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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | # | ||
| 4 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 5 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 6 : | # | ||
| 7 : | # This file is part of the SEED Toolkit. | ||
| 8 : | # | ||
| 9 : | # The SEED Toolkit is free software. You can redistribute | ||
| 10 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 11 : | # Public License. | ||
| 12 : | # | ||
| 13 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 14 : | # along with this program; if not write to the University of Chicago | ||
| 15 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 16 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 17 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 18 : | # | ||
| 19 : | |||
| 20 : | package FeatureSproutLoader; | ||
| 21 : | |||
| 22 : | use strict; | ||
| 23 : | use Tracer; | ||
| 24 : | use ERDB; | ||
| 25 : | use BioWords; | ||
| 26 : | use AliasAnalysis; | ||
| 27 : | parrello | 1.6 | use DBMaster; |
| 28 : | use HyperLink; | ||
| 29 : | use FFs; | ||
| 30 : | parrello | 1.1 | use base 'BaseSproutLoader'; |
| 31 : | |||
| 32 : | =head1 Sprout Feature Load Group Class | ||
| 33 : | |||
| 34 : | =head2 Introduction | ||
| 35 : | |||
| 36 : | The Feature Load Group includes all of the major feature-related tables. | ||
| 37 : | |||
| 38 : | =head3 new | ||
| 39 : | |||
| 40 : | parrello | 1.3 | my $sl = FeatureSproutLoader->new($erdb, $source, $options, @tables); |
| 41 : | parrello | 1.1 | |
| 42 : | parrello | 1.3 | Construct a new FeatureSproutLoader object. |
| 43 : | parrello | 1.1 | |
| 44 : | =over 4 | ||
| 45 : | |||
| 46 : | =item erdb | ||
| 47 : | |||
| 48 : | [[SproutPm]] object for the database being loaded. | ||
| 49 : | |||
| 50 : | =item options | ||
| 51 : | |||
| 52 : | Reference to a hash of command-line options. | ||
| 53 : | |||
| 54 : | =item tables | ||
| 55 : | |||
| 56 : | List of tables in this load group. | ||
| 57 : | |||
| 58 : | =back | ||
| 59 : | |||
| 60 : | =cut | ||
| 61 : | |||
| 62 : | sub new { | ||
| 63 : | # Get the parameters. | ||
| 64 : | parrello | 1.6 | my ($class, $erdb, $options) = @_; |
| 65 : | parrello | 1.1 | # Create the table list. |
| 66 : | my @tables = sort qw(Feature IsLocatedIn FeatureAlias IsAliasOf FeatureLink | ||
| 67 : | FeatureTranslation FeatureUpstream HasFeature HasRoleInSubsystem | ||
| 68 : | FeatureEssential FeatureVirulent FeatureIEDB CDD IsPresentOnProteinOf | ||
| 69 : | parrello | 1.6 | CellLocation IsPossiblePlaceFor IsAlsoFoundIn ExternalDatabase Keyword |
| 70 : | ProteinFamily IsFamilyForFeature ProteinFamilyName FeatureEC); | ||
| 71 : | parrello | 1.1 | # Create the BaseSproutLoader object. |
| 72 : | parrello | 1.6 | my $retVal = BaseSproutLoader::new($class, $erdb, $options, @tables); |
| 73 : | parrello | 1.2 | # Get the list of relevant attributes. |
| 74 : | parrello | 1.1 | # Bless and return it. |
| 75 : | bless $retVal, $class; | ||
| 76 : | return $retVal; | ||
| 77 : | } | ||
| 78 : | |||
| 79 : | =head2 Public Methods | ||
| 80 : | |||
| 81 : | =head3 Generate | ||
| 82 : | |||
| 83 : | $sl->Generate(); | ||
| 84 : | |||
| 85 : | Generate the data for the feature-related files. | ||
| 86 : | |||
| 87 : | =cut | ||
| 88 : | |||
| 89 : | sub Generate { | ||
| 90 : | # Get the parameters. | ||
| 91 : | my ($self) = @_; | ||
| 92 : | # Get the sprout object. | ||
| 93 : | my $sprout = $self->db(); | ||
| 94 : | # Get the FIG object. | ||
| 95 : | my $fig = $self->source(); | ||
