From 74acf9de75da97e580899cfa62fb6de78fb9b770 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 29 Mar 2025 19:35:31 -0400 Subject: [PATCH 1/2] Minor changes. --- api/models/canola_nssnp.py | 1 - api/models/homologs_db.py | 2 +- api/resources/snps.py | 13 +- api/utils/bar_utils.py | 6 +- api/utils/docking_utils.py | 0 config/BAR_API.cfg | 7 +- config/databases/canola_nssnp.sql | 281 +++++++++++------------------- config/databases/homologs_db.sql | 180 +++++++------------ config/init.sh | 5 +- requirements.txt | 36 ++-- tests/resources/test_snps.py | 4 +- 11 files changed, 197 insertions(+), 338 deletions(-) mode change 100755 => 100644 api/models/canola_nssnp.py mode change 100755 => 100644 api/resources/snps.py mode change 100755 => 100644 api/utils/docking_utils.py mode change 100755 => 100644 config/databases/canola_nssnp.sql mode change 100755 => 100644 config/databases/homologs_db.sql diff --git a/api/models/canola_nssnp.py b/api/models/canola_nssnp.py old mode 100755 new mode 100644 index 2c3fb2b..187ed42 --- a/api/models/canola_nssnp.py +++ b/api/models/canola_nssnp.py @@ -1,6 +1,5 @@ from typing import Optional from api import db -# from sqlalchemy.ext.declarative import declarative_base # CanolaBase = declarative_base() diff --git a/api/models/homologs_db.py b/api/models/homologs_db.py index a6f87a8..426d9b1 100644 --- a/api/models/homologs_db.py +++ b/api/models/homologs_db.py @@ -3,7 +3,7 @@ class homologs(db.Model): __bind_key__ = "homologs_db" - __tablename__ = 'homologs' + __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) diff --git a/api/resources/snps.py b/api/resources/snps.py old mode 100755 new mode 100644 index 038b267..b026b73 --- a/api/resources/snps.py +++ b/api/resources/snps.py @@ -19,7 +19,7 @@ ) from api.models.canola_nssnp import ( CanolaProteinReference as CanolaProteinReference, - CanolaSnpsToProtein as CanolaSnpsToProtein + CanolaSnpsToProtein as CanolaSnpsToProtein, ) from api.models.homologs_db import homologs as HomologsDB from api.utils.bar_utils import BARUtils @@ -557,13 +557,14 @@ def get(self, search_species="", search_gene="", target_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)): + 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 + 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 @@ -575,7 +576,7 @@ def get(self, search_species="", search_gene="", target_species=""): "result_species_name": target_species, "result_protein_name": homolog.result_protein_name, "Percent_id": float(homolog.Percent_id), - "e_score": float(homolog.e_score) + "e_score": float(homolog.e_score), } for homolog in results ] diff --git a/api/utils/bar_utils.py b/api/utils/bar_utils.py index b4f6a49..7fe0739 100644 --- a/api/utils/bar_utils.py +++ b/api/utils/bar_utils.py @@ -86,9 +86,9 @@ def is_cannabis_gene_valid(gene): @staticmethod def is_canola_gene_valid(gene): """This function verifies if canola gene (BnaC07g42830D) is valid - :param gene: - :return: - """ + :param gene: + :return: + """ if re.search(r"^Bna[AC]\d{2}g\d{5}[A-D]?$", gene, re.I): return True else: diff --git a/api/utils/docking_utils.py b/api/utils/docking_utils.py old mode 100755 new mode 100644 diff --git a/config/BAR_API.cfg b/config/BAR_API.cfg index 71363b1..f05a5fe 100755 --- a/config/BAR_API.cfg +++ b/config/BAR_API.cfg @@ -15,6 +15,7 @@ SQLALCHEMY_BINDS = { 'arachis': 'mysql://root:root@localhost/arachis', 'brassica_rapa': 'mysql://root:root@localhost/brassica_rapa', 'cannabis': 'mysql://root:root@localhost/cannabis', + 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', 'dna_damage': 'mysql://root:root@localhost/dna_damage', 'embryo': 'mysql://root:root@localhost/embryo', 'eplant2': 'mysql://root:root@localhost/eplant2', @@ -24,6 +25,7 @@ SQLALCHEMY_BINDS = { 'eplant_tomato' : 'mysql://root:root@localhost/eplant_tomato', 'fastpheno' : 'mysql://root:root@localhost/fastpheno', 'germination': 'mysql://root:root@localhost/germination', + 'homologs_db' : 'mysql://root:root@localhost/homologs_db', 'kalanchoe': 'mysql://root:root@localhost/kalanchoe', 'klepikova': 'mysql://root:root@localhost/klepikova', 'llama3': 'mysql://root:root@localhost/llama3', @@ -40,8 +42,5 @@ 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', - 'canola_nssnp' : 'mysql://root:root@localhost/canola_nssnp', - 'homologs_db' : 'mysql://root:root@localhost/homologs_db' - + 'triphysaria' : 'mysql://root:root@localhost/triphysaria' } diff --git a/config/databases/canola_nssnp.sql b/config/databases/canola_nssnp.sql old mode 100755 new mode 100644 index a89d10d..46f1cb8 --- a/config/databases/canola_nssnp.sql +++ b/config/databases/canola_nssnp.sql @@ -1,183 +1,98 @@ -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, 