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 -v
  43
  44 add data to map version provided. Conflicts with -i and -n.
  45
  46 =item -n
  47
  48 required if -i is not used. Provides the map name.
  49
  50 =item -l
  51
  52 specify name of linkage groups as a comma separated list:
  53 1,2,3,4,5,6,7,8,9,10,11,12
  54 default is names from one to twelve.
  55
  56 =item -f
  57
  58 force to 'unknown' protocol type if no protocol is provided.
  59
  60 =back
  61
  62 The tab-delimited map file has the following columns:
  63
  64  MARKER
  65  CONFIDENCE
  66  LINKAGE_GROUP
  67  POSITION (must be a float! 0.0 )
  68  PROTOCOL
  69
  70
  71 =head1 AUTHORS
  72
  73 John Binns, Adri Mills, Lukas Mueller, Naama Menda (among others).
  74
  75 Current maintainer: Lukas Mueller/Naama Menda.
  76
  77 =cut
  78
  79 use strict;
  80
  81 use Getopt::Std;
  82 use CXGN::Tools::List qw | str_in |;
  83 use CXGN::Tools::File::Spreadsheet;
  84 use CXGN::Tools::Text;
  85 use CXGN::Marker::Modifiable;
  86 use CXGN::Marker::Tools;
  87 use CXGN::Marker::Location;
  88 use CXGN::Map::Version;
  89 use CXGN::DB::Connection;
  90 use CXGN::DB::InsertDBH;
  91 use Data::Dumper;
  92
  93
  94 our ($opt_H, $opt_D, $opt_i, $opt_r, $opt_n, $opt_f, $opt_v, $opt_l);
  95
  96 getopts('H:D:i:rn:fv:l:');
  97
  98 my $map_id;
  99 my $map_file;
 100 # specify linkage groups
 101 # example: my $linkage_groups = ['1','2','3','4','5'];
 102
 103 my $linkage_groups;
 104 if ($opt_l) {
 105     $linkage_groups = [ split /\s*\,\s*/, $opt_l ];
 106 }
 107 else {
 108     $linkage_groups = [ qw | 1 2 3 4 5 6 7 8 9 10 11 12 | ];
 109 }
 110
 111 $map_id = $opt_i;
 112 my $map_version_id = $opt_v;
 113 $map_file = shift;
 114
 115 if (!$opt_H && !$opt_D) {
 116     die "-H and -D parameters are required.\n";
 117 }
 118  my $dbh = CXGN::DB::InsertDBH->new({
 119                                              dbname => $opt_D,
 120                                              dbhost => $opt_H,
 121                                              dbargs => {AutoCommit => 0,
 122                                                         RaiseError => 1}
 123                                             });
 124
 125 eval {
 126     if (!$map_id && !$map_version_id) {
 127         print "No map_id was provided. Insert a new map? ";
 128         my $key = <STDIN>;
 129         if ($key =~ /Y/i) {
 130             print "Inserting a new map...\n";
 131
 132             my $map = CXGN::Map->new_map($dbh, $opt_n);
 133
 134             $map_id = $map->get_map_id();
 135
 136             print "New map_id: $map_id\n";
 137
 138         }
 139         else {
 140             exit();
 141         }
 142     }
 143
 144     # we are creating a new map version every time we run this script,
 145     # as long as the transaction goes through
 146     my $new_map_version;
 147
 148     if ($map_id) {
 149         $new_map_version = CXGN::Map::Version->
 150             #new($dbh,{map_id=>$map_id});
 151             new($dbh,{map_id=>$map_id},$linkage_groups);
 152         # saving the new map version
 153         $map_version_id = $new_map_version->insert_into_database();
 154         print "map version = " . $new_map_version->as_string() . "\n";
 155         # make an object to give us the values from the spreadsheet
 156     }
 157     elsif ($map_version_id) {
 158         $new_map_version = CXGN::Map::Version->
 159             new($dbh, {map_version_id=>$map_version_id});
 160     }
 161     my $ss = CXGN::Tools::File::Spreadsheet->new($map_file);
 162     my @markers = $ss->row_labels(); # row labels are the marker names
 163     my @columns = $ss->column_labels(); # column labels are the headings for the data columns
 164     # make sure the spreadsheet is how we expect it to be
 165     @columns = qw | MARKER MARKER_ID LINKAGE_GROUP POSITION CONFIDENCE PROTOCOL | # modify columns as necessary
 166         or die"Column headings are not as expected";
 167
 168     # for all the (uncleaned) marker names in the spreadsheet
 169     #
 170     for my $dirty_marker_name(@markers) {
 171
 172         # clean it, meaning, get the subscript if it's there,
 173         # and convert the name into a canonical form so we can find it
 174         # if it already exists with a different spelling or something
 175         #
 176         my ($marker_name,$subscript) = ($dirty_marker_name, "");
 177             #CXGN::Marker::Tools::clean_marker_name($dirty_marker_name);
 178
 179         # get as many IDs as you can for a marker with a name like this
