org.opencb.cellbase.lib.variant.VariantAnnotationUtils Maven / Gradle / Ivy
/*
* Copyright 2015-2020 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.cellbase.lib.variant;
import org.apache.commons.lang3.StringUtils;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.annotation.ConsequenceTypeMappings;
import org.opencb.biodata.models.variant.annotation.exceptions.SOTermNotAvailableException;
import org.opencb.biodata.models.variant.avro.*;
import org.opencb.cellbase.lib.variant.annotation.UnsupportedURLVariantFormat;
import java.util.*;
/**
* Created by fjlopez on 22/06/15.
*/
public class VariantAnnotationUtils {
public static final char SEPARATOR_CHAR = ':';
public static final String THREEPRIME_OVERLAPPING_NCRNA = "3prime_overlapping_ncrna";
public static final String IG_C_GENE = "IG_C_gene";
public static final String IG_C_PSEUDOGENE = "IG_C_pseudogene";
public static final String IG_D_GENE = "IG_D_gene";
public static final String IG_J_GENE = "IG_J_gene";
public static final String IG_J_PSEUDOGENE = "IG_J_pseudogene";
public static final String IG_V_GENE = "IG_V_gene";
public static final String IG_V_PSEUDOGENE = "IG_V_pseudogene";
public static final String MT_RRNA = "Mt_rRNA";
public static final String MT_TRNA = "Mt_tRNA";
public static final String TR_C_GENE = "TR_C_gene";
public static final String TR_D_GENE = "TR_D_gene";
public static final String TR_J_GENE = "TR_J_gene";
public static final String TR_J_PSEUDOGENE = "TR_J_pseudogene";
public static final String TR_V_GENE = "TR_V_gene";
public static final String TR_V_PSEUDOGENE = "TR_V_pseudogene";
public static final String ANTISENSE = "antisense";
public static final String LINCRNA = "lincRNA";
public static final String MIRNA = "miRNA";
public static final String MISC_RNA = "misc_RNA";
public static final String POLYMORPHIC_PSEUDOGENE = "polymorphic_pseudogene";
public static final String PROCESSED_PSEUDOGENE = "processed_pseudogene";
public static final String PROCESSED_TRANSCRIPT = "processed_transcript";
public static final String PROTEIN_CODING = "protein_coding";
public static final String PSEUDOGENE = "pseudogene";
public static final String RRNA = "rRNA";
public static final String SENSE_INTRONIC = "sense_intronic";
public static final String SENSE_OVERLAPPING = "sense_overlapping";
public static final String SNRNA = "snRNA";
public static final String SNORNA = "snoRNA";
public static final String NONSENSE_MEDIATED_DECAY = "nonsense_mediated_decay";
public static final String NMD_TRANSCRIPT_VARIANT = "NMD_transcript_variant";
public static final String UNPROCESSED_PSEUDOGENE = "unprocessed_pseudogene";
public static final String TRANSCRIBED_UNPROCESSED_PSEUDGENE = "transcribed_unprocessed_pseudogene";
public static final String RETAINED_INTRON = "retained_intron";
public static final String NON_STOP_DECAY = "non_stop_decay";
public static final String UNITARY_PSEUDOGENE = "unitary_pseudogene";
public static final String TRANSLATED_PROCESSED_PSEUDOGENE = "translated_processed_pseudogene";
public static final String TRANSCRIBED_PROCESSED_PSEUDOGENE = "transcribed_processed_pseudogene";
public static final String TRNA_PSEUDOGENE = "tRNA_pseudogene";
public static final String SNORNA_PSEUDOGENE = "snoRNA_pseudogene";
public static final String SNRNA_PSEUDOGENE = "snRNA_pseudogene";
public static final String SCRNA_PSEUDOGENE = "scRNA_pseudogene";
public static final String RRNA_PSEUDOGENE = "rRNA_pseudogene";
public static final String MISC_RNA_PSEUDOGENE = "misc_RNA_pseudogene";
public static final String MIRNA_PSEUDOGENE = "miRNA_pseudogene";
public static final String NON_CODING = "non_coding";
