diff --git a/api/models/canola_nssnp.py b/api/models/canola_nssnp.py new file mode 100755 index 0000000..2c3fb2b --- /dev/null +++ b/api/models/canola_nssnp.py @@ -0,0 +1,37 @@ +from typing import Optional +from api import db +# from sqlalchemy.ext.declarative import declarative_base + + +# CanolaBase = declarative_base() +class CanolaProteinReference(db.Model): + __bind_key__ = "canola_nssnp" + __tablename__ = "protein_reference" + + protein_reference_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + gene_identifier: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + gene_name: db.Mapped[Optional[str]] = db.mapped_column(db.String(45), nullable=True) + + proteinsJoin = db.relationship("CanolaSnpsToProtein", backref="protein", cascade="all, delete-orphan") + + +class CanolaSnpsToProtein(db.Model): + __bind_key__ = "canola_nssnp" + __tablename__ = "snps_to_protein" + + snps_reference_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + protein_reference_id: db.Mapped[int] = db.mapped_column( + db.Integer(), db.ForeignKey("protein_reference.protein_reference_id", ondelete="CASCADE"), primary_key=True + ) + transcript_pos: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + chromosome: db.Mapped[str] = db.mapped_column(db.String(25), nullable=False) + chromosomal_loci: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + ref_DNA: db.Mapped[str] = db.mapped_column(db.String(1), nullable=False) + alt_DNA: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + aa_pos: db.Mapped[int] = db.mapped_column(db.Integer(), nullable=False) + ref_aa: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) + alt_aa: db.Mapped[str] = db.mapped_column(db.String(3), nullable=False) + type: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False) + effect_impact: db.Mapped[str] = db.mapped_column(db.String(50), nullable=False) + transcript_biotype: db.Mapped[Optional[str]] = db.mapped_column(db.String(45), nullable=True) + alt_freq: db.Mapped[float] = db.mapped_column(db.Numeric(10, 5), nullable=False) diff --git a/api/models/homologs_db.py b/api/models/homologs_db.py new file mode 100644 index 0000000..a6f87a8 --- /dev/null +++ b/api/models/homologs_db.py @@ -0,0 +1,14 @@ +from api import db + + +class homologs(db.Model): + __bind_key__ = "homologs_db" + __tablename__ = 'homologs' + + homologs_id: db.Mapped[int] = db.mapped_column(db.Integer(), primary_key=True, autoincrement=True) + search_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + result_protein_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + search_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + result_species_name: db.Mapped[str] = db.mapped_column(db.String(45), nullable=False) + Percent_id: db.Mapped[float] = db.mapped_column(db.Numeric(10, 5), nullable=False) + e_score: db.Mapped[str] = db.mapped_column(db.String(10), nullable=False) diff --git a/api/resources/snps.py b/api/resources/snps.py index 112c11d..038b267 100755 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -17,6 +17,11 @@ SnpsReference as SoybeanSnpsReference, SamplesLookup as SoybeanSampleNames, ) +from api.models.canola_nssnp import ( + CanolaProteinReference as CanolaProteinReference, + CanolaSnpsToProtein as CanolaSnpsToProtein +) +from api.models.homologs_db import homologs as HomologsDB from api.utils.bar_utils import BARUtils from flask import request import re @@ -141,7 +146,7 @@ class GeneNameAlias(Resource): def get(self, species="", gene_id=""): """Endpoint returns annotated SNP poplar data in order of (to match A th API format): AA pos (zero-indexed), sample id, 'missense_variant','MODERATE', 'MISSENSE', codon/DNA base change, - AA change (DH), pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype + AA change (DH), pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype (allele frequency for canola) values with single quotes are fixed""" results_json = [] @@ -160,43 +165,76 @@ def get(self, species="", gene_id=""): protein_reference = SoybeanProteinReference snps_to_protein = SoybeanSnpsToProtein snps_reference = SoybeanSnpsReference + elif species == "canola" and BARUtils.is_canola_gene_valid(gene_id): + protein_reference = CanolaProteinReference + snps_to_protein = CanolaSnpsToProtein else: return BARUtils.error_exit("Invalid gene id"), 400 - rows = ( - db.session.execute( - db.select(protein_reference, snps_to_protein, snps_reference) - .select_from(protein_reference) - .join(snps_to_protein) - .join(snps_reference) - .where(protein_reference.gene_identifier == gene_id) + if species == "canola" and BARUtils.is_canola_gene_valid(gene_id): + rows = ( + db.session.execute( + db.select(protein_reference, snps_to_protein) + .select_from(protein_reference) + .join(snps_to_protein) + .where(protein_reference.gene_identifier == gene_id) + ) + .tuples() + .all() + ) + for protein, snptoprotein in rows: + itm_lst = [ + snptoprotein.chromosome, + snptoprotein.aa_pos - 1, # zero index-ed + None, + "missense_variant", + "MODERATE", + "MISSENSE", + str(snptoprotein.transcript_pos) + snptoprotein.ref_DNA + ">" + snptoprotein.alt_DNA, + snptoprotein.ref_aa + snptoprotein.alt_aa, + None, + gene_id, + "protein_coding", + "CODING", + protein.gene_name, + float(snptoprotein.alt_freq), + ] + results_json.append(itm_lst) + else: + rows = ( + db.session.execute( + db.select(protein_reference, snps_to_protein, snps_reference) + .select_from(protein_reference) + .join(snps_to_protein) + .join(snps_reference) + .where(protein_reference.gene_identifier == gene_id) + ) + .tuples() + .all() ) - .tuples() - .all() - ) - # BAR A Th API format is chr, AA pos (zero-indexed), sample id, 'missense_variant', - # 'MODERATE', 'MISSENSE', codon/DNA base change, AA change (DH), - # pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype - for protein, snpsjoin, snpstbl in rows: - itm_lst = [ - snpstbl.chromosome, - # snpstbl.chromosomal_loci, - snpsjoin.aa_pos - 1, # zero index-ed - snpstbl.sample_id, - "missense_variant", - "MODERATE", - "MISSENSE", - str(snpsjoin.transcript_pos) + snpsjoin.ref_DNA + ">" + snpsjoin.alt_DNA, - snpsjoin.ref_aa + snpsjoin.alt_aa, - None, - re.sub(r".