 180         #
 181         my @marker_ids =  CXGN::Marker::Tools::marker_name_to_ids($dbh,$marker_name);
 182         # if we get more than one, our script needs to be made smarter
 183         # so it can differentiate between them, or maybe one of them
 184         # needs to be deleted from the database
 185         #
 186         if (@marker_ids>1) { die "Too many IDs found for marker '$marker_name'" }
 187         # just get the first ID in the list (if the list is longer than 1,
 188         # we've already died)
 189         #
 190         my ($marker_id) = @marker_ids;
 191         my $marker;
 192
 193         if($marker_id) {
 194             # if we have found an existing marker
 195             # make a modifiable marker object from it
 196             #
 197             print "Found existing marker: $marker_id, $marker_name\n";
 198             $marker = CXGN::Marker::Modifiable->new($dbh,$marker_id);
 199         }
 200         else {
 201             # if we are making a new marker
 202             # make a modifiable marker object and start to populate it
 203             #
 204             print "Loading new marker id from marker $marker_name\n";
 205             $marker = CXGN::Marker::Modifiable->new($dbh);
 206             $marker->set_marker_name($marker_name); #give it a name
 207
 208
 209             # marker must exist before locations can be added for it.
 210             # this is a db constraint. if you didn't do this, this script
 211             # would die later.
 212             #
 213             my $inserts = $marker->store_new_data();
 214
 215             # if any data was inserted for this marker (presumably it was,
 216             # because we're making a new one)
 217             #
 218             if ($inserts and @{$inserts}) { print"New marker inserted: $marker_name\n" }
 219             else { die "Oops, I thought I was inserting some new data" }
 220             $marker_id=$marker->marker_id();
 221
 222         }
 223
 224         print $marker->get_name()."\n";
 225
 226         my $loc=$marker->new_location(); #create a new location object
 227
 228         # some files have pos which contains chromsome and position
 229         #my $pos=$ss->value_at($dirty_marker_name,'Position')
 230             # get position from spreadsheet
 231             #or die "No position found for $marker_name";
 232         # extract linkage group name and cm position from string like '01.035'
 233         #my ($chromosome,$position) =
 234             #CXGN::Marker::Tools::lg_name_and_position($pos);
 235
 236 #       foreach my $me (@{$marker->current_mapping_experiments}) {
 237 #           print $me->{protocol}."\n";
 238 #       }
 239
 240         my $chromosome=$ss->value_at($dirty_marker_name,'LINKAGE_GROUP');           # get chromosome from spreadsheet
 241         if (!defined($chromosome)) {  die"No chromosome found for $marker_name"; }
 242
 243         if (! str_in($chromosome, @$linkage_groups)) {
 244             print STDERR "$marker_name skipped because linkage_group is $chromosome...\n";
 245             next;
 246         }
 247
 248         # some have separate fields for chromsome and position
 249         #
 250         my $position = $ss->value_at($dirty_marker_name,'POSITION');
 251             # get position from spreadsheet
 252              if (!defined($position)) {
 253                  print STDERR "No position found for $marker_name\n";
 254                  next;
 255          }
 256
 257         my $confidence;
 258
 259         # get confidence from spreadsheet
 260         #
 261         $confidence = $ss->value_at($dirty_marker_name,'CONFIDENCE') or $confidence='uncalculated';
 262         if ($confidence=~/^(\d+)$/) {
 263             if ($confidence == 0) { $confidence = "I"; }
 264             elsif ($confidence == 1) { $confidence = "I(LOD2)"; }
 265             elsif ($confidence == 2) { $confidence = "CF(LOD3)"; }
 266             elsif ($confidence == 3) { $confidence = "F(LOD3)"; }
 267             else { $confidence = "uncalculated"; }
 268         }
 269         # get protocol from spreadsheet
 270         #
 271         my $protocols_string=uc($ss->value_at($dirty_marker_name,'PROTOCOL'));
 272
 273         # some entries have been mapped to the same location by more than
 274         # one method separated in the spreadsheet by plus signs
 275         #
 276         my @protocols=split(/\+/,$protocols_string);
 277         if (@protocols) {