public static final String AMBIGUOUS_ORF = "ambiguous_orf";
public static final String KNOWN_NCRNA = "known_ncrna";
public static final String RETROTRANSPOSED = "retrotransposed";
public static final String TRANSCRIBED_UNITARY_PSEUDOGENE = "transcribed_unitary_pseudogene";
public static final String TRANSLATED_UNPROCESSED_PSEUDOGENE = "translated_unprocessed_pseudogene";
public static final String LRG_GENE = "LRG_gene";
public static final String INTERGENIC_VARIANT = "intergenic_variant";
public static final String REGULATORY_REGION_VARIANT = "regulatory_region_variant";
public static final String TF_BINDING_SITE_VARIANT = "TF_binding_site_variant";
public static final String UPSTREAM_GENE_VARIANT = "upstream_gene_variant";
public static final String TWOKB_UPSTREAM_VARIANT = "2KB_upstream_variant";
public static final String DOWNSTREAM_GENE_VARIANT = "downstream_gene_variant";
public static final String TWOKB_DOWNSTREAM_VARIANT = "2KB_downstream_variant";
public static final String SPLICE_DONOR_VARIANT = "splice_donor_variant";
public static final String SPLICE_ACCEPTOR_VARIANT = "splice_acceptor_variant";
public static final String INTRON_VARIANT = "intron_variant";
public static final String SPLICE_REGION_VARIANT = "splice_region_variant";
public static final String FIVE_PRIME_UTR_VARIANT = "5_prime_UTR_variant";
public static final String THREE_PRIME_UTR_VARIANT = "3_prime_UTR_variant";
public static final String INCOMPLETE_TERMINAL_CODON_VARIANT = "incomplete_terminal_codon_variant";
public static final String STOP_RETAINED_VARIANT = "stop_retained_variant";
public static final String START_RETAINED_VARIANT = "start_retained_variant";
public static final String SYNONYMOUS_VARIANT = "synonymous_variant";
public static final String INITIATOR_CODON_VARIANT = "initiator_codon_variant";
public static final String START_LOST = "start_lost";
public static final String STOP_GAINED = "stop_gained";
public static final String STOP_LOST = "stop_lost";
public static final String MISSENSE_VARIANT = "missense_variant";
public static final String MATURE_MIRNA_VARIANT = "mature_miRNA_variant";
public static final String NON_CODING_TRANSCRIPT_EXON_VARIANT = "non_coding_transcript_exon_variant";
public static final String NON_CODING_TRANSCRIPT_VARIANT = "non_coding_transcript_variant";
public static final String INFRAME_INSERTION = "inframe_insertion";
public static final String INFRAME_VARIANT = "inframe_variant";
public static final String FRAMESHIFT_VARIANT = "frameshift_variant";
public static final String CODING_SEQUENCE_VARIANT = "coding_sequence_variant";
public static final String TRANSCRIPT_ABLATION = "transcript_ablation";
public static final String TRANSCRIPT_AMPLIFICATION = "transcript_amplification";
public static final String COPY_NUMBER_CHANGE = "copy_number_change";
public static final String TERMINATOR_CODON_VARIANT = "terminator_codon_variant";
public static final String FEATURE_TRUNCATION = "feature_truncation";
public static final String FEATURE_VARIANT = "feature_variant";
public static final String STRUCTURAL_VARIANT = "structural_variant";
public static final String INFRAME_DELETION = "inframe_deletion";
public static final String CDS_START_NF = "cds_start_NF";
public static final String CDS_END_NF = "cds_end_NF";
public static final Map> IS_SYNONYMOUS_CODON = new HashMap<>();
public static final Map> MT_IS_SYNONYMOUS_CODON = new HashMap<>();
public static final Map SO_NAMES_CORRECTIONS = new HashMap<>();
public static final Map> A_TO_CODON = new HashMap<>();
public static final Map> MT_A_TO_CODON = new HashMap<>();
public static final Map CODON_TO_A = new HashMap<>();
public static final Map MT_CODON_TO_A = new HashMap<>();
public static final Map COMPLEMENTARY_NT = new HashMap<>();
public static final Map SIFT_DESCRIPTIONS = new HashMap<>();
public static final Map POLYPHEN_DESCRIPTIONS = new HashMap<>();
public static final Map SO_SEVERITY = new HashMap<>();
public static final Map ORIGIN_STRING_TO_ALLELE_ORIGIN = new HashMap<>();
public static final Set CODING_SO_NAMES = new HashSet<>();
public static final Map CLINVAR_CLINSIG_TO_ACMG = new HashMap<>();
public static final Map CLINVAR_CLINSIG_TO_TRAIT_ASSOCIATION = new HashMap<>();
public static final HashMap CLINVAR_REVIEW_TO_CONSISTENCY_STATUS = new HashMap<>();
// Currently left empty since the only item within DrugResponseClassification that seemed to match any clinvar
// tag ("responsive") was removed at some point from the model
public static final Map CLINVAR_CLINSIG_TO_DRUG_RESPONSE = new HashMap<>();
public static final String MT = "MT";
public static final String UNKNOWN_AMINOACID = "X";
public static final HashMap MODEOFINHERITANCE_MAP = new HashMap<>();
public static final HashMap COSMIC_SOMATICSTATUS_TO_ALLELE_ORIGIN = new HashMap<>();
public static final HashMap TO_ABBREVIATED_AA = new HashMap<>(40); // 22 AA
public static final HashMap TO_LONG_AA = new HashMap<>(40); // 22 AA
private static final String ATG = "ATG";
private static final String ATA = "ATA";
private static final String TAA = "TAA";
private static final String TAG = "TAG";
private static final String AGA = "AGA";
private static final String AGG = "AGG";
private static final String TGA = "TGA";
static {
MODEOFINHERITANCE_MAP.put("autosomal dominant inheritance", ModeOfInheritance.monoallelic);
MODEOFINHERITANCE_MAP.put("autosomal dominant inheritance with maternal imprinting",
ModeOfInheritance.monoallelic_maternally_imprinted);
MODEOFINHERITANCE_MAP.put("autosomal dominant inheritance with paternal imprinting",
ModeOfInheritance.monoallelic_paternally_imprinted);
MODEOFINHERITANCE_MAP.put("autosomal recessive inheritance",
ModeOfInheritance.biallelic);
MODEOFINHERITANCE_MAP.put("mitochondrial inheritance",
ModeOfInheritance.mitochondrial);
MODEOFINHERITANCE_MAP.put("sex-limited autosomal dominant",
ModeOfInheritance.monoallelic);
MODEOFINHERITANCE_MAP.put("x-linked dominant inheritance",
ModeOfInheritance.xlinked_monoallelic);
MODEOFINHERITANCE_MAP.put("x-linked recessive inheritance",
ModeOfInheritance.xlinked_biallelic);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("criteria_provided_conflicting_interpretations", ConsistencyStatus.conflict);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("criteria_provided_multiple_submitters_no_conflicts", ConsistencyStatus.congruent);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("criteria_provided_single_submitter", ConsistencyStatus.congruent);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("reviewed_by_expert_panel", ConsistencyStatus.congruent);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("conflicting interpretations", ConsistencyStatus.conflict);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("no conflicts", ConsistencyStatus.congruent);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("single submitter", ConsistencyStatus.congruent);
CLINVAR_REVIEW_TO_CONSISTENCY_STATUS.put("reviewed by expert panel", ConsistencyStatus.congruent);
CLINVAR_CLINSIG_TO_ACMG.put("benign", ClinicalSignificance.benign);
CLINVAR_CLINSIG_TO_ACMG.put("likely benign", ClinicalSignificance.likely_benign);
CLINVAR_CLINSIG_TO_ACMG.put("conflicting interpretations of pathogenicity", ClinicalSignificance.uncertain_significance);
CLINVAR_CLINSIG_TO_ACMG.put("likely pathogenic", ClinicalSignificance.likely_pathogenic);