\d$", "", protein.gene_identifier), - "protein_coding", - "CODING", - protein.gene_identifier, - None, - ] - results_json.append(itm_lst) + # BAR A Th API format is chr, AA pos (zero-indexed), sample id, 'missense_variant', + # 'MODERATE', 'MISSENSE', codon/DNA base change, AA change (DH), + # pro length, gene ID, 'protein_coding', 'CODING', transcript id, biotype + for protein, snpsjoin, snpstbl in rows: + itm_lst = [ + snpstbl.chromosome, + # snpstbl.chromosomal_loci, + snpsjoin.aa_pos - 1, # zero index-ed + snpstbl.sample_id, + "missense_variant", + "MODERATE", + "MISSENSE", + str(snpsjoin.transcript_pos) + snpsjoin.ref_DNA + ">" + snpsjoin.alt_DNA, + snpsjoin.ref_aa + snpsjoin.alt_aa, + None, + re.sub(r".\d$", "", protein.gene_identifier), + "protein_coding", + "CODING", + protein.gene_identifier, + None, + ] + results_json.append(itm_lst) # Return results if there are data if len(results_json) > 0: @@ -502,3 +540,49 @@ def get(self, pval="", araid="", popid=""): pop_both_sig_idx = HotspotUtils.get_sig_index(pop_both_sig) output = {"ara_id": araid, "pop_id": popid, "ara_hotspots": ara_both_sig_idx, "pop_hotspots": pop_both_sig_idx} return BARUtils.success_exit(output) + + +@snps.route("/homologs///") +class Homologs(Resource): + @snps.param("search_species", _in="path", default="canola") + @snps.param("search_gene", _in="path", default="BnaA07g31480D") + @snps.param("target_species", _in="path", default="arabidopsis") + def get(self, search_species="", search_gene="", target_species=""): + """This endpoint shows the homologs proteins of search_gene in target_species. + The endpoint returns a list of homologous pairs of proteins in following format: + Percent_id(percent identity get by blast); e score + """ + # Escape input + search_species = escape(search_species) + gene_id = escape(search_gene) + target_species = escape(target_species) + supported = ["arabidopsis", "canola"] + if (search_species not in supported) or (target_species not in supported): + return BARUtils.error_exit("Species not supported"), 400 + elif (search_species == "arabidopsis" and BARUtils.is_arabidopsis_gene_valid(gene_id)) or (search_species == "canola" and BARUtils.is_canola_gene_valid(gene_id)): + results = HomologsDB.query.filter_by( + search_protein_name=gene_id, + search_species_name=search_species, + result_species_name=target_species + ).all() + if not results: + return BARUtils.error_exit("No homologs found for the given query"), 400 + + homologs_list = [ + { + "search_species_name": search_species, + "search_protein_name": gene_id, + "result_species_name": target_species, + "result_protein_name": homolog.result_protein_name, + "Percent_id": float(homolog.Percent_id), + "e_score": float(homolog.e_score) + } + for homolog in results + ] + homologs_list.sort(key=lambda x: x["e_score"]) + if len(homologs_list) >= 5: + homologs_list = homologs_list[:5] + response = {"homologs": homologs_list} + return BARUtils.success_exit(response), 200 + else: + return BARUtils.error_exit("Invalid gene id"), 400 diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index 3dd6cfa..b4f6a49 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -83,6 +83,17 @@ def is_cannabis_gene_valid(gene): else: return False + @staticmethod + def is_canola_gene_valid(gene): + """This function verifies if canola gene (BnaC07g42830D) is valid + :param gene: + :return: + """ + if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I): + return True + else: + return False + @staticmethod def is_arachis_gene_valid(gene): """This function verifies if arachis gene is valid: Adur10000_comp0_c0_seq1 diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg old mode 100644 new mode 100755 index f6e0ab2..71363b1 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -40,5 +40,8 @@ SQLALCHEMY_BINDS = { 'striga' : 'mysql://root:root@localhost/striga', 'tomato_nssnp' : 'mysql://root:root@localhost/tomato_nssnp', 'tomato_sequence' : 'mysql://root:root@localhost/tomato_sequence', - 'triphysaria' : 'mysql://root:root@localhost/triphysaria' + 'triphysaria' : 'mysql://root:root@localhost/triphysaria', + 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', + 'homologs_db' : 'mysql://root:root@localhost/homologs_db' + } diff --git a/config/databases/canola_nssnp.sql b/config/databases/canola_nssnp.sql new file mode 100755 index 0000000..a89d10d --- /dev/null +++ b/config/databases/canola_nssnp.sql @@ -0,0 +1,183 @@ +SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0; +SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0; +SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION'; + +-- ----------------------------------------------------- +-- Schema nov24_canola_snps +-- ----------------------------------------------------- +DROP SCHEMA IF EXISTS `canola_nssnp` ; + +-- ----------------------------------------------------- +-- Schema nov24_canola_snps +-- ----------------------------------------------------- +CREATE SCHEMA IF NOT EXISTS `canola_nssnp` DEFAULT CHARACTER SET utf8 ; +USE `canola_nssnp` ; + +-- ----------------------------------------------------- +-- Table `canola_nssnp`.`protein_reference` +-- ----------------------------------------------------- +DROP TABLE IF EXISTS `canola_nssnp`.`protein_reference` ; + +create table protein_reference +( + protein_reference_id int auto_increment + primary key, + gene_identifier varchar(45) not null, + gene_name varchar(45) null +); + +-- ----------------------------------------------------- +-- Table `canola_nssnp`.`snps_to_protein` +-- ----------------------------------------------------- +DROP TABLE IF EXISTS `canola_nssnp`.