johnlees

jb_pubdistance <- function(
  v_pubs=c("The Cambridge Brew House","The Cambridge Blue",
           "King Street Run P.H.","The Elm Tree","The Regal"),
  v_location="Cambridge, UK",
  v_zoom=13,
  listpubs=FALSE,
  cam_pubs=TRUE,
  crow_distances=FALSE,
  units="minutes"){
  

johnlees

#!/usr/bin/env python
'''Python implementation of Firth regression by John Lees
See https://www.ncbi.nlm.nih.gov/pubmed/12758140'''

def firth_likelihood(beta, logit):
    return -(logit.loglike(beta) + 0.5*np.log(np.linalg.det(-logit.hessian(beta))))

# Do firth regression
# Note information = -hessian, for some reason available but not implemented in statsmodels
def fit_firth(y, X, start_vec=None, step_limit=1000, convergence_limit=0.0001):

johnlees

require(WGCNA)

# See:
# https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.pdf

SPV_2_name = read.delim("SPV_2_name.txt", header=FALSE)
colnames(SPV_2_name) = c("SPV", "gene")

# co-expression matrix from Veening lab
# https://www.biorxiv.org/content/early/2018/03/22/283739

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johnlees

johnlees

COG,Gene name,Average_aa_length,Aligned_sites,dS,dN,omega,Sites,pi_aa,dN_rate,pi_gene
CLS00002,adcB,268,268,56.5,10.5,0.0656766113998045,NA,0.000751449436378113,0.0391791044776119,0.201388448949334
CLS00003,adcC,234,234,50.5,14.5,0.134629916080151,NA,0.00391277647376286,0.061965811965812,0.915589694860509
CLS00004,adcR,146.941558441558,166,11,4,0.188155217627637,NA,0.00141473858168382,0.0240963855421687,0.207883891980019
CLS00005,dltD,420.982142857143,425,65,80,0.45168151934188,NA,0.00272578563815855,0.188235294117647,1.14750707892121
CLS00006,dltC,79,79,5,4,0.561513140654798,NA,0.0012429013818335,0.0506329113924051,0.0981892091648464
CLS00007,dltB,413.631493506493,422,84,84,0.429553902002596,NA,0.00524836591836688,0.199052132701422,2.17088943328267
CLS00013,glpF,233.165584415584,234,102,32,0.143771320439321,NA,0.0118706308630385,0.136752136752137,2.76782258256203
CLS00014,glpO,607.709415584416,608,413.75,128,0.164681667531972,NA,0.00827269833662607,0.210526315789474,5.0273966714572
CLS00022,phoB,217,217,86.6

johnlees

matrix_pow <- function(x, n) {
  if (abs(n - round(n)) < .Machine$double.eps^0.5) {
    stop(sprintf("Power %.1f is not an integer", n))
  }
  if (n < 0) {
    return(matrix_exp(solve(x), -n))
  } else if (n == 0) {
    return(1) 
  } else if (n == 1) {
    return(x) 

johnlees

import json
import random
import string

# Download from https://github.com/dwyl/english-words/raw/master/words_dictionary.json
with open('words_dictionary.json', 'r') as word_list:
    real_words = json.load(word_list)

vowels = ["a", "e", "i", "o", "u"]
trouble = ["q", "x", "y"]

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I0719 14:43:06.996543 139929070653184 run_docker.py:180] E0719 13:43:06.994233 139663816972096 hhblits.py:141] - 11:45:50.511 INFO: Searching 65983866 column state sequences.
I0719 14:43:06.996851 139929070653184 run_docker.py:180] E0719 13:43:06.994395 139663816972096 hhblits.py:141] - 11:45:51.265 INFO: Searching 15161831 column state sequences.
I0719 14:43:06.997076 139929070653184 run_docker.py:180] E0719 13:43:06.994539 139663816972096 hhblits.py:141] - 11:45:51.326 INFO: /mnt/fasta_path_0/dltA.fa is in A2M, A3M or FASTA format
I0719 14:43:06.997292 139929070653184 run_docker.py:180] E0719 13:43:06.994683 139663816972096 hhblits.py:141] - 11:45:51.327 INFO: Iteration 1
I0719 14:43:06.997498 139929070653184 run_docker.py:180] E0719 13:43:06.994824 139663816972096 hhblits.py:141] - 11:45:51.559 INFO: Prefiltering database
I0719 14:43:06.997703 139929070653184 run_docker.py:180] E0719 13:43:06.994960 139663816972096 hhblits.py:141] - 11:55:13.366 INFO: HMMs passed 1st prefilter (gapless profile-profile alig

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From 95ea1abb942e8da86faa1f1856fed316dcd95985 Mon Sep 17 00:00:00 2001
From: John Lees <[email protected]>
Date: Tue, 20 Jul 2021 15:44:19 +0100
Subject: [PATCH] Update CUDA version

---
 docker/Dockerfile | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docker/Dockerfile b/docker/Dockerfile