| 96 : | # Get the subsystem list. | ||
| 97 : | my $subHash = $self->GetSubsystems(); | ||
| 98 : | # Get the word stemmer. | ||
| 99 : | my $stemmer = $sprout->GetStemmer(); | ||
| 100 : | parrello | 1.6 | # Get access to FIGfams. |
| 101 : | my $figfam_data = &FIG::get_figfams_data(); | ||
| 102 : | my $ffs = new FFs($figfam_data); | ||
| 103 : | parrello | 1.1 | # Only proceed if this is not the global section. |
| 104 : | if (! $self->global()) { | ||
| 105 : | parrello | 1.4 | # Get the section ID. |
| 106 : | my $genomeID = $self->section(); | ||
| 107 : | parrello | 1.6 | # Connect to the ontology database. |
| 108 : | my $sqlite_db = "/home/mkubal/Temp/Ontology/ontology.sqlite"; | ||
| 109 : | my $ontology_dbmaster = DBMaster->new(-database => $sqlite_db, -backend => 'SQLite'); | ||
| 110 : | parrello | 1.1 | # Get the maximum sequence size. We need this later for splitting up the |
| 111 : | # locations. | ||
| 112 : | my $chunkSize = $sprout->MaxSegment(); | ||
| 113 : | Trace("Loading features for genome $genomeID.") if T(ERDBLoadGroup => 3); | ||
| 114 : | # Get the feature list for this genome. | ||
| 115 : | my $features = $fig->all_features_detailed_fast($genomeID); | ||
| 116 : | # Sort and count the list. | ||
| 117 : | my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features}; | ||
| 118 : | my $count = scalar @featureTuples; | ||
| 119 : | Trace("$count features found for genome $genomeID.") if T(ERDBLoadGroup => 3); | ||
| 120 : | # Get the attributes for this genome and put them in a hash by feature ID. | ||
| 121 : | parrello | 1.6 | my $attributes = $self->GetGenomeAttributes($genomeID, \@featureTuples); |
| 122 : | parrello | 1.1 | Trace("Looping through features for $genomeID.") if T(ERDBLoadGroup => 3); |
| 123 : | # Loop through the features. | ||
| 124 : | for my $featureTuple (@featureTuples) { | ||
| 125 : | # Split the tuple. | ||
| 126 : | parrello | 1.4 | my ($featureID, $locations, $aliases, $type, $minloc, $maxloc, $assignment, $user, $quality) = @{$featureTuple}; |
| 127 : | parrello | 1.1 | # Make sure this feature is active. |
| 128 : | if (! $fig->is_deleted_fid($featureID)) { | ||
| 129 : | # Handle missing assignments. | ||
| 130 : | if (! defined $assignment) { | ||
| 131 : | $assignment = ''; | ||
| 132 : | $user = ''; | ||
| 133 : | } else { | ||
| 134 : | # The default assignment-maker is FIG. | ||
| 135 : | $user ||= 'fig'; | ||
| 136 : | } | ||
| 137 : | # Count this feature. | ||
| 138 : | $self->Track(features => $featureID, 1000); | ||
| 139 : | # Fix the quality. It is almost always a space, but some odd stuff might sneak through, and the | ||
| 140 : | # Sprout database requires a single character. | ||
| 141 : | if (! defined($quality) || $quality eq "") { | ||
| 142 : | $quality = " "; | ||
| 143 : | } | ||
| 144 : | parrello | 1.6 | # Get the coupling count. The coupled features are returned as a list, |
| 145 : | # and we store it as a scalar to get the count. | ||
| 146 : | my $couplingCount = $fig->coupled_to($featureID); | ||
| 147 : | parrello | 1.1 | # Begin building the keywords. We start with the genome ID, the |
| 148 : | # feature ID, the taxonomy, and the organism name. | ||
| 149 : | my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID), | ||
| 150 : | $fig->taxonomy_of($genomeID)); | ||
| 151 : | # Create the aliases. | ||
| 152 : | parrello | 1.4 | for my $alias (split /,/, $aliases) { |
| 153 : | parrello | 1.1 | # Connect this alias to this feature and make an Alias record for it. |
| 154 : | parrello | 1.6 | $self->PutR(IsAliasOf => $alias, $featureID); |