`snps_to_protein` ; + +create table snps_to_protein +( + snps_reference_id int auto_increment, + protein_reference_id int not null, + transcript_pos int not null, + chromosome varchar(25) not null, + chromosomal_loci int not null, + ref_DNA varchar(1) not null, + alt_DNA varchar(45) not null, + aa_pos int not null, + ref_aa varchar(3) not null, + alt_aa varchar(3) not null, + type varchar(50) not null, + effect_impact varchar(50) not null, + transcript_biotype varchar(45) null, + alt_freq decimal(10, 5) not null, + primary key (snps_reference_id, protein_reference_id), + constraint protein_fk + foreign key (protein_reference_id) references protein_reference (protein_reference_id) +); + +create index protein_fk_idx + on snps_to_protein (protein_reference_id); + + +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (1, 'GSBRNA2T00000001001', 'BnaC09g12820D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (2, 'GSBRNA2T00000003001', 'BnaC09g12810D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (3, 'GSBRNA2T00000005001', 'BnaC09g12800D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (4, 'GSBRNA2T00000007001', 'BnaC09g12790D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (5, 'GSBRNA2T00000008001', 'BnaC09g12780D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (6, 'GSBRNA2T00000009001', 'BnaC09g12770D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (7, 'GSBRNA2T00000011001', 'BnaC09g12760D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (8, 'GSBRNA2T00000012001', 'BnaC09g12750D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (9, 'GSBRNA2T00000015001', 'BnaC09g12740D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (10, 'GSBRNA2T00000016001', 'BnaC09g12730D'); +INSERT INTO canola_nssnp.protein_reference (protein_reference_id, gene_name, gene_identifier) VALUES (63265, 'GSBRNA2T00102721001', 'BnaA07g31480D'); + +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142004, 63265, 52, 'chrA07', 21985117, 'A', 'C', 18, 'Met', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142005, 63265, 130, 'chrA07', 21985679, 'G', 'T', 44, 'Gly', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.04930); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142006, 63265, 163, 'chrA07', 21985712, 'C', 'G', 55, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.09210); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142007, 63265, 268, 'chrA07', 21985817, 'G', 'A', 90, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142008, 63265, 284, 'chrA07', 21985833, 'G', 'C', 95, 'Arg', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142009, 63265, 433, 'chrA07', 21985982, 'C', 'T', 145, 'Pro', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142010, 63265, 442, 'chrA07', 21985991, 'G', 'A', 148, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142011, 63265, 445, 'chrA07', 21985994, 'A', 'G', 149, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142012, 63265, 486, 'chrA07', 21986035, 'C', 'G', 162, 'His', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.08310); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142013, 63265, 500, 'chrA07', 21986049, 'T', 'G', 167, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08140); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142014, 63265, 526, 'chrA07', 21986075, 'G', 'A', 176, 'Gly', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.08390); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142015, 63265, 541, 'chrA07', 21986090, 'T', 'C', 181, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142016, 63265, 634, 'chrA07', 21986183, 'C', 'A', 212, 'Leu', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142017, 63265, 640, 'chrA07', 21986189, 'C', 'T', 214, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.08630); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142018, 63265, 694, 'chrA07', 21986243, 'G', 'T', 232, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142019, 63265, 769, 'chrA07', 21986318, 'T', 'C', 257, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.05180); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142020, 63265, 848, 'chrA07', 21986397, 'G', 'A', 283, 'Ser', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.05100); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142021, 63265, 859, 'chrA07', 21986408, 'T', 'C', 287, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.05920); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142022, 63265, 889, 'chrA07', 21986438, 'A', 'G', 297, 'Lys', 'Glu', 'missense_variant', 'MODERATE', 'protein_coding', 0.06330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142023, 63265, 979, 'chrA07', 21986528, 'C', 'G', 327, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142024, 63265, 995, 'chrA07', 21986544, 'C', 'T', 332, 'Thr', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142025, 63265, 1039, 'chrA07', 21986588, 'C', 'T', 347, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.07070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142026, 63265, 1042, 'chrA07', 21986591, 'T', 'C', 348, 'Trp', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142027, 63265, 1060, 'chrA07', 21986609, 'A', 'G', 354, 'Asn', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142028, 63265, 1075, 'chrA07', 21986624, 'T', 'C', 359, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142029, 63265, 1267, 'chrA07', 21986816, 'C', 'G', 423, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.07240); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142030, 63265, 1336, 'chrA07', 21986885, 'C', 'G', 446, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142031, 63265, 1363, 'chrA07', 21986912, 'G', 'A', 455, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.32150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142032, 63265, 1420, 'chrA07', 21986969, 'T', 'A', 474, 'Ser', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.01810); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142033, 