CLINVAR_CLINSIG_TO_ACMG.put("pathogenic", ClinicalSignificance.pathogenic);
CLINVAR_CLINSIG_TO_ACMG.put("uncertain significance", ClinicalSignificance.uncertain_significance);
CLINVAR_CLINSIG_TO_ACMG.put("conflicting data from submitters", ClinicalSignificance.uncertain_significance);
CLINVAR_CLINSIG_TO_TRAIT_ASSOCIATION.put("risk factor", TraitAssociation.established_risk_allele);
CLINVAR_CLINSIG_TO_TRAIT_ASSOCIATION.put("protective", TraitAssociation.protective);
///////////////////////////////////////////////////////////////////////
///// ClinVar and Cosmic allele origins to SO terms ///////////////
///////////////////////////////////////////////////////////////////////
ORIGIN_STRING_TO_ALLELE_ORIGIN.put("germline", AlleleOrigin.germline_variant);
ORIGIN_STRING_TO_ALLELE_ORIGIN.put("maternal", AlleleOrigin.maternal_variant);
ORIGIN_STRING_TO_ALLELE_ORIGIN.put("de novo", AlleleOrigin.de_novo_variant);
ORIGIN_STRING_TO_ALLELE_ORIGIN.put("paternal", AlleleOrigin.paternal_variant);
ORIGIN_STRING_TO_ALLELE_ORIGIN.put("somatic", AlleleOrigin.somatic_variant);
///////////////////////////////////////////////////////////////////////
///// GENETIC CODE ////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////
A_TO_CODON.put("ALA", new ArrayList());
A_TO_CODON.get("ALA").add("GCT");
A_TO_CODON.get("ALA").add("GCC");
A_TO_CODON.get("ALA").add("GCA");
A_TO_CODON.get("ALA").add("GCG");
A_TO_CODON.put("ARG", new ArrayList());
A_TO_CODON.get("ARG").add("CGT");
A_TO_CODON.get("ARG").add("CGC");
A_TO_CODON.get("ARG").add("CGA");
A_TO_CODON.get("ARG").add("CGG");
A_TO_CODON.get("ARG").add("AGA");
A_TO_CODON.get("ARG").add("AGG");
A_TO_CODON.put("ASN", new ArrayList());
A_TO_CODON.get("ASN").add("AAT");
A_TO_CODON.get("ASN").add("AAC");
A_TO_CODON.put("ASP", new ArrayList());
A_TO_CODON.get("ASP").add("GAT");
A_TO_CODON.get("ASP").add("GAC");
A_TO_CODON.put("CYS", new ArrayList());
A_TO_CODON.get("CYS").add("TGT");
A_TO_CODON.get("CYS").add("TGC");
A_TO_CODON.put("GLN", new ArrayList());
A_TO_CODON.get("GLN").add("CAA");
A_TO_CODON.get("GLN").add("CAG");
A_TO_CODON.put("GLU", new ArrayList());
A_TO_CODON.get("GLU").add("GAA");
A_TO_CODON.get("GLU").add("GAG");
A_TO_CODON.put("GLY", new ArrayList());
A_TO_CODON.get("GLY").add("GGT");
A_TO_CODON.get("GLY").add("GGC");
A_TO_CODON.get("GLY").add("GGA");
A_TO_CODON.get("GLY").add("GGG");
A_TO_CODON.put("HIS", new ArrayList());
A_TO_CODON.get("HIS").add("CAT");
A_TO_CODON.get("HIS").add("CAC");
A_TO_CODON.put("ILE", new ArrayList());
A_TO_CODON.get("ILE").add("ATT");
A_TO_CODON.get("ILE").add("ATC");
A_TO_CODON.get("ILE").add("ATA");
A_TO_CODON.put("LEU", new ArrayList());
A_TO_CODON.get("LEU").add("TTA");
A_TO_CODON.get("LEU").add("TTG");
A_TO_CODON.get("LEU").add("CTT");
A_TO_CODON.get("LEU").add("CTC");
A_TO_CODON.get("LEU").add("CTA");
A_TO_CODON.get("LEU").add("CTG");
A_TO_CODON.put("LYS", new ArrayList());
A_TO_CODON.get("LYS").add("AAA");
A_TO_CODON.get("LYS").add("AAG");
A_TO_CODON.put("MET", new ArrayList());
A_TO_CODON.get("MET").add("ATG");
A_TO_CODON.put("PHE", new ArrayList());
A_TO_CODON.get("PHE").add("TTT");
A_TO_CODON.get("PHE").add("TTC");
A_TO_CODON.put("PRO", new ArrayList());
A_TO_CODON.get("PRO").add("CCT");
A_TO_CODON.get("PRO").add("CCC");
A_TO_CODON.get("PRO").add("CCA");
A_TO_CODON.get("PRO").add("CCG");
A_TO_CODON.put("SER", new ArrayList());
A_TO_CODON.get("SER").add("TCT");
A_TO_CODON.get("SER").add("TCC");
A_TO_CODON.get("SER").add("TCA");
A_TO_CODON.get("SER").add("TCG");
A_TO_CODON.get("SER").add("AGT");
A_TO_CODON.get("SER").add("AGC");
A_TO_CODON.put("THR", new ArrayList());
A_TO_CODON.get("THR").add("ACT");