| 155 : | $self->PutE(FeatureAlias => $alias); | ||
| 156 : | parrello | 1.1 | # Add it to the keyword list. |
| 157 : | push @keywords, $alias; | ||
| 158 : | # If this is a locus tag, also add its natural form as a keyword. | ||
| 159 : | my $naturalName = AliasAnalysis::Type(LocusTag => $alias); | ||
| 160 : | if ($naturalName) { | ||
| 161 : | push @keywords, $naturalName; | ||
| 162 : | } | ||
| 163 : | } | ||
| 164 : | # Add the corresponding IDs. We ask for 2-tuples of the form (id, database). | ||
| 165 : | my @corresponders = $fig->get_corresponding_ids($featureID, 1); | ||
| 166 : | for my $tuple (@corresponders) { | ||
| 167 : | my ($id, $xdb) = @{$tuple}; | ||
| 168 : | parrello | 1.6 | # Ignore SEED: that's us. Also ignore contig IDs. Those are due to a bug. |
| 169 : | if ($xdb ne 'SEED' && ! ($xdb eq 'RefSeq' && $id =~ /^[A-Z][A-Z]_\d+$/)) { | ||
| 170 : | parrello | 1.1 | # Connect this ID to the feature and mark its database. |
| 171 : | parrello | 1.6 | $self->PutR(IsAlsoFoundIn => $featureID, $xdb, |
| 172 : | parrello | 1.1 | alias => $id); |
| 173 : | parrello | 1.6 | $self->PutE(ExternalDatabase => $xdb); |
| 174 : | # Add it as a keyword and an alias. | ||
| 175 : | parrello | 1.1 | push @keywords, $id; |
| 176 : | parrello | 1.6 | $self->PutR(IsAliasOf => $id, $featureID); |
| 177 : | $self->PutE(FeatureAlias => $id); | ||
| 178 : | parrello | 1.1 | } |
| 179 : | } | ||
| 180 : | Trace("Assignment for $featureID is: $assignment") if T(ERDBLoadGroup => 4); | ||
| 181 : | # Break the assignment into words and shove it onto the | ||
| 182 : | # keyword list. | ||
| 183 : | push @keywords, split(/\s+/, $assignment); | ||
| 184 : | parrello | 1.5 | # Add any EC numbers. |
| 185 : | parrello | 1.6 | my @ecs = BioWords::ExtractECs($assignment); |
| 186 : | for my $ec (@ecs) { | ||
| 187 : | push @keywords, $ec; | ||
| 188 : | $self->PutE(FeatureEC => $featureID, ec => $ec); | ||
| 189 : | } | ||
| 190 : | parrello | 1.1 | # Link this feature to the parent genome. |
| 191 : | parrello | 1.6 | $self->PutR(HasFeature => $genomeID, $featureID, |
| 192 : | parrello | 1.1 | type => $type); |
| 193 : | # Get the links. | ||
| 194 : | my @links = $fig->fid_links($featureID); | ||
| 195 : | for my $link (@links) { | ||
| 196 : | parrello | 1.6 | $self->PutE(FeatureLink => $featureID, link => $link); |
| 197 : | parrello | 1.1 | } |
| 198 : | # If this is a peg, generate the translation and the upstream. | ||
| 199 : | if ($type eq 'peg') { | ||
| 200 : | $self->Add(pegIn => 1); | ||
| 201 : | my $translation = $fig->get_translation($featureID); | ||
| 202 : | if ($translation) { | ||
| 203 : | parrello | 1.6 | $self->PutE(FeatureTranslation => $featureID, |
| 204 : | parrello | 1.1 | translation => $translation); |
| 205 : | } | ||
| 206 : | # We use the default upstream values of u=200 and c=100. | ||
| 207 : | my $upstream = $fig->upstream_of($featureID, 200, 100); | ||
| 208 : | if ($upstream) { | ||
| 209 : | parrello | 1.6 | $self->PutE(FeatureUpstream => $featureID, |
| 210 : | parrello | 1.1 | 'upstream-sequence' => $upstream); |
| 211 : | } | ||
| 212 : | } | ||
| 213 : | # Now we need to find the subsystems this feature participates in. | ||
| 214 : | my @ssList = $fig->subsystems_for_peg($featureID); | ||
| 215 : | # This hash prevents us from adding the same subsystem twice. | ||
| 216 : | my %seen = (); | ||
| 217 : | for my $ssEntry (@ssList) { | ||
| 218 : | # Get the subsystem and role. | ||
| 219 : | my ($subsystem, $role) = @{$ssEntry}; | ||
| 220 : | # Only proceed if we like this subsystem. | ||