63265, 1462, 'chrA07', 21987011, 'C', 'G', 488, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.04610); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142034, 63265, 1595, 'chrA07', 21987144, 'A', 'C', 532, 'Glu', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.04440); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142035, 63265, 1735, 'chrA07', 21987284, 'C', 'G', 579, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.29930); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142036, 63265, 1744, 'chrA07', 21987293, 'T', 'C', 582, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.02380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142037, 63265, 1865, 'chrA07', 21987414, 'C', 'T', 622, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142038, 63265, 2077, 'chrA07', 21987626, 'C', 'G', 693, 'His', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142039, 63265, 2086, 'chrA07', 21987635, 'C', 'A', 696, 'His', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142040, 63265, 2089, 'chrA07', 21987638, 'A', 'G', 697, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142041, 63265, 2215, 'chrA07', 21987764, 'A', 'T', 739, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142042, 63265, 2227, 'chrA07', 21987776, 'G', 'C', 743, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142043, 63265, 2233, 'chrA07', 21987782, 'T', 'C', 745, 'Tyr', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142044, 63265, 2254, 'chrA07', 21987803, 'C', 'T', 752, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142045, 63265, 2323, 'chrA07', 21987872, 'T', 'C', 775, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.28040); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142046, 63265, 2350, 'chrA07', 21987899, 'G', 'A', 784, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142047, 63265, 2395, 'chrA07', 21987944, 'C', 'G', 799, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00330); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142048, 63265, 2425, 'chrA07', 21987974, 'G', 'C', 809, 'Val', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142049, 63265, 2434, 'chrA07', 21987983, 'A', 'G', 812, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142050, 63265, 2446, 'chrA07', 21987995, 'A', 'G', 816, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142051, 63265, 2464, 'chrA07', 21988013, 'A', 'C', 822, 'Ser', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27140); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142052, 63265, 2518, 'chrA07', 21988067, 'C', 'G', 840, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.01150); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142053, 63265, 2521, 'chrA07', 21988070, 'T', 'G', 841, 'Leu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.24180); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142054, 63265, 2545, 'chrA07', 21988094, 'G', 'A', 849, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.31830); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142055, 63265, 2596, 'chrA07', 21988145, 'A', 'G', 866, 'Arg', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.26320); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142056, 63265, 2632, 'chrA07', 21988181, 'T', 'C', 878, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26730); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142057, 63265, 2737, 'chrA07', 21988286, 'G', 'A', 913, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.26640); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142058, 63265, 2770, 'chrA07', 21988319, 'G', 'A', 924, 'Val', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.27220); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142059, 63265, 2800, 'chrA07', 21988349, 'C', 'T', 934, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.05260); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142060, 63265, 2848, 'chrA07', 21988397, 'T', 'C', 950, 'Cys', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.27380); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142061, 63265, 2878, 'chrA07', 21988427, 'T', 'C', 960, 'Ser', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.27300); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142062, 63265, 2881, 'chrA07', 21988430, 'C', 'T', 961, 'Leu', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142063, 63265, 2890, 'chrA07', 21988439, 'G', 'A', 964, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.02800); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142064, 63265, 2908, 'chrA07', 21988457, 'G', 'C', 970, 'Asp', 'His', 'missense_variant', 'MODERATE', 'protein_coding', 0.01320); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142065, 63265, 2941, 'chrA07', 21988490, 'A', 'T', 981, 'Arg', 'Trp', 'missense_variant', 'MODERATE', 'protein_coding', 0.31170); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142066, 63265, 2968, 'chrA07', 21988517, 'C', 'T', 990, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.02880); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142067, 63265, 3163, 'chrA07', 21988712, 'G', 'A', 1055, 'Ala', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.27470); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142068, 63265, 3188, 'chrA07', 21988737, 'C', 'G', 1063, 'Ala', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.27550); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142069, 63265, 3199, 'chrA07', 21988748, 'A', 'T', 1067, 'Ser', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.32070); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142070, 63265, 3283, 'chrA07', 21988832, 'G', 'T', 1095, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (142071, 63265, 3289, 'chrA07', 21988838, 'G', 'T', 1097, 'Asp', 'Tyr', 'missense_variant', 'MODERATE', 'protein_coding', 0.04360); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327046, 1, 1319, 