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update_snp.py
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update_snp.py
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# -*- coding: utf-8 -*-
# __author__ = 'liubinxu'
import logging
import sys
import time
import json
from biocluster.config import Config
from concurrent.futures import ThreadPoolExecutor
import sqlite3
from collections import defaultdict
import re
from bson.objectid import ObjectId
class RefUpdate(object):
def __init__(self, project_type, bind_object=None):
super(RefUpdate, self).__init__()
self.db = Config().get_mongo_client(mtype=project_type, db_version=1)[Config().get_mongo_dbname(project_type, db_version=1)]
self._project_type = project_type
self.map_dict = dict()
def find_records(self, collection_name, query_dict):
conn = self.db[collection_name]
results = conn.find(query_dict)
print conn
return results
def update_record_by_dict(self, collection_name, query_dict, insert_dict):
conn = self.db[collection_name]
print collection_name
print query_dict
print insert_dict
conn.update(query_dict, {"$set": insert_dict}, upsert=True)
def find_record(self, collection_name, query_dict):
conn = self.db[collection_name]
result = conn.find_one(query_dict)
return result
def find_records(self, collection_name, query_dict):
conn = self.db[collection_name]
results = conn.find(query_dict)
print conn
return results
def update(self, task_id):
self.get_background_info(task_id)
self.replace_links(task_id)
def get_task(self, query_dict):
records = self.find_records("sg_geneset_kegg_enrich", query_dict)
task_id = [record['task_id'] for record in records]
return list(set(task_id))
def get_path_ko(self, main_id):
self.gene2ko = dict()
kegg_kos = self.find_records("sg_annotation_kegg_table", {"kegg_id": main_id})
for kegg_ko in kegg_kos:
self.gene2ko[kegg_ko["transcript_id"]] = kegg_ko["ko_id"]
def get_background_info(self, task_id):
kegg= self.find_record("sg_annotation_kegg", {"task_id": task_id})
if not kegg:
print "task wrong {}".format(task_id)
records = self.find_records("sg_annotation_kegg_level", {"kegg_id": kegg["main_id"]})
self.get_path_ko(kegg["main_id"])
for record in records:
pathway = record["pathway_id"]
links = record["hyperlink"].split("?")[1].split("/")
links.pop(0) # 去除掉map
dict = {}
for link in links:
ko = link.split("%09")[0] # K06101
color = link.split("%09")[1] # tomato
dict[ko] = color
self.map_dict[pathway] = dict # self.map_dict["map05340"] = {"K10887": "yellow"}
def get_geneset_detail(self, main_id):
geneset_detail = self.find_record("sg_geneset_detail", {"geneset_id": main_id})
geneset_ko = defaultdict(set)
regulate_gene = defaultdict(set)
geneset_ko["up"] = list()
geneset_ko["down"] = list()
dic = zip(geneset_detail["seq_list"], geneset_detail["regulate_list"])
regulate_gene["up"] = [k for k, v in dic if v == "up"]
regulate_gene["down"] = [k for k, v in dic if v == "down"]
for gene in regulate_gene["up"]:
if gene in self.gene2ko:
geneset_ko["up"].extend(self.gene2ko[gene].split(";"))
for gene in regulate_gene["down"]:
if gene in self.gene2ko:
geneset_ko["down"].extend(self.gene2ko[gene].split(";"))
self.category = geneset_ko
def replace_links(self, task_id):
enrich_records = self.find_records("sg_geneset_kegg_enrich", {"task_id": task_id})
for enrich_record in enrich_records:
if enrich_record["params"] == "":
continue
params = json.loads(enrich_record["params"])
gene_set = self.find_record("sg_geneset", {"main_id": ObjectId(params["geneset_id"])})
if gene_set.get("source", "") == "diff_exp" and enrich_record["status"] == "end":
self.get_geneset_detail(gene_set["main_id"])
print task_id, enrich_record["main_id"]
self.replace_link(enrich_record["main_id"])
def replace_link(self, main_id):
enrich_details = self.find_records("sg_geneset_kegg_enrich_detail", {"kegg_enrich_id": main_id})
for record in enrich_details:
links = record["hyperlink"]
if "multi_query" in links:
print main_id, "结果正确"
break
pathway = record["id"]
links_ko = links.split("?")[1].split("/")
links_ko.pop(0) # 去除掉map
lnk = links.split("?")[0] + "?map=" + pathway + "&multi_query="
ko_tmp = [x.split("%09")[0] for x in links_ko]
ko_link_all = []
ko_link_bg = []
if pathway in self.map_dict: # 含有背景色
for ko in self.map_dict[pathway].keys():
if ko == "":
continue
if ko in ko_tmp: # 基因ko显著富集
if self.get_color(ko):
ko_link_all.append(ko + "+{},{}%0d%0a".format(self.map_dict[pathway][ko], self.get_color(ko)))
else:
ko_link_bg.append(ko + "+{}%0d".format(self.map_dict[pathway][ko]))
else:
ko_link_bg.append(ko + "+{}%0d".format(self.map_dict[pathway][ko]))
else:
for ko in ko_tmp:
if ko == "":
continue
if self.get_color(ko):
ko_link_bg.append(ko + "+{},{}%0d%0a".format("white", self.get_color(ko)))
else:
pass
link_new = lnk + "".join(ko_link_all) + "".join(ko_link_bg)
# print links, link_new
self.update_record_by_dict("sg_geneset_kegg_enrich_detail", {"_id": record["_id"], "kegg_enrich_id": record["kegg_enrich_id"]}, {"hyperlink": link_new, "err_link": links})
def get_color(self, ko):
"""
根据基因的ko号，获取颜色
:param ko: 基因的ko号
:return:
"""
if len(self.category) == 1:
if ko in self.category[self.category.keys()[0]]:
return "red"
# return "blue"
else:
return False
elif len(self.category) == 2:
# if self.option('source') == 'diff_exp':
# lst = list(self.category.keys()) # 基因集列表
lst = ["up", "down"]
# lst.sort()
if ko in self.category[lst[0]] and ko in self.category[lst[1]]:
return "pink"
elif ko in self.category[lst[0]]:
return "red"
elif ko in self.category[lst[1]]:
return "blue"
else:
return False
if __name__ == '__main__':
logging.info('Usage: python add_batch.py <project_type>')
project_type = sys.argv[1]
if len(sys.argv) == 2:
ref = RefUpdate(project_type=project_type)
print "\n".join(ref.get_task({"created_ts": {"$gte": "2021-02-26"}}))
else:
task_id = sys.argv[2]
ref = RefUpdate(project_type=project_type)
ref.update(task_id=task_id)