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*/; + +USE `homologs_db`; + +-- +-- Table structure for table `homologs` +-- + +DROP TABLE IF EXISTS `homologs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; 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; + `homologs_id` int NOT NULL 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, + `is_result_structure` int NOT NULL, + PRIMARY KEY (`homologs_id`) +) ENGINE=InnoDB AUTO_INCREMENT=1356306 DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Dumping data for table `homologs` +-- + +LOCK TABLES `homologs` WRITE; +/*!40000 ALTER TABLE `homologs` DISABLE KEYS */; +INSERT INTO `homologs` VALUES 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+/*!40000 ALTER TABLE `homologs` ENABLE KEYS */; +UNLOCK TABLES; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; -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'); +-- Dump completed on 2025-03-29 19:28:31 diff --git a/config/init.sh b/config/init.sh index 50b7f10..68aff95 100755 --- a/config/init.sh +++ b/config/init.sh @@ -14,6 +14,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/arabidopsis_ecotypes.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/arachis.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/brassica_rapa.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/cannabis.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/canola_nssnp.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/dna_damage.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/embryo.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant2.sql @@ -23,6 +24,7 @@ mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_soybean.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/eplant_tomato.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/fastpheno.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/germination.sql +mysql -u $DB_USER -p$DB_PASS < ./config/databases/homologs_db.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/kalanchoe.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/klepikova.sql mysql -u $DB_USER -p$DB_PASS < ./config/databases/llama3.sql @@ -40,9 +42,6 @@ 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" echo "Please manually edit config file!" diff --git a/requirements.txt b/requirements.txt index 2657891..56cc25d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,31 +1,31 @@ aniso8601==10.0.0 async-timeout==5.0.1 -attrs==25.1.0 +attrs==25.3.0 black==25.1.0 blinker==1.9.0 cachelib==0.9.0 certifi==2025.1.31 charset-normalizer==3.4.1 click==8.1.8 -coverage==7.6.10 +coverage==7.7.1 Deprecated==1.2.18 -flake8==7.1.1 +flake8==7.2.0 Flask==3.1.0 -Flask-Caching==2.3.0 -Flask-Cors==5.0.0 -Flask-Limiter==3.10.1 +Flask-Caching==2.3.1 +flask-cors==5.0.1 +Flask-Limiter==3.12 flask-marshmallow==1.3.0 flask-restx==1.3.0 Flask-SQLAlchemy==3.1.1 greenlet==3.1.1 idna==3.10 importlib_resources==6.5.2 -iniconfig==2.0.0 +iniconfig==2.1.0 itsdangerous==2.2.0 -Jinja2==3.1.5 +Jinja2==3.1.6 jsonschema==4.23.0 jsonschema-specifications==2024.10.1 -limits==4.0.1 +limits==4.4.1 markdown-it-py==3.0.0 MarkupSafe==3.0.2 marshmallow==3.26.1 @@ -36,24 +36,24 @@ mysqlclient==2.2.7 ordered-set==4.1.0 packaging==24.2 pathspec==0.12.1 -platformdirs==4.3.6 +platformdirs==4.3.7 pluggy==1.5.0 -pycodestyle==2.12.1 -pyflakes==3.2.0 +pycodestyle==2.13.0 +pyflakes==3.3.0 Pygments==2.19.1 pyrsistent==0.20.0 -pytest==8.3.4 +pytest==8.3.5 python-dateutil==2.9.0.post0 -pytz==2025.1 +pytz==2025.2 redis==5.2.1 referencing==0.36.2 requests==2.32.3 rich==13.9.4 -rpds-py==0.22.3 -setuptools==75.8.0 +rpds-py==0.24.0 +setuptools==78.1.0 six==1.17.0 -SQLAlchemy==2.0.38 -typing_extensions==4.12.2 +SQLAlchemy==2.0.40 +typing_extensions==4.13.0 urllib3==2.3.0 Werkzeug==3.1.3 wheel==0.45.1 diff --git a/tests/resources/test_snps.py b/tests/resources/test_snps.py index c53156c..b634a88 100644 --- a/tests/resources/test_snps.py +++ b/tests/resources/test_snps.py @@ -115,9 +115,9 @@ def test_get_snps(self): "protein_coding", "CODING", "GSBRNA2T00000007001", - 0.0066 + 0.0066, ] - ] + ], } self.assertEqual(response.json, expected) From c23fddc1cdf9219dae08c259b73b2c0e91276740 Mon Sep 17 00:00:00 2001 From: asherpasha Date: Sat, 29 Mar 2025 19:44:46 -0400 Subject: [PATCH 2/2] Deprecated Python 3.9 --- .github/workflows/bar-api.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/bar-api.yml b/.github/workflows/bar-api.yml index d858b37..97890ad 100644 --- a/.github/workflows/bar-api.yml +++ b/.github/workflows/bar-api.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - python-version: [3.9, 3.10.15, 3.11, 3.12, 3.13] + python-version: [3.10.16, 3.11, 3.12, 3.13] services: redis: