "hash_direct";
  88         $stats{hash_direct}++;
  89
  90         my $stock_row = $schema->resultset("Stock::Stock")->find( { uniquename => { ilike => $uniquename } });
  91
  92         $stock_type = $stock_types{$stock_row->type_id};# "accession";
  93     }
  94     elsif( $g2s{$id}) {
  95         $uniquename = $g2s{$id};
  96         $match_type = "hash_modified";
  97         $stats{hash_modified}++;
  98
  99         my $stock_row = $schema->resultset("Stock::Stock")->find( { uniquename => { ilike => $uniquename } });
 100         $stock_type = $stock_types{$stock_row->type_id}; #"accession";
 101     }
 102     else {
 103
 104         my $stock_row = $schema->resultset("Stock::Stock")->find( { uniquename => { ilike => $id } });
 105
 106         if ($stock_row) {
 107             $uniquename = $stock_row->uniquename();
 108             $match_type = "direct";
 109             $stats{direct}++;
 110             $stock_type = $stock_types{$stock_row->type_id} || $stock_row->type_id;
 111         }
 112         else {
 113             my $syn_rs = $schema->resultset("Stock::Stockprop")->search( { value => { ilike => $id }, 'me.type_id' => $synonym_id }, { join => 'stock' } );
 114
 115
 116             if ($syn_rs->count() == 1) {
 117                 my $row = $syn_rs->first()->stock();
 118                 $uniquename = $row->uniquename();
 119                 $match_type = "synonym";
 120                 $stats{synonym}++;
 121                 $stock_type = $stock_types{$row->type_id()} || $row->type_id();
 122             }
 123             elsif ($syn_rs->count() > 1) {
 124                 while (my $r = $syn_rs->next()) {
 125                     $uniquename .= $r->stock->uniquename().",";
 126                     $match_type = "multiple synonyms";
 127                     $stats{multiple_synonyms}++;
 128                     $stock_type .= $stock_types{$r->stock->type_id()}.",";
 129                 }
 130             }
 131             else {
 132                 $uniquename = $line;
 133                 $match_type = "absent";
 134                 $stats{absent}++;
 135             }
 136         }
 137     }
 138
 139     my $out = join("\t", $line, $id, $uniquename, $match_type, $stock_type);
 140
 141     print "$out\n";
 142
 143
 144     if ($line_count % 100 == 0) {
 145         print STDERR "Processing: ".join (", ", (map { "$_ : $stats{$_}" } sort keys(%stats)))."\r";
 146     }
 147
 148
 149 }
 150
 151
 152 print STDERR "Done.\n";
 153 print STDERR "Complete.\n";