 278             print "Protocols found: ".CXGN::Tools::Text::list_to_string(@protocols)."\n";
 279         }
 280         else {
 281             if ($opt_f) {
 282                 print STDERR "Protocols not found for '$dirty_marker_name'";
 283                 @protocols = ('unknown' x scalar(@protocols));
 284             }
 285             else {
 286                 die "no protocol found for $dirty_marker_name. Use -f to force protocol to unknown.";
 287             }
 288         }
 289         for my $protocol(@protocols) {
 290             $protocol = uc($protocol);
 291             unless ($protocol eq 'AFLP' or $protocol eq 'CAPS' or $protocol eq 'RAPD'
 292                     or $protocol eq 'SNP' or $protocol eq 'SSR'
 293                     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  $protocol =~ /qtl/i )
 294             {
 295                 print STDERR "UNKNOWN protocol ($protocol)\n! ";
 296                 $protocol = 'unknown';
 297             }
 298
 299             if ($protocol eq 'DCAPS') { $protocol = 'dCAPS' }
 300             print "Protocol = $protocol\n";
 301
 302             # set the marker_id that will be at this location
 303             #
 304             $loc->marker_id($marker_id);
 305
 306             # set the map_version_id this location is found on
 307             # (this must be done before calling function lg_name)
 308             #
 309             $loc->map_version_id($map_version_id);
 310
 311             # set the linkage group name for this marker location
 312             # (the map_version_id must be already set for this to work,
 313             # else how would it be able to know different linkage groups on
 314             # different map versions from each other, when they all have the same names?)
 315             #
 316             $loc->lg_name($chromosome);
 317
 318             #set the position of the marker on this linkage group
 319             #
 320             $loc->position($position);
 321
 322             # set the confidence with which this marker is mapped at this position
 323             #
 324             $loc->confidence($confidence);
 325
 326             # set the subscript for this location, because the same marker
 327             # can be mapped to multiple locations, and these locations must be distinguishable
 328             #
 329             $loc->subscript($subscript);
 330
 331             # this method call represents the insertion into the
 332             # marker_experiment table. this is currently a troublesome
 333             # issue because this marker was probably mapped here via a
 334             # PCR or RFLP experiment. where is this experiment data?
 335             # well, it's in another spreadsheet, to be loaded later,
 336             # or maybe it has already been loaded. if it was previously
 337             # loaded, it was matched up with an old map version. how can we
 338             # match that existing PCR/RFLP data up with this new map
 339             # version? well, it will have to be done later by some other script.
 340             #
 341             print "Adding new experiment , marker_name = $marker_name, location = " . $loc->position . " protocol = '". $protocol . "'\n";
 342             $marker->add_experiment({location=>$loc,protocol=>$protocol});
 343         }
 344
 345         # store whatever new data you have (in this case, the new data
 346         # is the location we just assigned the marker)
 347         #
 348         print "Storing new marker data...\n";
 349         my $inserts = $marker->store_new_data();
 350
 351
 352         # if any data was inserted for this marker (presumably it was,
 353         # since we're adding locations on a brand new map version)
 354         #
 355         if ($inserts and @{$inserts}) {
 356             print "New marker data inserted:\n";#.Dumper($inserts);
 357             print $loc->as_string();
 358         }
 359
 360         else { die "Oops, I thought I was inserting some new data" }
 361     }
 362
 363     # deprecate the old map version and make the new one we just made the current one
 364     #
 365     $new_map_version->set_current();
 366
 367 };
 368
 369
 370 if ($@) {
 371     print $@;
 372     print "Failed; rolling back.\n";
 373     $dbh->rollback();
 374 }
 375 else {
 376     print"Succeeded.\n";
 377     if (!$opt_r) {
 378         print"Committing.\n";
 379         $dbh->commit();
 380     }
 381     else {
 382         print"Rolling back.\n";
 383         $dbh->rollback();
 384     }
 385 }