mpkocher

open System
open FSharp.Data
open FSharpx.Collections

// Example file filtered_subread_summary.csv 
// passedFilter = 1 True

// MovieName,HoleNumber,Start,End,Length,PassedFilter
// m120201_042231_42129_c100275262550000001523007907041260_s1_p0,9,0,1756,1756,1
// m120201_042231_42129_c100275262550000001523007907041260_s1_p0,11,1513,4949,3436,1

mpkocher

package com.github.mpkocher

import java.io.File

// This library is not very impressive, but it works.
// The main limitation is that it doesn't read in large chunks of the file.
import com.github.tototoshi.csv._

/*
filtered_summary.csv

mpkocher

function update_ve_pkgs() {
    echo "Updating pip packages"
    for i in $(pip freeze | tr "==" " " | awk '{print $1}') ; do pip install --upgrade $i; done
}

mpkocher

package com.github.mpkocher

import java.io.IOException
import java.nio.charset.Charset
import java.nio.file.Files
import java.nio.file.Paths
import java.util
import java.util.List
import java.util.ArrayList
import javax.script.ScriptEngineFactory

mpkocher

DI Task API Model inspired by angularjs

# Very simple task
one_proc = 1
opts_schema = {} # task has no options

mpkocher

import os
import functools

import numpy as np

from pbcore.io import FastaReader, FastaRecord


def _to_records(func, file_name):
    with FastaReader(file_name) as f:

mpkocher

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

mpkocher

# Install pbcore example
FROM mpkocher/docker-pacbiobase
MAINTAINER Michael Kocher

RUN cd /tmp && git clone https://github.com/PacificBiosciences/pbcore.git && cd pbcore && pip install .

mpkocher

package com.github.mpkocher.futuresdemo

import com.typesafe.scalalogging.LazyLogging

import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.duration._
import scala.concurrent.{Await, Future}
import scala.util.{Failure, Success}

mpkocher

import numpy as np

from pbcore.io.BasH5IO import BasH5Reader


class MovieResult(object):

    """Simple container class to hold the results of Movie (bax)"""

    def __init__(self, file_name, movie_name, read_lengths, accuracies, num_passes):