| 221 : | if (exists $subHash->{$subsystem}) { | ||
| 222 : | # If this is the first time we've seen this subsystem for | ||
| 223 : | # this peg, store the has-role link. | ||
| 224 : | if (! $seen{$subsystem}) { | ||
| 225 : | parrello | 1.6 | $self->PutR(HasRoleInSubsystem => $featureID, $subsystem, |
| 226 : | genome => $genomeID, type => $type); | ||
| 227 : | parrello | 1.5 | # Save the subsystem's keywords. |
| 228 : | parrello | 1.1 | push @keywords, split /[\s_]+/, $subsystem; |
| 229 : | } | ||
| 230 : | parrello | 1.5 | # Now add the role and any embedded EC nubmers to the keyword list. |
| 231 : | parrello | 1.1 | push @keywords, split /\s+/, $role; |
| 232 : | parrello | 1.5 | push @keywords, BioWords::ExtractECs($role); |
| 233 : | parrello | 1.1 | } |
| 234 : | } | ||
| 235 : | parrello | 1.5 | # For each hyphenated word, we also need the pieces. |
| 236 : | my @hyphenated = grep { $_ =~ /-/ } @keywords; | ||
| 237 : | for my $hyphenated (@hyphenated) { | ||
| 238 : | # Bust it into pieces. | ||
| 239 : | my @pieces = grep { length($_) > 2 } split /-/, $hyphenated; | ||
| 240 : | push @keywords, @pieces; | ||
| 241 : | } | ||
| 242 : | parrello | 1.1 | # There are three special attributes computed from property |
| 243 : | # data that we build next. If the special attribute is non-empty, | ||
| 244 : | # its name will be added to the keyword list. First, we get all | ||
| 245 : | # the attributes for this feature. They will come back as | ||
| 246 : | parrello | 1.6 | # 4-tuples: [peg, name, value, URL]. |
| 247 : | my @attributes = @{$attributes->{$featureID}}; | ||
| 248 : | parrello | 1.1 | # Now we process each of the special attributes. |
| 249 : | if ($self->SpecialAttribute($featureID, \@attributes, | ||
| 250 : | parrello | 1.6 | 2, [1,3], '^(essential|potential_essential)$', |
| 251 : | parrello | 1.1 | qw(FeatureEssential essential))) { |
| 252 : | push @keywords, 'essential'; | ||
| 253 : | $self->Add(essential => 1); | ||
| 254 : | } | ||
| 255 : | if ($self->SpecialAttribute($featureID, \@attributes, | ||
| 256 : | parrello | 1.6 | 1, [2,3], '^virulen', |
| 257 : | parrello | 1.1 | qw(FeatureVirulent virulent))) { |
| 258 : | push @keywords, 'virulent'; | ||
| 259 : | $self->Add(virulent => 1); | ||
| 260 : | } | ||
| 261 : | if ($self->SpecialAttribute($featureID, \@attributes, | ||
| 262 : | parrello | 1.6 | 1, [2,3], '^iedb_', |
| 263 : | parrello | 1.1 | qw(FeatureIEDB iedb))) { |
| 264 : | push @keywords, 'iedb'; | ||
| 265 : | $self->Add(iedb => 1); | ||
| 266 : | } | ||
| 267 : | # Now we have some other attributes we need to process. To get | ||
| 268 : | # through them, we convert the attribute list for this feature | ||
| 269 : | # into a two-layer hash: key => subkey => value. | ||
| 270 : | my %attributeHash = (); | ||
| 271 : | for my $attrRow (@{$attributes->{$featureID}}) { | ||
| 272 : | my (undef, $key, @values) = @{$attrRow}; | ||
| 273 : | my ($realKey, $subKey); | ||
| 274 : | if ($key =~ /^([^:]+)::(.+)/) { | ||
| 275 : | ($realKey, $subKey) = ($1, $2); | ||
| 276 : | } else { | ||
| 277 : | ($realKey, $subKey) = ($key, ""); | ||
| 278 : | } | ||
| 279 : | if (exists $attributeHash{$realKey}) { | ||
| 280 : | $attributeHash{$realKey}->{$subKey} = \@values; | ||
| 281 : | } else { | ||
| 282 : | $attributeHash{$realKey} = {$subKey => \@values}; | ||
| 283 : | } | ||
| 284 : | } | ||
| 285 : | parrello | 1.6 | TraceDump(AttributeHash => \%attributeHash) if T(FeatureLoadGroup => 4); |
| 286 : | parrello | 1.1 | # First we handle CDD. This is a bit complicated, because |
