jwillis0720

const { ApolloServer, gql } = require('apollo-server');
const fetch = require("node-fetch");


const typeDefs = `
  type Query {
    hello(name: String): String!
    getPersons: Person!
  }

jwillis0720

from multiprocessing import Process
import time

class JobDistributor():
    def __init__(self, jobs, limit=10, verbose=True):
        self.jobs = jobs
        self.limit = limit
        self.verbose = verbose
        self.sleep_time = 2

jwillis0720

jwillis0720

{"nbformat_minor": 0, "cells": [{"source": "#Load DB", "cell_type": "markdown", "metadata": {}}, {"execution_count": 2, "cell_type": "code", "source": "from pandas import DataFrame", "outputs": [], "metadata": {"collapsed": false, "trusted": true}}, {"execution_count": 5, "cell_type": "code", "source": "import sqlite3 as sql\nconn = sql.connect(\"/ipython_notebooks/germ_database.db3\")\ncursor = conn.cursor()", "outputs": [], "metadata": {"collapsed": false, "trusted": true}}, {"source": "#Query and convert to dataframe", "cell_type": "markdown", "metadata": {}}, {"execution_count": 75, "cell_type": "code", "source": "cursor_execute_long = cursor.execute('''\nSELECT\n\tone.struct_id,\n    one.resNum,\n    score_types.score_type_name,\n    one.score_value,\n    rpi.pdb_residue_number,\n    rpi.chain_id\n    hc.pdbnum as \"mutant_res\",\n    hc.germ,\n    hc.wt\nFROM\n\tresidue_scores_1b one\nINNER JOIN score_types ON score_types.score_type_id = one.score_type_id\ninner join residues r on r.resNum = one.resNum 

jwillis0720

def (line):
  l_s, l_l = line.split(), line.split().length()
  holder = []
  x = 0 
  y =0
  for i in l_s:
    holder.append(i)
  x++;
  y++;
  holder.append(' ')

jwillis0720

#!/usr/bin/env/python2.7
import sys
from Bio.Align.Applications import ClustalwCommandline as cw
import warnings
from multiprocessing import Pool
import argparse
import os
from Bio import AlignIO
from Bio.PDB import PDBExceptions
from Bio.PDB import PDBParser

jwillis0720

    Length     variable    value
1        1       Unique      154
2        2       Unique      258
3        3       Unique      370
4        4       Unique      548
5        5       Unique    16949
6        6       Unique    47841
7        7       Unique    60997
8        8       Unique   201506

jwillis0720

function print_usage(){
  print "###################################"
  print "USAGE: awk -f /home/kaufmakw/scripts/get_fasta_by_gi.awk -v gi=<int> -v filename=<string> -v email=<email for NCBI logging>"
  print "###################################"
  print "This script calls wget to retrieve the fasta file from the ncbi database."
  print "It accesses the sequence via the efetch eutils tool provided by NCBI"
  print "NCBI requests that you provide an email address for tracking and logging pruposes"
  print ""
}