bin/load_map_data.pl

   1 #!/usr/bin/perl
   2
   3 # basic script to load maps
   4
   5
   6 # copy and edit this file as necessary
   7 # common changes include the following:
   8 # specified linkage groups
   9 # different column headings
  10 # "pos" field versus separate "chromosome" and "position" fields
  11
  12 =head1 NAME
  13
  14 load_map_data.pl - a script to load maps into the SGN database.
  15
  16 =head1 DESCRIPTION
  17
  18 usage: load_map_data -H dbhost -D dbname [-r] [-n "map name"] [-i map_id] <map file>
  19
  20 example: load_map_data.pl -H devel -D sandbox -r -i 9 map-file.csv
  21
  22 Options:
  23
  24 =over 5
  25
  26 =item -H
  27
  28 The hostname of the server hosting the database.
  29
  30 =item -D
  31
  32 the name of the database
  33
  34 =item -r
  35
  36 (optional) if present, rollback after the script terminates. Database should not be affected. Good for test runs.
  37
  38 =item -i
  39
  40 (optional) the map_id. If not present, will insert a brand new map (confirm dialog).
  41
  42 =item -n
  43
  44 required if -i is not used. Provides the map name.
  45
  46 =item -f
  47
  48 force to 'unknown' protocol type if no protocol is provided.
  49
  50 =back
  51
  52 The tab-delimited map file has the following columns:
  53
  54  MARKER
  55  CONFIDENCE
  56  LINKAGE_GROUP
  57  POSITION (must be a float! 0.0 )
  58  PROTOCOL
  59
  60
  61 =head1 AUTHORS
  62
  63 John Binns, Adri Mills, Lukas Mueller, Naama Menda (among others).
  64
  65 Current maintainer: Lukas Mueller/Naama Menda.
  66
  67 =cut
  68
  69 use strict;
  70
  71 use Getopt::Std;
  72 use CXGN::Tools::List qw | str_in |;
  73 use CXGN::Tools::File::Spreadsheet;
  74 use CXGN::Tools::Text;
  75 use CXGN::Marker::Modifiable;
  76 use CXGN::Marker::Tools;
  77 use CXGN::Marker::Location;
  78 use CXGN::Map::Version;
  79 use CXGN::DB::Connection;
  80 use CXGN::DB::InsertDBH;
  81 use Data::Dumper;
  82
  83
  84 our ($opt_H, $opt_D, $opt_i, $opt_r, $opt_n, $opt_f);
  85
  86 getopts('H:D:i:rn:f');
  87
  88 my $map_id;
  89 my $map_file;
  90 # specify linkage groups
  91 # example: my $linkage_groups = ['1','2','3','4','5'];
  92 my $linkage_groups = [ qw | 1 2 3 4 5 6 7 8 9 10 11 12 | ];
  93
  94 $map_id = $opt_i;
  95
  96 $map_file = shift;
  97
  98 if (!$opt_H && !$opt_D) {
  99     die "-H and -D parameters are required.\n";
 100 }
 101  my $dbh = CXGN::DB::InsertDBH->new({
 102                                              dbname => $opt_D,
 103                                              dbhost => $opt_H,
 104                                              dbargs => {AutoCommit => 0,
 105                                                         RaiseError => 1}
 106                                             });
 107
 108 eval {
 109     if (!$map_id) {
 110         print "No map_id was provided. Insert a new map? ";
 111         my $key = <STDIN>;
 112         if ($key =~ /Y/i) {
 113             print "Inserting a new map...\n";
 114
 115             my $map = CXGN::Map->new_map($dbh, $opt_n);
 116
 117             $map_id = $map->get_map_id();
 118
 119             print "New map_id: $map_id\n";
 120
 121         }
 122         else {
 123             exit();
 124         }
 125     }
 126
 127     # we are creating a new map version every time we run this script,
 128     # as long as the transaction goes through
 129     my $new_map_version = CXGN::Map::Version->
 130         #new($dbh,{map_id=>$map_id});
 131        new($dbh,{map_id=>$map_id},$linkage_groups);
 132     # saving the new map version
 133     my $map_version_id = $new_map_version->insert_into_database();
 134     print "map version = " . $new_map_version->as_string() . "\n";
 135     # make an object to give us the values from the spreadsheet
 136     my $ss = CXGN::Tools::File::Spreadsheet->new($map_file);
 137     my @markers = $ss->row_labels(); # row labels are the marker names
 138     my @columns = $ss->column_labels(); # column labels are the headings for the data columns
 139     # make sure the spreadsheet is how we expect it to be
 140     @columns = qw | MARKER MARKER_ID LINKAGE_GROUP POSITION CONFIDENCE PROTOCOL | # modify columns as necessary
 141         or die"Column headings are not as expected";
 142
 143     # for all the (uncleaned) marker names in the spreadsheet
 144     for my $dirty_marker_name(@markers) {
 145         # clean it, meaning, get the subscript if it's there,