'chrC09', 9319194, 'G', 'A', 440, 'Ser', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327047, 1, 1085, 'chrC09', 9319428, 'C', 'T', 362, 'Arg', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327045, 2, 200, 'chrC09', 9311197, 'A', 'C', 67, 'His', 'Pro', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327036, 3, 385, 'chrC09', 9301658, 'T', 'A', 129, 'Phe', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327037, 3, 419, 'chrC09', 9301692, 'A', 'G', 140, 'Glu', 'Gly', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327038, 3, 726, 'chrC09', 9301999, 'C', 'G', 242, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00580); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327039, 3, 896, 'chrC09', 9302169, 'T', 'A', 299, 'Val', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00250); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327040, 3, 1106, 'chrC09', 9302379, 'G', 'T', 369, 'Arg', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00510); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327041, 3, 1220, 'chrC09', 9302493, 'A', 'T', 407, 'Glu', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327042, 3, 1307, 'chrC09', 9302580, 'A', 'T', 436, 'His', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327043, 3, 1576, 'chrC09', 9302849, 'T', 'A', 526, 'Cys', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00820); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327044, 3, 1697, 'chrC09', 9302970, 'A', 'C', 566, 'Asn', 'Thr', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327035, 4, 67, 'chrC09', 9282013, 'C', 'A', 23, 'Val', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327033, 5, 661, 'chrC09', 9273716, 'G', 'C', 221, 'Pro', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327034, 5, 481, 'chrC09', 9274017, 'A', 'T', 161, 'Leu', 'Met', 'missense_variant', 'MODERATE', 'protein_coding', 0.00990); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327030, 6, 17, 'chrC09', 9267233, 'A', 'T', 6, 'Lys', 'Ile', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327031, 6, 305, 'chrC09', 9267521, 'G', 'C', 102, 'Gly', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327032, 6, 2093, 'chrC09', 9270136, 'G', 'T', 698, 'Gly', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00490); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327022, 7, 2450, 'chrC09', 9234630, 'G', 'T', 817, 'Ala', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.00010); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327023, 7, 1718, 'chrC09', 9237814, 'A', 'C', 573, 'Ile', 'Ser', 'missense_variant', 'MODERATE', 'protein_coding', 0.00900); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327024, 7, 1408, 'chrC09', 9238193, 'T', 'C', 470, 'Ile', 'Val', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327025, 7, 865, 'chrC09', 9238736, 'C', 'T', 289, 'Asp', 'Asn', 'missense_variant', 'MODERATE', 'protein_coding', 0.00200); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327026, 7, 825, 'chrC09', 9238776, 'G', 'T', 275, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.01230); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327027, 7, 763, 'chrC09', 9238838, 'A', 'G', 255, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00740); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327028, 7, 673, 'chrC09', 9238928, 'C', 'T', 225, 'Glu', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327029, 7, 612, 'chrC09', 9238989, 'A', 'T', 204, 'Asn', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00660); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327020, 8, 67, 'chrC09', 9230756, 'C', 'T', 23, 'Arg', 'Cys', 'missense_variant', 'MODERATE', 'protein_coding', 0.00350); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327021, 8, 81, 'chrC09', 9230770, 'G', 'C', 27, 'Glu', 'Asp', 'missense_variant', 'MODERATE', 'protein_coding', 0.43170); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327018, 9, 169, 'chrC09', 9195157, 'T', 'C', 57, 'Phe', 'Leu', 'missense_variant', 'MODERATE', 'protein_coding', 0.00130); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327019, 9, 457, 'chrC09', 9195518, 'A', 'G', 153, 'Thr', 'Ala', 'missense_variant', 'MODERATE', 'protein_coding', 0.00160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327014, 10, 191, 'chrC09', 9191243, 'G', 'A', 64, 'Ser', 'Phe', 'missense_variant', 'MODERATE', 'protein_coding', 0.44000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327015, 10, 188, 'chrC09', 9191246, 'G', 'T', 63, 'Pro', 'Gln', 'missense_variant', 'MODERATE', 'protein_coding', 0.00000); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327016, 10, 164, 'chrC09', 9191270, 'C', 'T', 55, 'Arg', 'Lys', 'missense_variant', 'MODERATE', 'protein_coding', 0.44160); +INSERT INTO canola_nssnp.snps_to_protein (snps_reference_id, protein_reference_id, transcript_pos, chromosome, chromosomal_loci, ref_DNA, alt_DNA, aa_pos, ref_aa, alt_aa, type, effect_impact, transcript_biotype, alt_freq) VALUES (327017, 10, 43, 'chrC09', 9191391, 'C', 'T', 15, 'Gly', 'Arg', 'missense_variant', 'MODERATE', 'protein_coding', 0.43260); + + + + + + + +SET SQL_MODE=@OLD_SQL_MODE; +SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS; +SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS; + diff --git a/config/databases/homologs_db.sql b/config/databases/homologs_db.sql new file mode 100755 index 0000000..2f5e2ae --- /dev/null +++ b/config/databases/homologs_db.sql @@ -0,0 +1,120 @@ +SET SQL_MODE = "NO_AUTO_VALUE_ON_ZERO"; +START TRANSACTION; +SET time_zone = "+00:00"; +CREATE SCHEMA IF NOT EXISTS `homologs_db` DEFAULT CHARACTER SET utf8 ; +USE homologs_db; +DROP TABLE IF EXISTS `homologs_db`.