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# $Id: vim-keys.conf,v 1.2 2010-09-18 09:36:15 nicm Exp $
#
# vim-keys.conf, v1.2 2010/09/12
#
# By Daniel Thau.  Public domain.
#
# This configuration file binds many vi- and vim-like bindings to the
# appropriate tmux key bindings.  Note that for many key bindings there is no
# tmux analogue.  This is intended for tmux 1.3, which handles pane selection
# differently from the previous versions

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# Functions for parallelizing things

def init_spark(nproc=-1, appname="sparksession"):
    """Function to start a Spark executor."""
    from pyspark.sql import SparkSession
    if nproc == -1:
        # Use all CUPs
        spark = SparkSession.builder.master(
                "local[*]").appName(appname).getOrCreate()
    else:

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blastp -db fasta.fa -query database.fa \
    -outfmt "6 std stitle qcovs" -num_threads 10 -out out.blast

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#!/bin/bash
TYPE=${TYPE:-prot}
[[ ! -z ${1} ]] && INFILE=${1} || exit 1
shift
makeblastdb -in ${INFILE} -dbtype ${TYPE} -parse_seqids ${@} -blastdb_version 5

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#!/usr/bin/env python

import pandas as pd
import click
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO


@click.command()

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# List unique values in a DataFrame column
pd.unique(df.column_name.ravel())

# Convert Series datatype to numeric, getting rid of any non-numeric values
df['col'] = df['col'].astype(str).convert_objects(convert_numeric=True)

# Grab DataFrame rows where column has certain values
valuelist = ['value1', 'value2', 'value3']
df = df[df.column.isin(valuelist)]

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def flatten_json(y):
    out = {}

    def flatten(x, name=''):
        if type(x) is dict:
            for a in x:
                flatten(x[a], name + a + '_')
        elif type(x) is list:
            i = 0
            for a in x:

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#!/usr/bin/env python

# Sequence alignment using PyMOL
# The purpose of this script is to generate a sequence alignment between
# the original crystal structure of the apo and holo models, and the sequence
# of the finalised, ungapped Rosetta models. This allows us to get a 1 to 1
# corresponcence between the residue numberings in both structures.

# USAGE: Run once from the project root.
# "pockets.csv" contains the information about apo holo pairs.

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Databricks Programming Guidance

This document contains lessons learned with regard to Databricks programming, but also contains some best practices

Mapping to a Azure Data Lake Generation 2

blobname = "miraw"  
storageaccount = "rdmidlgen2"  
mountname = "/rdmi"

configs = {"fs.azure.account.auth.type": "OAuth",