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Researching 'em microbes...

Christian Diener cdiener

Researching 'em microbes...
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cdiener /
Last active May 20, 2020
Convert image to ascii art
import sys; from PIL import Image; import numpy as np
chars = np.asarray(list(' .,:;irsXA253hMHGS#9B&@'))
if len(sys.argv) != 4: print( 'Usage: ./ image scale factor' ); sys.exit()
f, SC, GCF, WCF = sys.argv[1], float(sys.argv[2]), float(sys.argv[3]), 7/4
img =
S = ( round(img.size[0]*SC*WCF), round(img.size[1]*SC) )
img = np.sum( np.asarray( img.resize(S) ), axis=2)
cdiener /
Created Apr 13, 2014 now with documentation
# This line imports the modules we will need. The first is the sys module used
# to read the command line arguments. Second the Python Imaging Library to read
# the image and third numpy, a linear algebra/vector/matrix module.
import sys; from PIL import Image; import numpy as np
# This is a list of characters from low to high "blackness" in order to map the
# intensities of the image to ascii characters
chars = np.asarray(list(' .,:;irsXA253hMHGS#9B&@'))
# Check whether all necessary command line arguments were given, if not exit and show a
cdiener /
Last active Aug 29, 2015
Learning Topics

Learning List

Next topics to learn:

  • webservers
  • node.js
  • Django or Pyramid [maybe Jinja2+Tornado a better option for smaller projects]
  • Plone plugins [too complex, substituded by FormGen]
  • D3
  • Python testing frameworks
cdiener / overload.R
Last active Aug 23, 2019
R operator overloading
View overload.R
a = "bla"
b = "so on"
class(a) = append("my_class", class(a))
'+.my_class' = function(x,y) paste(x,y,sep=" and ")
cdiener / points
Last active Aug 29, 2015
ggplot2 grouped points with horizontal means
View points
emsa_plot = ggplot(emsa, aes(x=Name, y=intensity, shape=charge_ratio, col=charge_ratio, width=0.8)) +
geom_point(size=3, position=position_dodge(width=0.8)) +
stat_summary(, mult=0, color="black", geom="errorbar", size=1, position=position_dodge(width=0.8)) +
scale_color_grey(start=0, end=0.5,name="charge ratio") +
scale_shape(name="charge ratio") +
scale_y_continuous(limits=c(-0.05,1), breaks=seq(0,1,by=0.2), label=percent) +
cdiener / cache.R
Last active Aug 29, 2015
cache operator for R
View cache.R
# Caching operator executes command if there is no saved version of the data
# just delete the saved file and code will be run again
'%c%' = function(ex, file) if(file.exists(file), env=parent.frame(4)) load(file) else evalq(ex))
# Example
# first execution
{ x <- rnorm(1e6); save(x, file="cache.Rd") } %c% "cache.Rd" # executes the sampling
cdiener / eset_reduce.R
Last active Feb 3, 2016
ExpressionSet reducer - allows you to reduce the features of an expression set from an nxn grouping, for instance probesets to genes/transcripts etc.
View eset_reduce.R
#' Reduces an ExpressionSet by an n-to-n map of features to groups. All entries
#' in \code{features} must exist in \code{eset}. \code{features} and
#' \code{groups} must have the same length.
#' @param eset An ExpressionSet object.
#' @param features A character vector of features to be grouped.
#' @param groups A factor or character vector mapping the entries in
#' \code{features} to groups.
#/usr/bin/env python
from cobra.test import create_test_model
from cobra.flux_analysis import single_gene_deletion
cobra_model = create_test_model("textbook")
dels = {"b0008": 0.87, "b0114": 0.71, "b0116": 0.56, "b2276": 0.11, "b1779": 0.00}
rates, statuses = single_gene_deletion(cobra_model, gene_list=dels.keys(),
method="moma", solver="mosek")
cdiener / enrichment.R
Created May 4, 2016
Small GSEA implementation
View enrichment.R
ES <- function(p, w, pws, both=FALSE) {
n <- length(pws)
nr <- sum(abs(w[pws == p]))
nh <- sum(pws == p)
scores <- vector(length=n)
scores[pws == p] <- abs(w[pws == p])/nr
scores[pws != p] <- -1/(n - nh)
r <- range(cumsum(scores))
i <- which.max(abs(r))
cdiener /
Last active Mar 6, 2017
Compare pytest benchmarks
import json
import pandas as pd
from sys import argv, exit
def benchmark_to_df(json_file):
with open(json_file) as jf:
content = json.load(jf)
df = pd.DataFrame(columns=("test", "time [ms]"))
for b in content["benchmarks"]:
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