callahantiff

#!/usr/bin/env python3.6.2
# -*- coding: utf-8 -*-

# run script from command line via python3 keyword_search_github_repositories.py

import click
import datetime
import time

from github import Github

callahantiff

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# import needed libraries
import glob
import json
import os
import pickle
import random
import requests

callahantiff

############
## PURPOSE: Generate gene-centric edge lists for collaboration with PNNL
## Master Repo: https://github.com/callahantiff/PheKnowLator/wiki/v2.0.0
## Edge Data: https://github.com/callahantiff/PheKnowLator/wiki/v2-Data-Sources
###########

# import needed libraries
import pandas
import pickle
import json

callahantiff

-- Query 1: Search for specific patients using specific vocabulary codes
SELECT DISTINCT
  CONCAT('"', CAST(c1.concept_id AS STRING), '"') AS OMOP_ID,
  c1.concept_name AS OMOP_LABEL,
  CONCAT('"', CAST(c.concept_code AS STRING), '"') AS CLINICAL_CODE, 
  CONCAT('"', CAST(c1.concept_code AS STRING), '"') AS SNOMED_CODE,
  c.vocabulary_id AS VOCABULARY

FROM CHCO_DeID_Oct2018.concept c 
  JOIN CHCO_DeID_Oct2018.concept_relationship r ON r.concept_id_1 = c.concept_id 

callahantiff

SELECT * FROM
(SELECT patient_id, disease_group_label, disease_group_num, disease_group_abbreviation, condition_concept_id AS concept_id, visit_occurrence_id, visit_start_interval
 FROM CHCO_DeID_Oct2018.Med2Mech_RareDisease_Conditions
 WHERE visit_start_interval>0 AND visit_end_interval>0)

UNION ALL

(SELECT patient_id, disease_group_label, disease_group_num, disease_group_abbreviation, drug_concept_id AS concept_id, visit_occurrence_id, visit_start_interval 
 FROM CHCO_DeID_Oct2018.Med2Mech_RareDisease_Medications
 WHERE visit_start_interval>0 AND visit_end_interval>0)

callahantiff

-- get unique counts of source and standard codes for each phenotype

-- CHCO
SELECT standard_code_set, COUNT(DISTINCT source_code) AS source_code_count, COUNT(DISTINCT standard_code) AS standard_code_count
FROM CHCO_DeID_Oct2018.ADHD_COHORT_VARS
WHERE standard_code_set is NOT NULL
GROUP BY standard_code_set

SELECT standard_code_set, COUNT(DISTINCT source_code) AS source_code_count, COUNT(DISTINCT standard_code) AS standard_code_count
FROM CHCO_DeID_Oct2018.APPENDICITIS_COHORT_VARS

callahantiff

WITH rx_case_inclusion_criteria_1 AS (
SELECT de.person_id, cohort.standard_code_set AS code_set 
FROM 
  {database}.drug_exposure de, 
  {database}.STEROIDINDUCEDOSTEONECROSIS_COHORT_VARS cohort 
WHERE de.route_concept_id IN (4132161, 4171047, 4302612)
  AND de.drug_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1
  AND cohort.standard_code_set = {code_set_group}
GROUP BY

callahantiff

WITH dx_case_inclusion_criteria_1 AS (
  SELECT co.person_id, cohort.standard_code_set AS code_set
  FROM 
    {database}.condition_occurrence co,
    {database}.HYPOTHYROIDISM_COHORT_VARS cohort
  WHERE 
    co.condition_concept_id = CAST(cohort.standard_concept_id AS int64)
    AND cohort.phenotype_definition_number = 0
    AND cohort.standard_code_set = {code_set_group}
  GROUP BY co.person_id, cohort.standard_code_set

callahantiff

WITH all_case_inclusion_criteria_1 AS (
SELECT person_id, {code_set_group} AS code_set FROM
(SELECT co.person_id
FROM 
  {database}.condition_occurrence co, 
  {database}.PEANUTALLERGY_COHORT_VARS cohort 
WHERE 
  co.condition_concept_id = CAST(cohort.standard_concept_id AS int64) 
  AND cohort.phenotype_definition_number = 1 
  AND cohort.standard_code_set = {code_set_group}

callahantiff

#!/usr/bin/python
# -*- coding: utf-8 -*-

def xpath_soup(element):
    """
    Generate xpath from BeautifulSoup4 element

    :param element: BeautifulSoup4 element.
    :type element: bs4.element.Tag or bs4.element.NavigableString
    :return: xpath as string