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willfurnass / ruffus_simple_test.py
Created Jan 11, 2017
Simple test of the Ruffus workflow manager
View ruffus_simple_test.py
#!/usr/bin/env python
from __future__ import print_function
from ruffus import transform, suffix, pipeline_run
# A test of using Ruffus to locally run a very simple pipeline comprised of
# tasks defined as Python functions
# Can run this from a conda environnment created using
# conda create -n drmaatest -c bioconda python=2.7 ruffus drmaa
@willfurnass
willfurnass / bng.py
Created Mar 1, 2016
Convert alphanumeric British National Grid references to/from easting northing integer pairs
View bng.py
import numpy as np
myriad_codes = np.array((
None, None, None, None, "HP", None, None,
None, None, None, "HT", "HU", None, None,
None, "HW", "HX", "HY", "HZ", None, None,
"NA", "NB", "NC", "ND", None, None, None,
"NF", "NG", "NH", "NJ", "NK", None, None,
"NL", "NM", "NN", "NO", None, None, None,
None, "NR", "NS", "NT", "NU", None, None,
@willfurnass
willfurnass / zotero_shorttitle_as_bibtex_key.patch
Created Feb 20, 2016
Patch Zotero's translators/BibTeX.js so non-empty shortTitle values used as BibTeX key when exporting Zotero library.
View zotero_shorttitle_as_bibtex_key.patch
--- BibTeX.js.orig 2015-07-03 07:18:37.000000000 +0100
+++ BibTeX.js 2015-08-09 14:21:08.779706944 +0100
@@ -1176,7 +1176,11 @@
if(!type) type = "misc";
// create a unique citation key
- var citekey = buildCiteKey(item, citekeys);
+ if (item.shortTitle==''){
+ var citekey = buildCiteKey(item, citekeys);
+ } else {
@willfurnass
willfurnass / shear_stress.m
Last active Aug 29, 2015
Calculate steady-state boundary shear stress in pressurised water pipes
View shear_stress.m
function tau_a = shear_stress(D, Q, k_s, T, den)
%{ Hydraulic shear stress at pipe wall (in Pa).
%
% Params:
% D -- internal diameter (m)
% Q -- flow (m^3s^-1)
% k_s -- roughness height (m)
% T -- temperature; defaults to 10degC)
% den -- density defaults to 1000kg/m^3
%