| 287 : | # there are multiple CDDs per protein. | ||
| 288 : | if (exists $attributeHash{CDD}) { | ||
| 289 : | # Get the hash of CDD IDs to scores for this feature. We | ||
| 290 : | # already know it exists because of the above IF. | ||
| 291 : | my $cddHash = $attributeHash{CDD}; | ||
| 292 : | parrello | 1.6 | my @cddData = sort keys %$cddHash; |
| 293 : | parrello | 1.1 | for my $cdd (@cddData) { |
| 294 : | # Extract the score for this CDD and decode it. | ||
| 295 : | my ($codeScore) = split(/\s*[,;]\s*/, $cddHash->{$cdd}->[0]); | ||
| 296 : | my $realScore = FIGRules::DecodeScore($codeScore); | ||
| 297 : | # We can't afford to crash because of a bad attribute | ||
| 298 : | # value, hence the IF below. | ||
| 299 : | if (! defined($realScore)) { | ||
| 300 : | # Bad score, so count it. | ||
| 301 : | $self->Add(badCDDscore => 1); | ||
| 302 : | Trace("CDD score \"$codeScore\" for feature $featureID invalid.") if T(ERDBLoadGroup => 3); | ||
| 303 : | } else { | ||
| 304 : | # Create the connection and a CDD record. | ||
| 305 : | parrello | 1.6 | $self->PutR(IsPresentOnProteinOf => $cdd, $featureID, |
| 306 : | score => $realScore); | ||
| 307 : | $self->PutE(CDD => $cdd); | ||
| 308 : | } | ||
| 309 : | } | ||
| 310 : | } | ||
| 311 : | # A similar situation exists for protein families. | ||
| 312 : | if (exists $attributeHash{PFAM}) { | ||
| 313 : | # Get the hash of PFAMs to scores for this feature. | ||
| 314 : | my $pfamHash = $attributeHash{PFAM}; | ||
| 315 : | for my $pfam (sort keys %$pfamHash) { | ||
| 316 : | # Extract the range. | ||
| 317 : | my $codeScore = $pfamHash->{$pfam}->[0]; | ||
| 318 : | $codeScore =~ /;(.+)/; | ||
| 319 : | my $range = $1; | ||
| 320 : | # Strip off the PFAM id from the source. | ||
| 321 : | my ($pfamID) = split /_/, $pfam, 2; | ||
| 322 : | # Emit the ProteinFamily record. | ||
| 323 : | $self->PutE(ProteinFamily => $pfamID); | ||
| 324 : | # Connect it to the feature. | ||
| 325 : | $self->PutR(IsFamilyForFeature => $pfamID, $featureID, | ||
| 326 : | range => $range); | ||
| 327 : | # Get its name from the ontology database. There can | ||
| 328 : | # be at most one. | ||
| 329 : | my $dt_objs = | ||
| 330 : | $ontology_dbmaster->pfam->get_objects({id => $pfamID}); | ||
| 331 : | if (defined $dt_objs->[0]) { | ||
| 332 : | $self->PutE(ProteinFamilyName => $pfamID, | ||
| 333 : | common_name => $dt_objs->[0]->term()); | ||
| 334 : | parrello | 1.1 | } |
| 335 : | } | ||
| 336 : | } | ||
| 337 : | # Next we do PSORT cell locations. here the confidence value | ||
| 338 : | # could have the value "unknown", which we translate to -1. | ||
| 339 : | if (exists $attributeHash{PSORT}) { | ||
| 340 : | # This will be a hash of cell locations to confidence | ||
| 341 : | # factors. | ||
| 342 : | my $psortHash = $attributeHash{PSORT}; | ||
| 343 : | for my $psort (keys %{$psortHash}) { | ||
| 344 : | # Get the confidence, and convert it to a number if necessary. | ||
| 345 : | parrello | 1.6 | my $confidence = $psortHash->{$psort}->[0]; |
| 346 : | parrello | 1.1 | if ($confidence eq 'unknown') { |
| 347 : | $confidence = -1; | ||
| 348 : | } | ||
| 349 : | parrello | 1.6 | $self->PutR(IsPossiblePlaceFor => $psort, $featureID, |
| 350 : | confidence => $confidence); | ||
| 351 : | $self->PutE(CellLocation => $psort); | ||
| 352 : | parrello | 1.1 | # If this is a significant location, add it as a keyword. |
| 353 : | if ($confidence > 2.5) { | ||
| 354 : | parrello | 1.6 | # Before we add it as a keyword, we convert it from |
