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eclarke /
Created April 30, 2012 22:01
modifying plain wikilinks in wikitext
eclarke /
Created May 1, 2012 21:30
apache http client inanity
postParams.add(new BasicNameValuePair("longestOnly","false"));
postParams.add(new BasicNameValuePair("wholeWordOnly","true"));
postParams.add(new BasicNameValuePair("filterNumber", "true"));
postParams.add(new BasicNameValuePair("stopWords","protein,gene,disease,disorder,cell,syndrome,CAN"));
postParams.add(new BasicNameValuePair("withDefaultStopWords","true"));
postParams.add(new BasicNameValuePair("isTopWordsCaseSensitive","false"));
postParams.add(new BasicNameValuePair("mintermSize","3"));
postParams.add(new BasicNameValuePair("scored", "true"));
postParams.add(new BasicNameValuePair("withSynonyms","true"));
postParams.add(new BasicNameValuePair("ontologiesToExpand", ""));
eclarke /
Created May 2, 2012 21:33
filter obsolete go terms
#!/usr/bin/env python
import re
import json
import clint
def import_go(gofile='go.json'):
return json.loads(json.load(open(gofile)))
except IOError:
eclarke /
Created June 15, 2012 19:03
Spawning processes in Python
import sqlite3
import multiprocessing
store_results_sql = """ some sql code here """
select_results_sql = """ some other sql code here """
def find_enriched(**kwargs):
# do some heavy computation task here
results = enrichment_analysis(**kwargs)
# sqlite is not ideal for parallel processing, but with a timeout it should be fine
eclarke /
Created June 26, 2013 19:28
Taxonomy fixer
#!/usr/bin/env python
"""Usage: python [FILE]
Converts an ITS taxonomy file to eliminate taxa marked as unidentified,
swaps [kpcofg]__unidentified;s__Fungi to k__Fungi, and eliminates species
taxa that are simply s__[genus]_sp.
Writes to stdout.
# Erik Clarke <>
eclarke /
Last active August 29, 2015 13:57
A hackety hack function to toggle SSH/SOCKS proxy on OS X Mavericks
function toggleproxy {
# checks to see if SOCKS proxy is enabled
if [[ $(networksetup -getsocksfirewallproxy Wi-Fi | grep '^Enabled') == "Enabled: No" ]]; then
networksetup -setsocksfirewallproxystate Wi-Fi on
echo "SOCKS on!"
# checks to see if there's an existing SSH tunnel and if not, it starts one
if [[ -z $(ps aux | grep '[0-9] ssh -D 8080') ]]; then
echo -ne "Don't see a ssh tunnel on 8080 active, starting one now..."
ssh -D 8080 -f -C -q -N USERNAME@HOSTNAME.EDU # Change this from the defaults!
[[ $? == 0 ]] && echo " success!" || echo " failed :("
eclarke / ggheatmaps.R
Created April 8, 2014 19:37
Some r code relating to heatmaps and OTU counts
prop_presence_absence <- function(, groups) {
# Creates a proportional presence-absence melted dataframe suitable for use in
# ggplot heatmaps to show varying within-group proportions of species.
# Args:
# Matrix of presence-absence data. Columns are samples, rows are
# species.
# groups: Grouping data frame. A column named "SampleID" should be unique
# list of sample identifiers that match the column names of
# The other column, named "group", should correspond to the group
# Multiple plot function
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols: Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
eclarke / ggheatmap.R
Last active October 29, 2019 21:04
heatmaps ggplot style, with annotations and dendrograms
plot_ggheatmap <- function(obj, n=nrow(obj), norm=TRUE, log=TRUE,"NewSampleID",
col.annotation.width=4) {
eclarke / lab-notebook.el
Created October 21, 2014 23:26
Minor mode and functions for a lab notebook in emacs
(defun ensure-in-vc-or-checkin ()
(if (file-exists-p (format "%s" (buffer-file-name)))
(progn (vc-next-action nil) (message "Committed"))
(ding) (message "File not checked in.")))
(defun export-bibtex ()
"Exports Papers library using a custom applescript."
(message "Exporting papers library...")