hammer’s gists

hammer / platform-input-support-config.yaml

Last active July 8, 2019 20:28

Configuration organized by ES index; note that this will not parse correctly! It's for purely pedagogical purposes.

	# [invalid-]evidence-data
	evidences:
	gs_output_dir: evidence-files
	downloads:
	- bucket: otar000-evidence_input/CRISPR/json
	output_filename: crispr-{suffix}.json.gz
	resource: input-file
	subset_key:
	- target
	- id

hammer / mrtarget.data.19.06.yml

Last active July 7, 2019 19:46

Configuration organized by ES index

	# relation-data
	ddr:
	evidence-count: 3
	score-threshold: 0.1

	# association-data
	scoring_weights:
	crisp: 1
	europepmc: 0.2
	expression_atlas: 0.2

hammer / Dockerfile

Last active February 24, 2018 20:39 — forked from flying-sheep/Dockerfile

scanpy-locale-setup

	FROM ubuntu:17.10

	ENV LANG C.UTF-8

	RUN apt-get update && \
	apt-get install -y python3 python3-pip libxml2-dev zlib1g-dev wget git cmake && \
	apt-get clean

	RUN apt-get install -y python3-numpy # not necessary in scanpy 0.2.9.2/0.2.10

hammer / cosmic_sigs.R

Last active January 9, 2017 21:19

Exploring COSMIC signatures

	# deconstructSigs signatures.cosmic
	library("deconstructSigs")
	library("tibble")
	signatures.cosmic.tidy <- tibble::rownames_to_column(as.data.frame(t(signatures.cosmic)))

	# COSMIC http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt
	cosmic.current <- read.delim("http://cancer.sanger.ac.uk/cancergenome/assets/signatures_probabilities.txt", check.names = F)
	cosmic.current.clean <- cosmic.current[ , colnames(cosmic.current) != ""]
	cosmic.current.tidy <- cosmic.current.clean[,names(cosmic.current.clean) not in c("Substitution Type","Trinucleotide")]

hammer / seqs2bed.py

Created January 11, 2016 22:20

Convert DeepSEA training sequences a BED file

	import h5py

	# HDF5 file with two arrays: 'trainxdata' (samples) and 'traindata' (labels)
	INFILE_SAMPLES = ''
	INFILE_REFERENCE_FASTA = ''
	OUTFILE_FASTA = 'deepsea_train10k.fa'
	OUTFILE_BED = 'deepsea_train10k.bed'

	def onehot2base(onehot):
	if onehot == [1,0,0,0]:

hammer / sgd.ml

Created December 9, 2014 20:33

	type sample = {
	x : float;
	y : float
	}

	type model = {
	theta : float;
	beta : float
	}

hammer / jpmp

Created June 4, 2014 21:45

	#!/bin/bash
	pid=$1
	nsamples=$2
	sleeptime=$3

	for x in $(seq 1 $nsamples)
	do
	jstack $pid
	sleep $sleeptime
	done \| \

hammer / HelloKryo.scala

Created May 4, 2014 23:22

Demonstration of problems with chill-avro (twitter/chill #183)

	import com.twitter.bijection.avro.{GenericAvroCodec, GenericAvroCodecs}
	import com.twitter.bijection.Injection
	import com.twitter.chill._
	import org.apache.avro.generic.{GenericRecord, GenericRecordBuilder}
	import org.apache.avro.SchemaBuilder
	import scala.util.{Failure, Success}

	object HelloKryo {
	def main(args: Array[String]) {
	// Build a schema

hammer / HelloAvro.scala

Last active October 17, 2022 04:16

Concise example of how to write an Avro record out as JSON in Scala

	import java.io.{IOException, File, ByteArrayOutputStream}
	import org.apache.avro.file.{DataFileReader, DataFileWriter}
	import org.apache.avro.generic.{GenericDatumReader, GenericDatumWriter, GenericRecord, GenericRecordBuilder}
	import org.apache.avro.io.EncoderFactory
	import org.apache.avro.SchemaBuilder
	import org.apache.hadoop.fs.Path
	import parquet.avro.{AvroParquetReader, AvroParquetWriter}
	import scala.util.control.Breaks.break

	object HelloAvro {

hammer / server_side_datatable.py

Created January 21, 2014 15:58

Implementation of a server-side DataTable (cf. http://datatables.net/release-datatables/examples/data_sources/server_side.html) using Flask, Flask-RESTful, and Psycopg. You should only have to edit source_database, source_table, and source_columns to make it work. Of course you'll probably want to edit the resource name and URL as well.

	from string import Template
	from distutils.util import strtobool

	from flask import Flask, request
	from flask.ext.restful import Api, Resource
	import psycopg2


	# Flask-RESTful Api object
	app = Flask(__name__)

Jeff Hammerbacher hammer