| 355 : | # capital-case to hyphenated by inserting hyphens at | ||
| 356 : | # case transition points. | ||
| 357 : | $psort =~ s/([a-z])([A-Z])/$1-$2/g; | ||
| 358 : | parrello | 1.1 | push @keywords, $psort; |
| 359 : | } | ||
| 360 : | } | ||
| 361 : | } | ||
| 362 : | # Phobius data is next. This consists of the signal peptide location and | ||
| 363 : | # the transmembrane locations. | ||
| 364 : | my $signalList = ""; | ||
| 365 : | my $transList = ""; | ||
| 366 : | parrello | 1.6 | my $transCount = 0; |
| 367 : | parrello | 1.1 | if (exists $attributeHash{Phobius}) { |
| 368 : | # This will be a hash of two keys (transmembrane and signal) to | ||
| 369 : | parrello | 1.6 | # location lists. GetCommaList converts them into comma-separated |
| 370 : | # location strings. If there's no value, it returns an empty string. | ||
| 371 : | parrello | 1.1 | $signalList = $self->GetCommaList($attributeHash{Phobius}->{signal}); |
| 372 : | parrello | 1.6 | my $transList = $attributeHash{Phobius}->{transmembrane}; |
| 373 : | my @transMap = split /\s*,\s*/, $transList; | ||
| 374 : | $transCount = (defined $transList ? scalar(@transMap) : 0); | ||
| 375 : | parrello | 1.1 | } |
| 376 : | # Here are some more numbers: isoelectric point, molecular weight, and | ||
| 377 : | # the similar-to-human flag. | ||
| 378 : | my $isoelectric = 0; | ||
| 379 : | if (exists $attributeHash{isoelectric_point}) { | ||
| 380 : | parrello | 1.6 | $isoelectric = $attributeHash{isoelectric_point}->{""}->[0]; |
| 381 : | parrello | 1.1 | } |
| 382 : | my $similarToHuman = 0; | ||
| 383 : | parrello | 1.6 | if (exists $attributeHash{similar_to_human} && $attributeHash{similar_to_human}->{""}->[0] eq 'yes') { |
| 384 : | parrello | 1.1 | $similarToHuman = 1; |
| 385 : | } | ||
| 386 : | my $molecularWeight = 0; | ||
| 387 : | if (exists $attributeHash{molecular_weight}) { | ||
| 388 : | parrello | 1.6 | $molecularWeight = $attributeHash{molecular_weight}->{""}->[0]; |
| 389 : | parrello | 1.1 | } |
| 390 : | # Join the keyword string. | ||
| 391 : | my $keywordString = join(" ", @keywords); | ||
| 392 : | # Get rid of annoying punctuation. | ||
| 393 : | parrello | 1.5 | $keywordString =~ s/[();@#\/,]/ /g; |
| 394 : | parrello | 1.6 | # Get the list of keywords in the keyword string, minus the delimiters. |
| 395 : | my @realKeywords = grep { $stemmer->IsWord($_) } | ||
| 396 : | $stemmer->Split($keywordString); | ||
| 397 : | parrello | 1.1 | # We need to do two things here: create the keyword string for the feature table |
| 398 : | # and write records to the keyword table for the keywords. | ||
| 399 : | my (%keys, %stems, @realStems); | ||
| 400 : | for my $keyword (@realKeywords) { | ||
| 401 : | # Compute the stem and phonex for this keyword. | ||
| 402 : | my ($stem, $phonex) = $stemmer->StemLookup($keyword); | ||
| 403 : | # Only proceed if a stem comes back. If no stem came back, it's a | ||
| 404 : | # stop word and we throw it away. | ||
| 405 : | if ($stem) { | ||
| 406 : | $keys{$keyword} = $stem; | ||
| 407 : | $stems{$stem} = $phonex; | ||
| 408 : | push @realStems, $stem; | ||
| 409 : | } | ||
| 410 : | } | ||
| 411 : | # Now create the keyword string. | ||
| 412 : | my $cleanWords = join(" ", @realStems); | ||
| 413 : | Trace("Keyword string for $featureID: $cleanWords") if T(ERDBLoadGroup => 4); | ||
| 414 : | # Create keyword table entries for the keywords found. | ||
| 415 : | for my $key (keys %keys) { | ||
| 416 : | my $stem = $keys{$key}; | ||
| 417 : | parrello | 1.6 | $self->PutE(Keyword => $key, stem => $stem, phonex => $stems{$stem}); |