 146         # and convert the name into a canonical form so we can find it
 147         # if it already exists with a different spelling or something
 148         my ($marker_name,$subscript) =
 149             CXGN::Marker::Tools::clean_marker_name($dirty_marker_name);
 150         # get as many IDs as you can for a marker with a name like this
 151         my @marker_ids =  CXGN::Marker::Tools::marker_name_to_ids($dbh,$marker_name);
 152         # if we get more than one, our script needs to be made smarter
 153         # so it can differentiate between them, or maybe one of them
 154         # needs to be deleted from the database
 155         if (@marker_ids>1) { die "Too many IDs found for marker '$marker_name'" }
 156         # just get the first ID in the list (if the list is longer than 1, we've already died)
 157         my($marker_id) = @marker_ids;
 158         my $marker;
 159         if($marker_id) { # if we have found an existing marker
 160             # make a modifiable marker object from it
 161             print "Found existing marker: $marker_id, $marker_name\n";
 162             $marker = CXGN::Marker::Modifiable->new($dbh,$marker_id);
 163         }
 164         else { # if we are making a new marker
 165             # make a modifiable marker object and start to populate it
 166             $marker = CXGN::Marker::Modifiable->new($dbh);
 167             $marker->set_marker_name($marker_name); #give it a name
 168             print "Loading new marker id from marker $marker_name\n";
 169             # marker must exist before locations can be added for it.
 170             # this is a db constraint. if you didn't do this, this script would die later.
 171             my $inserts = $marker->store_new_data();
 172             # if any data was inserted for this marker (presumably it was,
 173             # because we're making a new one)
 174             if ($inserts and @{$inserts}) { print"New marker inserted: $marker_name\n" }
 175             else { die "Oops, I thought I was inserting some new data" }
 176             $marker_id=$marker->marker_id();
 177
 178         }
 179         print $marker->name_that_marker()."\n";
 180         my $loc=$marker->new_location(); #create a new location object
 181
 182         # some files have pos which contains chromsome and position
 183         #my $pos=$ss->value_at($dirty_marker_name,'Position')
 184             # get position from spreadsheet
 185             #or die "No position found for $marker_name";
 186         # extract linkage group name and cm position from string like '01.035'
 187         #my ($chromosome,$position) =
 188             #CXGN::Marker::Tools::lg_name_and_position($pos);
 189
 190 #       foreach my $me (@{$marker->current_mapping_experiments}) {
 191 #           print $me->{protocol}."\n";
 192 #       }
 193
 194         my $chromosome=$ss->value_at($dirty_marker_name,'LINKAGE_GROUP')
 195             # get chromosome from spreadsheet
 196             or die"No chromosome found for $marker_name";
 197
 198
 199         if (! str_in($chromosome, @$linkage_groups)) {
 200             print STDERR "$marker_name skipped because linkage_group is $chromosome...\n";
 201             next;
 202         }
 203         # some have separate fields for chromsome and position
 204         my $position = $ss->value_at($dirty_marker_name,'POSITION');
 205             # get position from spreadsheet
 206              if (!defined($position)) {
 207                  print STDERR "No position found for $marker_name\n";
 208                  next;
 209          }
 210
 211         my $conf;
 212         # get confidence from spreadsheet
 213         $conf = $ss->value_at($dirty_marker_name,'CONFIDENCE') or $conf='uncalculated';
 214         if ($conf=~/^(\d+)$/) {
 215             if ($conf == 0) { $conf = "I"; }
 216             elsif ($conf == 1) { $conf = "I(LOD2)"; }
 217             elsif ($conf == 2) { $conf = "CF(LOD3)"; }
 218             elsif ($conf == 3) { $conf = "F(LOD3)"; }
 219             else { $conf = "uncalculated"; }
 220         }
 221         # get protocol from spreadsheet
 222         my $protocols_string=uc($ss->value_at($dirty_marker_name,'PROTOCOL'));
 223         # some entries have been mapped to the same location by more than
 224         # one method separated in the spreadsheet by plus signs
 225         my @protocols=split(/\+/,$protocols_string);