`homologs` ; +CREATE TABLE `homologs` ( + `homologs_id` INT auto_increment, + `search_protein_name` varchar(45) NOT NULL, + `result_protein_name` varchar(45) NOT NULL, + `search_species_name` varchar(45) NOT NULL, + `result_species_name` varchar(45) NOT NULL, + `Percent_id` decimal(10, 5) NOT NULL, + `e_score` varchar(10) NOT NULL, + `is_search_structure` INT NOT NULL,/*1 represent has structure*/ + `is_result_structure` INT NOT NULL, + PRIMARY KEY (homologs_id) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; + + +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1, 'AT5G16970.1', 'BnaC09g40930D', 'arabidopsis', 'canola', 86.04700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (2, 'AT5G16970.1', 'BnaA10g17570D', 'arabidopsis', 'canola', 86.04700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (3, 'AT5G16970.1', 'BnaC03g08130D', 'arabidopsis', 'canola', 85.08800, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (4, 'AT5G16970.1', 'BnaA05g32330D', 'arabidopsis', 'canola', 81.63300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (5, 'AT5G16970.1', 'BnaCnng06210D', 'arabidopsis', 'canola', 80.87000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (6, 'AT5G16970.1', 'BnaA03g06330D', 'arabidopsis', 'canola', 85.37300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (7, 'AT5G16970.1', 'BnaA09g28840D', 'arabidopsis', 'canola', 77.90700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (8, 'AT5G16970.1', 'BnaC05g20410D', 'arabidopsis', 'canola', 77.32600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (9, 'AT5G16970.1', 'BnaC02g06960D', 'arabidopsis', 'canola', 76.23200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (10, 'AT5G16970.1', 'BnaA02g03340D', 'arabidopsis', 'canola', 75.94200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (11, 'AT4G32100.1', 'BnaC01g06360D', 'arabidopsis', 'canola', 55.28500, '2.18e-39'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (12, 'AT4G32100.1', 'BnaA01g04810D', 'arabidopsis', 'canola', 55.28500, '1.46e-38'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (13, 'AT4G32100.1', 'BnaA01g04820D', 'arabidopsis', 'canola', 52.84600, '6.47e-38'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (14, 'AT4G32100.1', 'BnaAnng05770D', 'arabidopsis', 'canola', 53.33300, '1.23e-37'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (15, 'AT4G32100.1', 'BnaC01g06960D', 'arabidopsis', 'canola', 51.61300, '1.19e-36'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (16, 'AT4G32100.1', 'BnaC07g18640D', 'arabidopsis', 'canola', 51.66700, '6.37e-36'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (17, 'AT4G32100.1', 'BnaA01g34870D', 'arabidopsis', 'canola', 49.19400, '4.15e-35'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (18, 'AT4G32100.1', 'BnaA02g24080D', 'arabidopsis', 'canola', 49.13800, '3.63e-27'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (19, 'AT4G32100.1', 'BnaA02g24090D', 'arabidopsis', 'canola', 48.27600, '6.69e-27'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (20, 'AT4G32100.1', 'BnaC02g31830D', 'arabidopsis', 'canola', 47.41400, '2.72e-25'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (21, 'AT2G43120.2', 'BnaC04g02730D', 'arabidopsis', 'canola', 90.96600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (22, 'AT2G43120.2', 'BnaC03g24040D', 'arabidopsis', 'canola', 91.27700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (23, 'AT2G43120.2', 'BnaA03g20050D', 'arabidopsis', 'canola', 90.65400, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824264, 'BnaC07g23540D', 'AT5G65470.1', 'canola', 'arabidopsis', 39.72900, '9.91e-109'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824265, 'BnaC07g23540D', 'AT4G24530.1', 'canola', 'arabidopsis', 36.96500, '1.03e-108'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824266, 'BnaC07g23540D', 'AT2G01480.1', 'canola', 'arabidopsis', 41.78400, '2.97e-107'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824267, 'BnaC07g23540D', 'AT2G01480.2', 'canola', 'arabidopsis', 43.07700, '6.19e-104'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824268, 'BnaC07g23540D', 'AT1G14970.2', 'canola', 'arabidopsis', 40.00000, '1.03e-103'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824269, 'BnaC07g23540D', 'AT1G14970.1', 'canola', 'arabidopsis', 40.00000, '2.33e-102'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824270, 'BnaC07g23540D', 'AT1G14970.3', 'canola', 'arabidopsis', 40.24700, '2.02e-101'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824271, 'BnaC07g23540D', 'AT1G38065.2', 'canola', 'arabidopsis', 39.86200, '2.00e-95'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824272, 'BnaC07g23550D', 'AT3G26400.1', 'canola', 'arabidopsis', 77.19600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824273, 'BnaC07g23550D', 'AT1G13020.1', 'canola', 'arabidopsis', 67.31400, '1.71e-180'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824274, 'BnaC07g23560D', 'AT3G26410.1', 'canola', 'arabidopsis', 93.21100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824275, 'BnaC07g23570D', 'AT3G26420.1', 'canola', 'arabidopsis', 79.75700, '1.69e-126'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824276, 'BnaC07g23570D', 'AT2G21660.1', 'canola', 'arabidopsis', 60.49400, '1.99e-30'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824277, 'BnaC07g23570D', 'AT4G39260.3', 'canola', 'arabidopsis', 57.31700, '6.84e-30'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824278, 'BnaC07g23570D', 'AT5G04280.1', 'canola', 'arabidopsis', 41.95100, '2.88e-29'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824279, 'BnaC07g23570D', 'AT4G39260.2', 'canola', 'arabidopsis', 58.02500, '4.78e-29'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824280, 'BnaC07g23570D', 'AT1G60650.2', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824281, 'BnaC07g23570D', 'AT1G60650.1', 'canola', 'arabidopsis', 40.44100, '3.40e-28'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824282, 'BnaC07g23570D', 'AT4G39260.4', 'canola', 'arabidopsis', 56.06100, '2.46e-21'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824283, 'BnaC07g23580D', 'AT3G26430.1', 'canola', 