rob-p

import networkx as nx
import random
import copy

def isValidPair(G, Gp):
  '''
  This function checks if the weighted, undirected graphs G and Gp
  constitute a valid pair.
  G and Gp constitute a valid pair if, for every vertex u in G and Gp,
  the multiset of weights for u is the same in both graphs.

rob-p

#include <cstdio>
#include <cstdlib>
#include <vector>
#include <thread>
#include <atomic>
#include <iostream>
#include "unistd.h"
#include "fcntl.h"
extern "C" {
  #include "kseq.h"

rob-p

{
 "metadata": {
  "name": "",
  "signature": "sha256:a6e570cf0bd55a345c51e9845a0be441853a5108bc5ac8bec032e8c0b89b057d"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

rob-p

seqtk mergepe ${leftIn} ${rightIn} | pv -r -b | paste - - - - - - - - | shuf | tr "\t" "\n" | tee >(seqtk seq -1 - > ${outBase}_1.fastq) | seqtk seq -2 - > ${outBase}_2.fastq

rob-p

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [

rob-p

Keybase proof

I hereby claim:

• I am rob-p on github.
• I am rob_p (https://keybase.io/rob_p) on keybase.
• I have a public key whose fingerprint is C7B0 CCB0 FCB8 E9C3 DFB8 A9BF 2EAB 9D25 7707 B487

To claim this, I am signing this object:

rob-p

#!/bin/bash

cmd="$@"
interleaved_file=`echo $cmd | sed -n 's/.*--interleaved\s\+\(\S\+\)\s\+.*/\1/p'`

if [ -z "$interleaved_file" ]
then
    #Run normally in this branch
    ${@}
else

rob-p

 def effLen(L, pmf, meanLen):
    if L < meanLen:
        return L
    minVal = 0
    maxVal = len(pmf)-1
    mval = maxVal
    clen = minVal
    maxLen = min(L, mval)
    effectiveLength = 0
    while (clen <= maxLen):

rob-p

#!/bin/bash
set -e

# Activate Holy Build Box environment.
source /hbb_exe/activate

set -x

# Install things we need
yum install -y --quiet wget

rob-p

import argparse
import pandas as pd
import numpy as np
import sys

def main(args):
    gtable = pd.read_table(args.ginput).set_index('Name')
    ttable = pd.read_table(args.tinput).set_index('Name')
    tgmap = pd.read_table(args.tgmap, names=['t', 'g']).set_index('t')
    gene_lengths = {}