Chris Friedline cfriedline
cfriedline
/ gist:7138580
Last active
December 26, 2015 10:39
Poor man's IPython notebook manager, now that there's multidir. Put this into a new notebook, assumes that all notebooks are under a common directory, albeit in their own directories. Should help (me) with git.
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| manager_name = 'Manager.ipynb' | |
| import os | |
| from IPython.display import FileLink, FileLinks, display, HTML, display_html | |
| notebooks = !find . | grep .ipynb$ | grep -v checkpoint | |
| notebooks = sorted(notebooks) | |
| root_dir = [os.path.dirname(os.path.abspath(x)) for x in notebooks if manager_name in x] | |
| paths = [] | |
| for n in notebooks: | |
| u = os.path.abspath(n).replace(root_dir[0], '/notebooks') | |
| display_html(HTML('<li><a href=%s target=_new>%s' % (u, u))) |
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| def run_diginorm_renamer(args): | |
| from Bio.SeqIO.QualityIO import FastqGeneralIterator | |
| infile, outfile = args | |
| with open(outfile, "w") as o: | |
| for i, (name, seq, qual) in enumerate(FastqGeneralIterator(open(infile))): | |
| add = 1 | |
| if i % 2 != 0: | |
| add = 2 | |
| o.write("@%s_%d\n%s\n+\n%s\n" % (name, add, seq, qual)) | |
| if i % 100000 == 0: |
cfriedline
/ diginorm_renamer.ipynb
Created
October 28, 2013 20:30
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cfriedline
/ latexify.js
Created
November 14, 2013 21:07
Create LaTeX table from selected text in Google Spreadsheet
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| function latexify() { | |
| var app = UiApp.createApplication(); | |
| height = "400" | |
| width = "500" | |
| app.setHeight(height) | |
| app.setWidth(width) | |
| app.setTitle("LaTeXified!") | |
| panel = app.createVerticalPanel() | |
| panel.setHeight("350"); | |
| panel.setWidth(width); |
cfriedline
/ snp_sim
Created
December 4, 2013 16:45
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| { | |
| "metadata": { | |
| "name": "snp_sim" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ | |
| { |
cfriedline
/ cegma_blast.ipynb
Created
January 24, 2014 16:21
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cfriedline
/ gist:9104739
Last active
August 29, 2015 13:56
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| rTraitDisc2 <- | |
| function(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2, | |
| rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k), | |
| ancestor = FALSE, root.value = 1, ...) | |
| { | |
| if (is.null(phy$edge.length)) | |
| stop("tree has no branch length") | |
| if (any(phy$edge.length < 0)) | |
| stop("at least one branch length negative") | |
cfriedline
/ test_mp_rpy2.ipynb.json
Created
June 4, 2014 05:08
testing multiprocessing and rpy2 (ape)
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:04f733fe38a12e7bbe8ee8d3f2900d3fecf0ae7a83ba728cd84650110e26b216" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
cfriedline
/ test_mp_rpy2.ipynb-2.json
Created
June 4, 2014 06:06
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:24625e0326d219f8b77f0317e421df165d0adfb7925fac44e4f9cc5c35a28bd6" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
cfriedline
/ test_mp_rpy2.ipynb-3.json
Created
June 4, 2014 07:30
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| { | |
| "metadata": { | |
| "name": "", | |
| "signature": "sha256:5507a20bf985d7ff9c8b454bf414997a33b671d82b7ceaaf24f89a61d1397ce0" | |
| }, | |
| "nbformat": 3, | |
| "nbformat_minor": 0, | |
| "worksheets": [ | |
| { | |
| "cells": [ |
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