A_TO_CODON.get("THR").add("ACC");
A_TO_CODON.get("THR").add("ACA");
A_TO_CODON.get("THR").add("ACG");
A_TO_CODON.put("TRP", new ArrayList());
A_TO_CODON.get("TRP").add("TGG");
A_TO_CODON.put("TYR", new ArrayList());
A_TO_CODON.get("TYR").add("TAT");
A_TO_CODON.get("TYR").add("TAC");
A_TO_CODON.put("VAL", new ArrayList());
A_TO_CODON.get("VAL").add("GTT");
A_TO_CODON.get("VAL").add("GTC");
A_TO_CODON.get("VAL").add("GTA");
A_TO_CODON.get("VAL").add("GTG");
A_TO_CODON.put("STOP", new ArrayList());
A_TO_CODON.get("STOP").add("TAA");
A_TO_CODON.get("STOP").add("TGA");
A_TO_CODON.get("STOP").add("TAG");
for (String aa : A_TO_CODON.keySet()) {
for (String codon : A_TO_CODON.get(aa)) {
IS_SYNONYMOUS_CODON.put(codon, new HashMap());
CODON_TO_A.put(codon, aa);
}
}
for (String codon1 : IS_SYNONYMOUS_CODON.keySet()) {
Map codonEntry = IS_SYNONYMOUS_CODON.get(codon1);
for (String codon2 : IS_SYNONYMOUS_CODON.keySet()) {
codonEntry.put(codon2, false);
}
}
for (String aa : A_TO_CODON.keySet()) {
for (String codon1 : A_TO_CODON.get(aa)) {
for (String codon2 : A_TO_CODON.get(aa)) {
IS_SYNONYMOUS_CODON.get(codon1).put(codon2, true);
}
}
}
///////////////////////////////////////////////////////////////////////
///// MITOCHONDRIAL GENETIC CODE //////////////////////////////////
///////////////////////////////////////////////////////////////////////
MT_A_TO_CODON.put("ALA", new ArrayList());
MT_A_TO_CODON.get("ALA").add("GCT");
MT_A_TO_CODON.get("ALA").add("GCC");
MT_A_TO_CODON.get("ALA").add("GCA");
MT_A_TO_CODON.get("ALA").add("GCG");
MT_A_TO_CODON.put("ARG", new ArrayList());
MT_A_TO_CODON.get("ARG").add("CGT");
MT_A_TO_CODON.get("ARG").add("CGC");
MT_A_TO_CODON.get("ARG").add("CGA");
MT_A_TO_CODON.get("ARG").add("CGG");
MT_A_TO_CODON.put("ASN", new ArrayList());
MT_A_TO_CODON.get("ASN").add("AAT");
MT_A_TO_CODON.get("ASN").add("AAC");
MT_A_TO_CODON.put("ASP", new ArrayList());
MT_A_TO_CODON.get("ASP").add("GAT");
MT_A_TO_CODON.get("ASP").add("GAC");
MT_A_TO_CODON.put("CYS", new ArrayList());
MT_A_TO_CODON.get("CYS").add("TGT");
MT_A_TO_CODON.get("CYS").add("TGC");
MT_A_TO_CODON.put("GLN", new ArrayList());
MT_A_TO_CODON.get("GLN").add("CAA");
MT_A_TO_CODON.get("GLN").add("CAG");
MT_A_TO_CODON.put("GLU", new ArrayList());
MT_A_TO_CODON.get("GLU").add("GAA");
MT_A_TO_CODON.get("GLU").add("GAG");
MT_A_TO_CODON.put("GLY", new ArrayList());
MT_A_TO_CODON.get("GLY").add("GGT");
MT_A_TO_CODON.get("GLY").add("GGC");
MT_A_TO_CODON.get("GLY").add("GGA");
MT_A_TO_CODON.get("GLY").add("GGG");
MT_A_TO_CODON.put("HIS", new ArrayList());
MT_A_TO_CODON.get("HIS").add("CAT");
MT_A_TO_CODON.get("HIS").add("CAC");
MT_A_TO_CODON.put("ILE", new ArrayList());
MT_A_TO_CODON.get("ILE").add("ATT");
MT_A_TO_CODON.get("ILE").add("ATC");
MT_A_TO_CODON.put("LEU", new ArrayList());
MT_A_TO_CODON.get("LEU").add("TTA");
MT_A_TO_CODON.get("LEU").add("TTG");
MT_A_TO_CODON.get("LEU").add("CTT");
MT_A_TO_CODON.get("LEU").add("CTC");
MT_A_TO_CODON.get("LEU").add("CTA");
MT_A_TO_CODON.get("LEU").add("CTG");
MT_A_TO_CODON.put("LYS", new ArrayList());
MT_A_TO_CODON.get("LYS").add("AAA");
MT_A_TO_CODON.get("LYS").add("AAG");
MT_A_TO_CODON.put("MET", new ArrayList());
MT_A_TO_CODON.get("MET").add("ATG");
MT_A_TO_CODON.get("MET").add("ATA");
MT_A_TO_CODON.put("PHE", new ArrayList());
MT_A_TO_CODON.get("PHE").add("TTT");
MT_A_TO_CODON.get("PHE").add("TTC");
MT_A_TO_CODON.put("PRO", new ArrayList());
MT_A_TO_CODON.get("PRO").add("CCT");
MT_A_TO_CODON.get("PRO").add("CCC");
MT_A_TO_CODON.get("PRO").add("CCA");
MT_A_TO_CODON.get("PRO").add("CCG");
// A_TO_CODON.put("SEC", new ArrayList<>());
// A_TO_CODON.get("SEC").add("TGA");
MT_A_TO_CODON.put("SER", new ArrayList());