'arabidopsis', 84.21100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824284, 'BnaC07g23580D', 'AT1G67830.1', 'canola', 'arabidopsis', 60.58800, '2.97e-155'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (824285, 'BnaC07g23580D', 'AT5G14450.1', 'canola', 'arabidopsis', 50.66000, '4.50e-131'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320148, 'BnaA10g09850D', 'BnaA10g09850D', 'canola', 'canola', 100.00000, '5.68e-110'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320149, 'BnaA10g09850D', 'BnaC09g32290D', 'canola', 'canola', 93.59000, '5.28e-93'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320150, 'BnaA10g09850D', 'BnaC02g12890D', 'canola', 'canola', 72.85700, '3.68e-26'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320151, 'BnaA10g09860D', 'BnaA10g09860D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320152, 'BnaA10g09860D', 'BnaC09g32300D', 'canola', 'canola', 86.68300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320153, 'BnaA10g09860D', 'BnaA02g08940D', 'canola', 'canola', 69.50900, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320154, 'BnaA10g09860D', 'BnaC02g12870D', 'canola', 'canola', 83.58500, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320155, 'BnaA10g09860D', 'BnaC08g12230D', 'canola', 'canola', 58.34400, '1.15e-177'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320156, 'BnaA10g09860D', 'BnaA01g15750D', 'canola', 'canola', 55.24900, '1.77e-162'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320157, 'BnaA10g09860D', 'BnaC01g18800D', 'canola', 'canola', 62.35600, '5.48e-116'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320158, 'BnaA10g09860D', 'BnaA06g19020D', 'canola', 'canola', 34.15200, '4.23e-50'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320159, 'BnaA10g09860D', 'BnaC09g05960D', 'canola', 'canola', 44.25500, '2.79e-46'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320160, 'BnaA10g09860D', 'BnaA06g22700D', 'canola', 'canola', 42.16900, '2.31e-43'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320161, 'BnaA10g09870D', 'BnaA10g09870D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320162, 'BnaA10g09870D', 'BnaC09g32310D', 'canola', 'canola', 90.82800, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320163, 'BnaA10g09870D', 'BnaA02g08930D', 'canola', 'canola', 72.72700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320164, 'BnaA10g09870D', 'BnaC02g12860D', 'canola', 'canola', 70.51700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320165, 'BnaA10g09870D', 'BnaA03g11280D', 'canola', 'canola', 70.32600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320166, 'BnaA10g09870D', 'BnaC03g71710D', 'canola', 'canola', 87.03700, '1.49e-113'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320167, 'BnaA10g09880D', 'BnaA10g09880D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320168, 'BnaA10g09880D', 'BnaC09g32320D', 'canola', 'canola', 98.12600, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320169, 'BnaA10g09880D', 'BnaA02g08870D', 'canola', 'canola', 85.38300, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320170, 'BnaA10g09880D', 'BnaA01g20560D', 'canola', 'canola', 51.22000, '1.02e-130'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320171, 'BnaA10g09880D', 'BnaC01g25850D', 'canola', 'canola', 51.81100, '9.19e-130'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1320172, 'BnaA10g09880D', 'BnaA06g19130D', 'canola', 'canola', 51.24000, '4.00e-128'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690828, 'BnaA07g31480D', 'AT1G74360.1', 'canola', 'arabidopsis', 84.02200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690829, 'BnaA07g31480D', 'AT2G01950.1', 'canola', 'arabidopsis', 32.34200, '3.57e-149'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690830, 'BnaA07g31480D', 'AT1G55610.1', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690831, 'BnaA07g31480D', 'AT1G55610.2', 'canola', 'arabidopsis', 31.71500, '9.47e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690832, 'BnaA07g31480D', 'AT1G17230.1', 'canola', 'arabidopsis', 32.44000, '7.99e-146'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690833, 'BnaA07g31480D', 'AT1G17230.2', 'canola', 'arabidopsis', 32.44000, '1.34e-145'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690834, 'BnaA07g31480D', 'AT4G39400.1', 'canola', 'arabidopsis', 33.15200, '5.71e-145'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690835, 'BnaA07g31480D', 'AT3G13380.1', 'canola', 'arabidopsis', 32.44600, '3.05e-143'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690836, 'BnaA07g31480D', 'AT5G63930.1', 'canola', 'arabidopsis', 33.05600, '1.84e-142'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (690837, 'BnaA07g31480D', 'AT5G63930.2', 'canola', 'arabidopsis', 33.23900, '3.94e-141'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356296, 'BnaA07g31480D', 'BnaA07g31480D', 'canola', 'canola', 100.00000, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356297, 'BnaA07g31480D', 'BnaC06g35270D', 'canola', 'canola', 96.79400, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356298, 'BnaA07g31480D', 'BnaCnng50590D', 'canola', 'canola', 75.29100, '5.45e-180'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356299, 'BnaA07g31480D', 'BnaA02g11590D', 'canola', 'canola', 74.41900, '3.01e-178'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356300, 'BnaA07g31480D', 'BnaC05g13410D', 'canola', 'canola', 32.51300, '7.21e-153'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356301, 'BnaA07g31480D', 'BnaA06g11580D', 'canola', 'canola', 33.08800, '1.36e-152'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356302, 'BnaA07g31480D', 'BnaC07g47240D', 'canola', 'canola', 33.42600, '6.47e-151'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356303, 'BnaA07g31480D', 'BnaA01g05490D', 'canola', 'canola', 33.58100, '3.69e-148'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356304, 