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ensp,position,residue
ENSP00000367263,1441,M
ENSP00000367263,1572,M
ENSP00000367263,5030,M
ENSP00000367263,5550,M
ENSP00000350990,1428,M
ENSP00000437271,1428,M
ENSP00000350990,1443,C
ENSP00000437271,1443,C
ENSP00000263801,551,M

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## getJournalsFreq.R
## author: David Ochoa <dogcaesar@gmail.com>
## The script displays the number of manuscripts in each journal stored in the Mekentosj's Papers database 

topN <- 20 #Top journals to display
lastyears <- 5 #Last n years

journalsquery <- "osascript -ss -e 'tell application \"Papers\" to get bundle name of publication items'"
yearsquery <- "osascript -e 'tell application \"Papers\" to get publication year of publication items'"

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import rdflib
import pandas as pd

## Path to efo local or remote
owlpath = "https://github.com/EBISPOT/efo/releases/download/v3.18.0/efo_otar_slim.owl"
## File downloaded from
## https://docs.google.com/spreadsheets/d/1CV_shXJy1ACM09HZBB_-3Nl6l_dfkrA26elMAF0ttHs/edit
mappingFile = "/Users/ochoa/Downloads/OTAR project EFO mappings for disease profile pages - Sheet1-2.csv"
intraneturl = "http://home.opentargets.org/"
outputFile = "/Users/ochoa/Desktop/output.json"

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import argparse
import array
import struct
import pyspark.sql.functions as F
from pyspark import SparkConf
from pyspark.sql import SparkSession
from pyspark.sql import DataFrame, StructType, ArrayType, StringType
from typing import Iterable
from functools import reduce

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#!/usr/bin/env python3

# Import relevant libraries for HTTP request and JSON formatting
import requests
import json

# Set gene_id variable
gene_id = "ENSG00000244734"

# Build query string

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from pyspark.sql import SparkSession
from pyspark.sql import Window as W
from pyspark.sql import functions as F

# genetics portal studies
studiesPath = "/Users/ochoa/Datasets/study-index/"
failedPath = "/Users/ochoa/Datasets/failedEvidence"
evidenceFailedPath = "/Users/ochoa/Datasets/evidenceFailed"
diseasePath = "/Users/ochoa/Datasets/diseases"

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import pyspark.sql.functions as F
from pyspark import SparkConf
from pyspark.sql import SparkSession

sparkConf = SparkConf()

spark = (
    SparkSession.builder
    .config(conf=sparkConf)
    .master('local[*]')

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from pyspark.sql import SparkSession
from pyspark.context import SparkContext
from pyspark.sql import functions as F
from pyspark.ml.feature import Word2VecModel
from pyspark.sql.types import DoubleType
from pyspark.ml.feature import Normalizer

# establish spark connection
spark = (
    SparkSession.builder

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from pymol import cmd

cmd.load("/Users/ochoa/Downloads/AF-Q9HC29-F1-model_v1.cif")

cmd.bg_color("grey95")

cmd.set_color("veryHigh", [0, 83, 214])
cmd.set_color("confident", [101, 203, 243])
cmd.set_color("low", [255, 219, 19])
cmd.set_color("veryLow", [255, 125, 69])

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import pyspark.sql.functions as F
from pyspark import SparkConf
from pyspark.sql import SparkSession

sparkConf = SparkConf()
sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.mode', 'AUTO')
sparkConf = sparkConf.set('spark.hadoop.fs.gs.requester.pays.project.id', 'open-targets-eu-dev')

spark = (
    SparkSession.builder