MT_A_TO_CODON.get("SER").add("TCT");
MT_A_TO_CODON.get("SER").add("TCC");
MT_A_TO_CODON.get("SER").add("TCA");
MT_A_TO_CODON.get("SER").add("TCG");
MT_A_TO_CODON.get("SER").add("AGT");
MT_A_TO_CODON.get("SER").add("AGC");
MT_A_TO_CODON.put("THR", new ArrayList());
MT_A_TO_CODON.get("THR").add("ACT");
MT_A_TO_CODON.get("THR").add("ACC");
MT_A_TO_CODON.get("THR").add("ACA");
MT_A_TO_CODON.get("THR").add("ACG");
MT_A_TO_CODON.put("TRP", new ArrayList());
MT_A_TO_CODON.get("TRP").add("TGG");
MT_A_TO_CODON.get("TRP").add("TGA");
MT_A_TO_CODON.put("TYR", new ArrayList());
MT_A_TO_CODON.get("TYR").add("TAT");
MT_A_TO_CODON.get("TYR").add("TAC");
MT_A_TO_CODON.put("VAL", new ArrayList());
MT_A_TO_CODON.get("VAL").add("GTT");
MT_A_TO_CODON.get("VAL").add("GTC");
MT_A_TO_CODON.get("VAL").add("GTA");
MT_A_TO_CODON.get("VAL").add("GTG");
MT_A_TO_CODON.put("STOP", new ArrayList());
MT_A_TO_CODON.get("STOP").add("TAA");
MT_A_TO_CODON.get("STOP").add("TAG");
MT_A_TO_CODON.get("STOP").add("AGA");
MT_A_TO_CODON.get("STOP").add("AGG");
for (String aa : MT_A_TO_CODON.keySet()) {
for (String codon : MT_A_TO_CODON.get(aa)) {
MT_IS_SYNONYMOUS_CODON.put(codon, new HashMap());
MT_CODON_TO_A.put(codon, aa);
}
}
for (String codon1 : MT_IS_SYNONYMOUS_CODON.keySet()) {
Map codonEntry = MT_IS_SYNONYMOUS_CODON.get(codon1);
for (String codon2 : MT_IS_SYNONYMOUS_CODON.keySet()) {
codonEntry.put(codon2, false);
}
}
for (String aa : MT_A_TO_CODON.keySet()) {
for (String codon1 : MT_A_TO_CODON.get(aa)) {
for (String codon2 : MT_A_TO_CODON.get(aa)) {
MT_IS_SYNONYMOUS_CODON.get(codon1).put(codon2, true);
}
}
}
/*
Aminoacid abbreviation map
*/
TO_ABBREVIATED_AA.put("ALA", "A");
TO_ABBREVIATED_AA.put("ARG", "R");
TO_ABBREVIATED_AA.put("ASN", "N");
TO_ABBREVIATED_AA.put("ASP", "D");
TO_ABBREVIATED_AA.put("ASX", "B");
TO_ABBREVIATED_AA.put("CYS", "C");
TO_ABBREVIATED_AA.put("GLU", "E");
TO_ABBREVIATED_AA.put("GLN", "Q");
TO_ABBREVIATED_AA.put("GLX", "Z");
TO_ABBREVIATED_AA.put("GLY", "G");
TO_ABBREVIATED_AA.put("HIS", "H");
TO_ABBREVIATED_AA.put("ILE", "I");
TO_ABBREVIATED_AA.put("LEU", "L");
TO_ABBREVIATED_AA.put("LYS", "K");
TO_ABBREVIATED_AA.put("MET", "M");
TO_ABBREVIATED_AA.put("PHE", "F");
TO_ABBREVIATED_AA.put("PRO", "P");
TO_ABBREVIATED_AA.put("SEC", "U");
TO_ABBREVIATED_AA.put("SER", "S");
TO_ABBREVIATED_AA.put("THR", "T");
TO_ABBREVIATED_AA.put("TRP", "W");
TO_ABBREVIATED_AA.put("TYR", "Y");
TO_ABBREVIATED_AA.put("VAL", "V");
TO_ABBREVIATED_AA.put("STOP", "O");
for (String aa : TO_ABBREVIATED_AA.keySet()) {
TO_LONG_AA.put(TO_ABBREVIATED_AA.get(aa), buildUpperLowerCaseString(aa));
}
COMPLEMENTARY_NT.put('A', 'T');
COMPLEMENTARY_NT.put('C', 'G');
COMPLEMENTARY_NT.put('G', 'C');
COMPLEMENTARY_NT.put('T', 'A');
COMPLEMENTARY_NT.put('N', 'N');
POLYPHEN_DESCRIPTIONS.put(0, "probably damaging");
POLYPHEN_DESCRIPTIONS.put(1, "possibly damaging");
POLYPHEN_DESCRIPTIONS.put(2, "benign");
POLYPHEN_DESCRIPTIONS.put(3, "unknown");
SIFT_DESCRIPTIONS.put(0, "tolerated");
SIFT_DESCRIPTIONS.put(1, "deleterious");
SO_SEVERITY.put("copy_number_change", 42);
SO_SEVERITY.put("transcript_ablation", 41);
SO_SEVERITY.put("structural_variant", 40);
SO_SEVERITY.put("splice_acceptor_variant", 39);
SO_SEVERITY.put("splice_donor_variant", 38);
SO_SEVERITY.put("stop_gained", 37);
SO_SEVERITY.put("frameshift_variant", 36);
SO_SEVERITY.put("stop_lost", 35);
SO_SEVERITY.put("terminator_codon_variant", 34);
SO_SEVERITY.put("start_lost", 34);
SO_SEVERITY.put("initiator_codon_variant", 33);
SO_SEVERITY.put("transcript_amplification", 32);
SO_SEVERITY.put("inframe_insertion", 31);
SO_SEVERITY.put("inframe_deletion", 30);
SO_SEVERITY.put("inframe_variant", 29);