| 418 : | parrello | 1.1 | } |
| 419 : | # Now we need to process the feature's locations. First, we split them up. | ||
| 420 : | my @locationList = split /\s*,\s*/, $locations; | ||
| 421 : | # Next, we convert them to Sprout location objects. | ||
| 422 : | my @locObjectList = map { BasicLocation->new("$genomeID:$_") } @locationList; | ||
| 423 : | # Assemble them into a sprout location string for later. | ||
| 424 : | my $locationString = join(", ", map { $_->String } @locObjectList); | ||
| 425 : | # We'll store the sequence length in here. | ||
| 426 : | my $sequenceLength = 0; | ||
| 427 : | # This part is the roughest. We need to relate the features to contig | ||
| 428 : | # locations, and the locations must be split so that none of them exceed | ||
| 429 : | # the maximum segment size. This simplifies the genes_in_region processing | ||
| 430 : | # for Sprout. To start, we create the location position indicator. | ||
| 431 : | my $i = 1; | ||
| 432 : | # Loop through the locations. | ||
| 433 : | for my $locObject (@locObjectList) { | ||
| 434 : | # Record the length. | ||
| 435 : | $sequenceLength += $locObject->Length; | ||
| 436 : | # Split this location into a list of chunks. | ||
| 437 : | my @locOList = (); | ||
| 438 : | while (my $peeling = $locObject->Peel($chunkSize)) { | ||
| 439 : | $self->Add(peeling => 1); | ||
| 440 : | push @locOList, $peeling; | ||
| 441 : | } | ||
| 442 : | push @locOList, $locObject; | ||
| 443 : | # Loop through the chunks, creating IsLocatedIn records. The variable | ||
| 444 : | # "$i" will be used to keep the location index. | ||
| 445 : | for my $locChunk (@locOList) { | ||
| 446 : | parrello | 1.6 | $self->PutR(IsLocatedIn => $featureID, $locChunk->Contig, |
| 447 : | beg => $locChunk->Left, dir => $locChunk->Dir, | ||
| 448 : | len => $locChunk->Length, locN => $i); | ||
| 449 : | parrello | 1.1 | $i++; |
| 450 : | } | ||
| 451 : | } | ||
| 452 : | parrello | 1.6 | # Check for figfams. In case we find any, we need the range. |
| 453 : | # It's the whole sequence. | ||
| 454 : | my $range = "1-$sequenceLength"; | ||
| 455 : | # Ask for the figfams. | ||
| 456 : | my @fams = $ffs->families_containing_peg($featureID); | ||
| 457 : | # Connect them to the feature (if any). | ||
| 458 : | for my $fam (@fams) { | ||
| 459 : | $self->PutE(ProteinFamily => $fam); | ||
| 460 : | $self->PutR(IsFamilyForFeature => $fam, $featureID, | ||
| 461 : | range => $range); | ||
| 462 : | } | ||
| 463 : | parrello | 1.1 | # Now we get some ancillary flags. |
| 464 : | my $locked = $fig->is_locked_fid($featureID); | ||
| 465 : | my $in_genbank = $fig->peg_in_gendb($featureID); | ||
| 466 : | # Create the feature record. | ||
| 467 : | parrello | 1.6 | $self->PutE(Feature => $featureID, 'assignment-maker' => $user, |
| 468 : | parrello | 1.1 | 'assignment-quality' => $quality, 'feature-type' => $type, |
| 469 : | 'in-genbank' => $in_genbank, 'isoelectric-point' => $isoelectric, | ||
| 470 : | locked => $locked, 'molecular-weight' => $molecularWeight, | ||
| 471 : | 'sequence-length' => $sequenceLength, | ||
| 472 : | 'signal-peptide' => $signalList, 'similar-to-human' => $similarToHuman, | ||
| 473 : | assignment => $assignment, keywords => $cleanWords, | ||
| 474 : | 'location-string' => $locationString, | ||
| 475 : | parrello | 1.6 | 'transmembrane-map' => $transList, |
| 476 : | 'conserved-neighbors' => $couplingCount, | ||
| 477 : | 'transmembrane-domain-count' => $transCount); | ||
| 478 : | parrello | 1.1 | } |
| 479 : | } | ||
| 480 : | } | ||
| 481 : | } | ||
| 482 : | |||
| 483 : | |||