'BnaA07g31480D', 'BnaC07g21390D', 'canola', 'canola', 32.23900, '2.77e-147'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (1356305, 'BnaA07g31480D', 'BnaA06g34400D', 'canola', 'canola', 31.89600, '3.39e-147'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86750, 'AT1G74360.1', 'BnaC06g35270D', 'arabidopsis', 'canola', 84.27700, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86751, 'AT1G74360.1', 'BnaA07g31480D', 'arabidopsis', 'canola', 84.02200, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86752, 'AT1G74360.1', 'BnaA02g11590D', 'arabidopsis', 'canola', 77.97100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86753, 'AT1G74360.1', 'BnaCnng50590D', 'arabidopsis', 'canola', 77.97100, '0.0'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86754, 'AT1G74360.1', 'BnaA08g00410D', 'arabidopsis', 'canola', 31.84900, '5.39e-154'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86755, 'AT1G74360.1', 'BnaA06g11580D', 'arabidopsis', 'canola', 33.86600, '3.20e-153'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86756, 'AT1G74360.1', 'BnaA02g16780D', 'arabidopsis', 'canola', 67.03000, '2.11e-152'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86757, 'AT1G74360.1', 'BnaA06g34400D', 'arabidopsis', 'canola', 32.93200, '1.50e-151'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86758, 'AT1G74360.1', 'BnaA08g16520D', 'arabidopsis', 'canola', 33.89500, '1.68e-150'); +INSERT INTO homologs_db.homologs (homologs_id, search_protein_name, result_protein_name, search_species_name, result_species_name, Percent_id, e_score) VALUES (86759, 'AT1G74360.1', 'BnaC07g47240D', 'arabidopsis', 'canola', 33.88700, '3.05e-150'); diff --git a/config/init.sh b/config/init.sh index 23bd482..50b7f10 100755 --- a/config/init.sh +++ b/config/init.sh @@ -40,6 +40,8 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/striga.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/tomato_sequence.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/triphysaria.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql echo "Data are now loaded. Preparing API config" diff --git a/tests/data/get_canola_homolog_information.json b/tests/data/get_canola_homolog_information.json new file mode 100644 index 0000000..e11763c --- /dev/null +++ b/tests/data/get_canola_homolog_information.json @@ -0,0 +1,47 @@ +{ + "wasSuccessful": true, + "data": { + "homologs": [ + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC09g40930D", + "Percent_id": 86.047, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA10g17570D", + "Percent_id": 86.047, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaC03g08130D", + "Percent_id": 85.088, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaA05g32330D", + "Percent_id": 81.633, + "e_score": 0.0 + }, + { + "search_species_name": "arabidopsis", + "search_protein_name": "AT5G16970.1", + "result_species_name": "canola", + "result_protein_name": "BnaCnng06210D", + "Percent_id": 80.87, + "e_score": 0.0 + } + ] + } +} diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index 61e6d4b..c53156c 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -1,6 +1,7 @@ from api import app from unittest import TestCase import pytest +from json import load class TestIntegrations(TestCase): @@ -95,6 +96,31 @@ def test_get_snps(self): } self.assertEqual(response.json, expected) + # Valid request canola + response = self.app_client.get("/snps/canola/BnaC09g12790D") + expected = { + "wasSuccessful": True, + "data": [ + [ + "chrC09", + 22, + None, + "missense_variant", + "MODERATE", + "MISSENSE", + "67C>A", + "ValPhe", + None, + "BnaC09g12790D", + "protein_coding", + "CODING", + "GSBRNA2T00000007001", + 0.0066 + ] + ] + } + self.assertEqual(response.json, expected) + # Invalid gene id response = self.app_client.get("/snps/poplar/abc") expected = {"wasSuccessful": False, "error": "Invalid gene id"} @@ -108,6 +134,19 @@ def test_get_snps(self): } self.assertEqual(response.json, expected) + # Invalid gene id for canola + response = self.app_client.get("/snps/canola/abc") + expected = {"wasSuccessful": False, "error": "Invalid gene id"} + self.assertEqual(response.json, expected) + + # Gene does not exist for canola + response = self.app_client.get("/snps/canola/BnaC07g99930D") + expected = { + "wasSuccessful": False, + "error": "There are no data found for the given gene", + } + self.assertEqual(response.json, expected) + def test_get_sample_definitions(self): """ Test cases for sample definition @@ -218,3 +257,41 @@ def test_pymol_snps_pymol_unneeded(self): response = self.app_client.get("/snps/pymol/Potri.016G107900.1?snps=25l&chain=None") expected = {"wasSuccessful": False, "error": "Invalid SNP string format"} self.assertEqual(response.json, expected) + + def test_homologs(self): + + # test for get homologs + response = self.app_client.get("/snps/homologs/arabidopsis/AT5G16970.1/canola") + with open("tests/data/get_canola_homolog_information.json") as file: + expected = load(file) + self.assertEqual(response.json, expected) + + # test for invalid input + response = self.app_client.get("/snps/homologs/rice/AT3G18710.1/canola") + expected = { + "wasSuccessful": False, + "error": "Species not supported", + } + self.assertEqual(response.json, expected) + + response = self.app_client.get("/snps/homologs/arabidopsis/AT3G18710.1/rice") + expected = { + "wasSuccessful": False, + "error": "Species not supported", + } + self.assertEqual(response.json, expected) + + response = self.app_client.get("/snps/homologs/arabidopsis/abc/canola") + expected = { + "wasSuccessful": False, + "error": "Invalid gene id", + } + self.assertEqual(response.json, expected) + + # test for no homologs data + response = self.app_client.get("/snps/homologs/arabidopsis/AT3G18710.1/canola") + expected = { + "wasSuccessful": False, + "error": "No homologs found for the given query", + } + self.assertEqual(response.json, expected)