SO_SEVERITY.put("missense_variant", 28);
SO_SEVERITY.put("splice_region_variant", 27);
SO_SEVERITY.put("incomplete_terminal_codon_variant", 26);
SO_SEVERITY.put("stop_retained_variant", 25);
SO_SEVERITY.put("start_retained_variant", 24);
SO_SEVERITY.put("synonymous_variant", 23);
SO_SEVERITY.put("coding_sequence_variant", 22);
SO_SEVERITY.put("mature_miRNA_variant", 21);
SO_SEVERITY.put("5_prime_UTR_variant", 20);
SO_SEVERITY.put("3_prime_UTR_variant", 19);
SO_SEVERITY.put("non_coding_transcript_exon_variant", 18);
SO_SEVERITY.put("intron_variant", 17);
SO_SEVERITY.put("NMD_transcript_variant", 16);
SO_SEVERITY.put("non_coding_transcript_variant", 15);
SO_SEVERITY.put("2KB_upstream_variant", 14);
SO_SEVERITY.put("upstream_gene_variant", 13);
SO_SEVERITY.put("2KB_downstream_variant", 12);
SO_SEVERITY.put("downstream_gene_variant", 11);
SO_SEVERITY.put("TFBS_ablation", 10);
SO_SEVERITY.put("TFBS_amplification", 9);
SO_SEVERITY.put("TF_binding_site_variant", 8);
SO_SEVERITY.put("regulatory_region_ablation", 7);
SO_SEVERITY.put("regulatory_region_amplification", 6);
SO_SEVERITY.put("regulatory_region_variant", 5);
SO_SEVERITY.put("feature_elongation", 4);
SO_SEVERITY.put("feature_truncation", 3);
SO_SEVERITY.put("feature_variant", 2);
SO_SEVERITY.put("intergenic_variant", 1);
CODING_SO_NAMES.add(STOP_RETAINED_VARIANT);
CODING_SO_NAMES.add(START_RETAINED_VARIANT);
CODING_SO_NAMES.add(SYNONYMOUS_VARIANT);
CODING_SO_NAMES.add(STOP_GAINED);
CODING_SO_NAMES.add(INITIATOR_CODON_VARIANT);
CODING_SO_NAMES.add(START_LOST);
CODING_SO_NAMES.add(STOP_LOST);
CODING_SO_NAMES.add(MISSENSE_VARIANT);
SO_NAMES_CORRECTIONS.put("nc_transcript_variant", "non_coding_transcript_variant");
SO_NAMES_CORRECTIONS.put("non_coding_exon_variant", "non_coding_transcript_exon_variant");
}
public static String buildUpperLowerCaseString(String aa) {
if (StringUtils.isEmpty(aa)) {
return null;
}
StringBuilder stringBuilder = new StringBuilder(aa);
for (int i = 1; i < stringBuilder.length(); i++) {
stringBuilder.setCharAt(i, String.valueOf(stringBuilder.charAt(i)).toLowerCase().charAt(0));
}
return stringBuilder.toString();
}
public static Boolean isSynonymousCodon(String codon1, String codon2) {
return isSynonymousCodon(false, codon1, codon2);
}
public static Boolean isSynonymousCodon(Boolean mitochondrialCode, String codon1, String codon2) {
// Map geneticCode = null;
if (mitochondrialCode) {
return MT_IS_SYNONYMOUS_CODON.get(codon1.toUpperCase()).get(codon2.toUpperCase());
} else {
return IS_SYNONYMOUS_CODON.get(codon1.toUpperCase()).get(codon2.toUpperCase());
}
}
public static Boolean isStopCodon(String codon) {
return isStopCodon(false, codon);
}
public static Boolean isStopCodon(boolean mitochondrialCode, String codon) {
if (mitochondrialCode) {
if (codon.equals(TAA) || codon.equals(TAG) || codon.equals(AGA) || codon.equals(AGG)) {
return true;
}
} else {
if (codon.equals(TAA) || codon.equals(TGA) || codon.equals(TAG)) {
return true;
}
}
return false;
}
public static boolean isStartCodon(boolean mitochondrialCode, String codon) {
if (mitochondrialCode) {
if (codon.equals(ATG) || codon.equals(ATA)) {
return true;
}
} else {
if (codon.equals(ATG)) {
return true;
}
}
return false;
}
public static String getAminoacid(boolean mitochondrialCode, String codon) {
if (mitochondrialCode) {
return MT_CODON_TO_A.get(codon);
} else {
return CODON_TO_A.get(codon);
}
}
public static List getSequenceOntologyTerms(Iterable soNames) throws SOTermNotAvailableException {
List sequenceOntologyTerms = new ArrayList<>();
for (String name : soNames) {
name = fixSONameIfNeeded(name);
sequenceOntologyTerms.add(newSequenceOntologyTerm(name));
}
