michaelbarton’s gists

michaelbarton / gist:1954109

Created March 1, 2012 23:53

	#!/usr/bin/env ruby
	require 'csv'
	require 'yaml'
	require 'bio'

	def records(file)
	Hash[Bio::GFF::GFF3.new(File.read(file)).records.map{\|i\| [i.id,i]}]
	end

	bad = records("assembly/bad.gff")

michaelbarton / gist:1950645

Created March 1, 2012 15:52

	#!/usr/bin/env ruby
	require 'csv'
	require 'yaml'
	require 'bio'

	def records(file)
	Hash[Bio::GFF::GFF3.new(File.read(file)).records.map{\|i\| [i.id,i]}]
	end

	bad = records("assembly/bad.gff")

michaelbarton / gist:1941327

Created February 29, 2012 14:52

	#!/usr/bin/env ruby
	require 'csv'
	require 'yaml'
	require 'bio'

	gff = "/Users/mike/Dropbox/bad.gff"
	re = /\w[a-z]{2}[A-Z]/


	reformatted = Bio::GFF::GFF3.new(File.read(gff)).records.each do \|record\|

michaelbarton / gist:1894210

Created February 23, 2012 18:23

	all: build

	build: plasmid.sqn

	plasmid.fsa:
	genomer view fasta \
	--identifier=PRJNA68653 \
	--organism='Pseudomonas fluorescens' \
	--strain='R124' \
	--gcode='11' \

michaelbarton / EDAM_topics.tree

Created January 19, 2012 18:28 — forked from robsyme/EDAM_topics.tree

Bioinformatics topics from EDAM (http://voxel.dl.sourceforge.net/project/edamontology/EDAM_beta12.obo)

	* Topic
	\|---+ Biological data resources
	\| \|---+ Laboratory resources
	\| \|---> Microarrays
	\| \|---> Cell culture resources
	\| +---> Medical informatics resources
	\| +---+ Biological science resources
	\|---> Cell biology resources
	\|---+ Developmental biology resources
	\| +---> Embryology resources

michaelbarton / descend.m

Created October 27, 2011 18:50

	%!test assert(descend([[1 1 1]' [2 2 2]'],[2 2 2]',[0 1]',1) == 0,
	%! "should return 0 for theta_0 when x maps onto y")
	%!
	%!test assert(descend([[1 1 1]' [2 2 2]'],[2 2 2]',[0 1]',2) == 0,
	%! "should return 0 for theta_1 when x maps onto y")
	%!
	%!test assert(descend([[1 1 1]' [4 4 4]'],[2 2 2]',[0 1]',1) == 2,
	%! "should return error for theta_0 when x doesn't map onto y")
	%!
	%!test assert(descend([[1 1 1]' [4 4 4]'],[2 2 2]',[0 1]',2) == 8,

michaelbarton / gist:1177441

Created August 29, 2011 00:14

	(ns download
	(:require [clojure.contrib.io :as io])
	(:import [java.io File FileOutputStream]))

	(defn download-binary [to from]
	(with-open [out (FileOutputStream. to)]
	(.write out
	(io/to-byte-array
	(io/input-stream
	(io/as-url from))))))

michaelbarton / gist:1177434

Created August 29, 2011 00:09

Download binary files from a url

	(nsdownload
	(:require [clojure.contrib.io :as io])
	(:import [java.io File]))

	(defn download-binary [to from]
	(with-open [in (io/input-stream (io/as-url from))]
	(io/copy in (File. to))))

michaelbarton / gist:1168959

Created August 24, 2011 19:29

	/Users/mike/.gem/gems/ffi-1.0.7/lib/ffi_c.bundle: [BUG] Segmentation fault
	ruby 1.9.2p290 (2011-07-09 revision 32553) [x86_64-darwin10.8.0]

	-- control frame ----------
	c:0045 p:-542296850 s:0139 b:0139 l:000138 d:000138 TOP
	c:0044 p:---- s:0137 b:0137 l:000136 d:000136 CFUNC :require
	c:0043 p:0029 s:0133 b:0133 l:000129 d:000132 BLOCK /Users/mike/.gem/gems/ffi-1.0.7/lib/ffi.rb:8
	c:0042 p:0056 s:0130 b:0130 l:000129 d:000129 TOP /Users/mike/.gem/gems/ffi-1.0.7/lib/ffi.rb:1
	c:0041 p:---- s:0128 b:0128 l:000127 d:000127 FINISH
	c:0040 p:---- s:0126 b:0126 l:000125 d:000125 CFUNC :require

michaelbarton / database.clj

Created August 20, 2011 21:08

	(ns leiningen.database
	(:import (org.biojava.bio.seq.io SeqIOTools))
	(:require [clj-redis.client :as redis])
	(:use [clojure.contrib.duck-streams :only (reader)]))

	(defn sequence-stream [file]
	(SeqIOTools/readFastaDNA (reader file)))

	(defn sequences [stream]
	(lazy-seq

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