Paul Magwene pmagwene

pmagwene / Pandas indexing on Rows

Created September 23, 2014 23:25

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pmagwene / Accent.py

Created December 6, 2012 05:42 — forked from endolith/Accent.py

Documenting the matplotlib colormaps

	# https://github.com/matplotlib/matplotlib/issues/881
	# Several of the ColorBrewer maps are "qualitative", meaning
	# they are just a group of colors that can be used together
	# for categories of data. So I remapped Accent to segments
	# instead of continuous:

	# Actually, these should be used with ListedColormap, and
	# the number of colors should depend on the number of
	# categories in the data, with colors removed from the
	# list in a certain order?

pmagwene / gist:2220955

Created March 27, 2012 22:21

samtools mpileup example

	samtools mpileup -uf ../../yeast-genome-Feb2011/yeast-genome-Feb2011.fasta aln.sorted.bam \| bcftools view -bvcg - > var.raw.bcf


	bcftools view var.raw.bcf \| vcfutils.pl varFilter -D400 > var.flt.vcf

pmagwene / gist:2212148

Created March 27, 2012 03:09

Lato based preamble for LaTeXit

	\documentclass[10pt]{article}
	\usepackage[usenames]{color} %used for font color
	\usepackage{amssymb} %maths
	\usepackage{amsmath} %maths\documentclass[10pt,letterpaper]{article}

	%\usepackage[usenames]{color} %used for font color
	\usepackage[HTML,dvipsnames,svgnames,x11names,hyperref]{xcolor}
	\usepackage{amssymb} %maths
	\usepackage{amsmath} %maths
	\usepackage[utf8]{inputenc} %useful to type directly diacritic characters

pmagwene / gist:2023405

Created March 12, 2012 17:09

build vim 7.3 on OS X w/non-system python and lua support

If using brew version of python

Make sure you brew as:

brew install --framework python

pmagwene / gist:1991040

Created March 7, 2012 05:08

crude dotplot in matplotlib

	# assumes pyplot and numpy are in namespace

	import string
	x = [1,4,5,9,9,11,13,14,18,20]
	cats = [i for i in string.letters[:10]]
	maxx = max(x)*1.10
	ax = axes([0,0,1,1])
	xlim(0,maxx)
	ylim(0,11)
	ticks = ax.yaxis.set_ticks(range(1,11))

pmagwene / gist:1367153

Created November 15, 2011 14:05

Prevent TextMate from restoring files from last session

	If you want to change this behavior, open Terminal.app and type

	defaults write com.macromates.textmate OakDisableSessionRestore 1

	This will make Textmate not remember the last session.

	Change the 1 by 0 if you want the default behavior.

pmagwene / gist:1298331

Created October 19, 2011 13:50

Get SNPs for gene from our Illumina data

	from yeastgenome import samsnp
	from yeastgenome import yeastgff as yff
	from yeastgenome import yeastsnp
	from yeastgenome import gff, gffsnp as gs


	flist = gff.parse_GFFfeatures('./yeast-genome-Feb2011/saccharomyces_cerevisiae.gff')
	gdict = gff.fasta_asdict('../yeast-genome-feb2011/saccharomyces_cerevisiae.gff')

	bwa70 = samsnp.parse_samsnp('./PMY070/bwa.Feb2011/final.pileup')

pmagwene / gist:1290415

Created October 16, 2011 01:55

create a numpy recarray from a matrix

nr1 = np.core.records.fromarrays(d1.transpose(), names=labels,formats=['f8']*191)

pmagwene / gist:1257022

Created October 2, 2011 03:57

emacs stuff


	(custom-set-variables
	;; custom-set-variables was added by Custom.
	;; If you edit it by hand, you could mess it up, so be careful.
	;; Your init file should contain only one such instance.
	;; If there is more than one, they won't work right.
	'(LaTeX-command "latex -synctex=1")
	'(TeX-view-program-selection (quote ((output-dvi "open") (output-pdf "Skim") (output-html "open"))))
	'(org-agenda-files (quote ("~/synchronized/org-notes/work.org" "~/synchronized/org-notes/home.org" "~/synchronized/org-notes/teaching.org" "~/synchronized/org-notes/research.org"))))
	;(custom-set-faces