 226         if (@protocols) {
 227             print "Protocols found: ".CXGN::Tools::Text::list_to_string(@protocols)."\n";
 228         }
 229         else {
 230             if ($opt_f) {
 231                 print STDERR "Protocols not found for '$dirty_marker_name'";
 232                 @protocols = ('unknown');
 233             }
 234             else {
 235                 die "no protocol found for $dirty_marker_name. Use -f to force protocol to unknown.";
 236             }
 237         }
 238         for my $protocol(@protocols) {
 239             $protocol =~ tr/[a-z]/[A-Z]/;
 240             unless ($protocol eq 'AFLP' or $protocol eq 'CAPS' or $protocol eq 'RAPD'
 241                     or $protocol eq 'SNP' or $protocol eq 'SSR'
 242                     or $protocol eq 'RFLP' or $protocol eq 'PCR' or $protocol eq 'DCAPS' or $protocol =~/DArt/i or $protocol =~ /OPA/i or $protocol =~ /INDEL/i or $protocol =~ /ASPE/i or  $protocol =~ /qtl/i )
 243             {
 244                 print STDERR "UNKNOWN protocol ($protocol)\n! ";
 245                 $protocol = 'unknown';
 246             }
 247
 248             if ($protocol eq 'DCAPS') { $protocol = 'dCAPS' }
 249             print "Protocol = $protocol\n";
 250             # set the marker_id that will be at this location
 251             $loc->marker_id($marker_id);
 252             # set the map_version_id this location is found on
 253             # (this must be done before calling function lg_name)
 254             $loc->map_version_id($map_version_id);
 255             # set the linkage group name for this marker location
 256             # (the map_version_id must be already set for this to work,
 257             # else how would it be able to know different linkage groups on
 258             # different map versions from each other, when they all have the same names?)
 259             $loc->lg_name($chromosome);
 260
 261             #set the position of the marker on this linkage group
 262             $loc->position($position);
 263
 264             # set the confidence with which this marker is mapped at this position
 265             $loc->confidence($conf);
 266
 267             # set the subscript for this location, because the same marker
 268             # can be mapped to multiple locations, and these locations must be distinguishable
 269             $loc->subscript($subscript);
 270
 271             # this method call represents the insertion into the
 272             # marker_experiment table. this is currently a troublesome
 273             # issue because this marker was probably mapped here via a
 274             # PCR or RFLP experiment. where is this experiment data?
 275             # well, it's in another spreadsheet, to be loaded later,
 276             # or maybe it has already been loaded. if it was previously
 277             # loaded, it was matched up with an old map version. how can we
 278             # match that existing PCR/RFLP data up with this new map
 279             # version? well, it will have to be done later by some other script.
 280             print "Adding new experiment , marker_name = $marker_name, location = " . $loc->position . " protocol = '". $protocol . "'\n";
 281             $marker->add_experiment({location=>$loc,protocol=>$protocol});
 282         }
 283
 284         # store whatever new data you have (in this case, the new data
 285         #  is the location we just assigned the marker)
 286         my $inserts = $marker->store_new_data();
 287
 288
 289         # if any data was inserted for this marker (presumably it was,
 290         # since we're adding locations on a brand new map version)
 291         if ($inserts and @{$inserts}) {
 292             print "New marker data inserted:\n";#.Dumper($inserts);
 293             print $loc->as_string();
 294         }
 295
 296         else { die "Oops, I thought I was inserting some new data" }
 297     }
 298
 299     # deprecate the old map version and make the new one we just made the current one
 300     $new_map_version->set_current();
 301
 302 };
 303
 304
 305 if ($@) {
 306     print $@;
 307     print "Failed; rolling back.\n";
 308     $dbh->rollback();
 309 }
 310 else {
 311     print"Succeeded.\n";
 312     if (!$opt_r) {
 313         print"Committing.\n";
 314         $dbh->commit();
 315     }
 316     else {
 317         print"Rolling back.\n";
 318         $dbh->rollback();
 319     }
 320 }