| 484 : | =head3 SpecialAttribute | ||
| 485 : | |||
| 486 : | my $count = $sl->SpecialAttribute($id, \@attributes, $idxMatch, \@idxValues, $pattern, $tableName, $field); | ||
| 487 : | |||
| 488 : | Look for special attributes of a given type. A special attribute is found by comparing one of | ||
| 489 : | the columns of the incoming attribute list to a search pattern. If a match is found, then | ||
| 490 : | a set of columns is put into an output table connected to the specified ID. | ||
| 491 : | |||
| 492 : | For example, when processing features, the attribute list we look at has three columns: attribute | ||
| 493 : | name, attribute value, and attribute value HTML. The IEDB attribute exists if the attribute name | ||
| 494 : | begins with C<iedb_>. The call signature is therefore | ||
| 495 : | |||
| 496 : | my $found = SpecialAttribute($fid, \@attributeList, 0, [0,2], '^iedb_', 'FeatureIEDB', 'iedb'); | ||
| 497 : | |||
| 498 : | The pattern is matched against column 0, and if we have a match, then column 2's value is put | ||
| 499 : | to the output along with the specified feature ID. | ||
| 500 : | |||
| 501 : | =over 4 | ||
| 502 : | |||
| 503 : | =item id | ||
| 504 : | |||
| 505 : | ID of the object whose special attributes are being loaded. This forms the first column of the | ||
| 506 : | output. | ||
| 507 : | |||
| 508 : | =item attributes | ||
| 509 : | |||
| 510 : | Reference to a list of tuples. | ||
| 511 : | |||
| 512 : | =item idxMatch | ||
| 513 : | |||
| 514 : | Index in each tuple of the column to be matched against the pattern. If the match is | ||
| 515 : | successful, an output record will be generated. | ||
| 516 : | |||
| 517 : | =item idxValues | ||
| 518 : | |||
| 519 : | parrello | 1.6 | Reference to a list containing the indexes of the value and URL to put in the |
| 520 : | second column of the output. | ||
| 521 : | parrello | 1.1 | |
| 522 : | =item pattern | ||
| 523 : | |||
| 524 : | Pattern to be matched against the specified column. The match will be case-insensitive. | ||
| 525 : | |||
| 526 : | =item tableName | ||
| 527 : | |||
| 528 : | Name of the table to contain the attribute values found. | ||
| 529 : | |||
| 530 : | =item fieldName | ||
| 531 : | |||
| 532 : | Name of the field to contain the attribute values in the output table. | ||
| 533 : | |||
| 534 : | =item RETURN | ||
| 535 : | |||
| 536 : | Returns a count of the matches found. | ||
| 537 : | |||
| 538 : | =item | ||
| 539 : | |||
| 540 : | =back | ||
| 541 : | |||
| 542 : | =cut | ||
| 543 : | |||
| 544 : | sub SpecialAttribute { | ||
| 545 : | # Get the parameters. | ||
| 546 : | my ($self, $id, $attributes, $idxMatch, $idxValues, $pattern, $tableName, $fieldName) = @_; | ||
| 547 : | # Declare the return variable. | ||
| 548 : | my $retVal = 0; | ||
| 549 : | # Loop through the attribute rows. | ||
| 550 : | for my $row (@{$attributes}) { | ||
| 551 : | # Check for a match. | ||
| 552 : | if ($row->[$idxMatch] =~ m/$pattern/i) { | ||
| 553 : | parrello | 1.6 | # We have a match, so output a row. |
| 554 : | my $value = HyperLink->new(map { $row->[$_] } @$idxValues); | ||
| 555 : | $self->PutE($tableName => $id, $fieldName => $value); | ||
| 556 : | parrello | 1.1 | $retVal++; |
| 557 : | } | ||
| 558 : | } | ||
| 559 : | Trace("$retVal special attributes found for $id and table $tableName.") if T(ERDBLoadGroup => 4) && $retVal; | ||
| 560 : | # Return the number of matches. | ||
| 561 : | return $retVal; | ||
| 562 : | } | ||
| 563 : | |||
| 564 : | 1; |
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