return sequenceOntologyTerms;
}
private static String fixSONameIfNeeded(String name) {
String fixedName = SO_NAMES_CORRECTIONS.get(name);
return fixedName == null ? name : fixedName;
}
public static SequenceOntologyTerm newSequenceOntologyTerm(String name) throws SOTermNotAvailableException {
return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name);
}
public static String buildVariantId(String chromosome, int start, String reference, String alternate) {
StringBuilder stringBuilder = new StringBuilder();
appendChromosome(chromosome, stringBuilder)
.append(SEPARATOR_CHAR)
.append(StringUtils.leftPad(Integer.toString(start), 10, " "))
.append(SEPARATOR_CHAR);
// if (reference.length() > Variant.SV_THRESHOLD) {
// stringBuilder.append(new String(CryptoUtils.encryptSha1(reference)));
// } else if (!(reference == null || reference.isEmpty() || reference.equals("-"))) {
if (!(reference == null || reference.isEmpty() || reference.equals("-"))) {
stringBuilder.append(reference);
}
stringBuilder.append(SEPARATOR_CHAR);
// if (alternate.length() > Variant.SV_THRESHOLD) {
// stringBuilder.append(new String(CryptoUtils.encryptSha1(alternate)));
// } else if (!(alternate == null || alternate.isEmpty() || alternate.equals("-"))) {
if (!(alternate == null || alternate.isEmpty() || alternate.equals("-"))) {
stringBuilder.append(alternate);
}
return stringBuilder.toString();
}
protected static StringBuilder appendChromosome(String chromosome, StringBuilder stringBuilder) {
if (chromosome.length() == 1 && Character.isDigit(chromosome.charAt(0))) {
stringBuilder.append(' ');
}
return stringBuilder.append(chromosome);
}
public static VariantType getVariantType(Variant variant) throws UnsupportedURLVariantFormat {
if (variant.getType() == null) {
variant.setType(Variant.inferType(variant.getReference(), variant.getAlternate()));
}
// FIXME: remove the if block below as soon as the Variant.inferType method is able to differentiate between
// FIXME: insertions and deletions
// if (variant.getType().equals(VariantType.INDEL) || variant.getType().equals(VariantType.SV)) {
if (variant.getType().equals(VariantType.INDEL)) {
if (variant.getReference().isEmpty()) {
// variant.setType(VariantType.INSERTION);
return VariantType.INSERTION;
} else if (variant.getAlternate().isEmpty()) {
// variant.setType(VariantType.DELETION);
return VariantType.DELETION;
} else {
return VariantType.MNV;
}
}
return variant.getType();
// return getVariantType(variant.getReferenceStart(), variant.getAlternate());
}
public static String reverseComplement(String string) {
StringBuilder stringBuilder = new StringBuilder(string).reverse();
for (int i = 0; i < stringBuilder.length(); i++) {
char nextNt = stringBuilder.charAt(i);
// Protection against weird characters, e.g. alternate:"TBS" found in ClinVar
if (VariantAnnotationUtils.COMPLEMENTARY_NT.containsKey(nextNt)) {
stringBuilder.setCharAt(i, VariantAnnotationUtils.COMPLEMENTARY_NT.get(nextNt));
} else {
return null;
}
}
return stringBuilder.toString();
}
public static String translate(String dnaSequence) {
return translate(dnaSequence, "-");
}
public static String translate(String dnaSequence, String separator) {
StringBuilder aaSequence = new StringBuilder();
dnaSequence = dnaSequence.toUpperCase();
dnaSequence = dnaSequence.replaceAll("T", "U");
for (int i = 0; i < dnaSequence.length(); i += 3) {
if (i + 2 < dnaSequence.length()) {
aaSequence.append(CODON_TO_A.get(dnaSequence.charAt(i) + dnaSequence.charAt(i + 1) + dnaSequence.charAt(i + 2)));
if (i + 3 < dnaSequence.length()) {
aaSequence.append(separator);
}
}
}
return aaSequence.toString();
}
}
© 2015 - 2024 Weber Informatics LLC | Privacy Policy