Benjamin Langmead BenLangmead

Associate Professor of Computer Science at Johns Hopkins University

BenLangmead / DeBruijn.py

Last active September 26, 2023 15:39

Demonstration of de Bruijn graph construction and Eulerian path/cycle finding.

	class DeBruijnGraph:
	""" A de Bruijn multigraph built from a collection of strings.
	User supplies strings and k-mer length k. Nodes of the de
	Bruijn graph are k-1-mers and edges correspond to the k-mer
	that joins a left k-1-mer to a right k-1-mer. """

	@staticmethod
	def chop(st, k):
	""" Chop a string up into k mers of given length """
	for i in xrange(0, len(st)-(k-1)):

BenLangmead / ErrorCorrection.py

Last active December 15, 2015 22:18

	def neighbors1mm(kmer, alpha):
	""" Generate all neighbors at Hamming distance 1 from kmer """
	for j in xrange(len(kmer)-1, -1, -1):
	for c in alpha:
	if c == kmer[j]: continue
	yield kmer[:j] + c + kmer[j+1:]

	def correct1mm(read, k, kmerhist, alpha, thresh):
	""" Return an error-corrected version of read. k = k-mer length
	for k-mer count profile. kmerhist maps distinct kmers to their

BenLangmead / CpGIslandMarkovChain.py

Last active December 16, 2015 00:59

	import re
	import sys
	import string
	import numpy
	import math

	def fastaKmerParser(fns, k):
	""" Parse all (overlapping) k-mers of length k from all the FASTA
	filenames provided. """
	for fn in fns:

BenLangmead / HMM.py

Last active December 16, 2015 05:38

	import numpy

	class HMM(object):
	""" Simple Hidden Markov Model implementation. User provides
	transition, emission and initial probabilities as dictionaries.
	Transition and emission probabilities are expressed as a dict
	mapping a 2-character code onto the floating-point probability
	for that table entry. States and emissions are represented
	with single characters. """

BenLangmead / gtf_flux_fix.py

Created September 2, 2013 15:50

Transforms a genes.gtf file from an iGenomes tarball into a new .gtf file formatted more like Flux Simulator expects.

	"""
	gtf_flux_fix.py

	Author: Ben Langmead ([email protected])
	Date: Sept 2, 2013

	Remove GTF records for sequence IDs that don't appear in any of the specified
	FASTA files. Move the transcript_id attribute into the first attribute
	position. Output transformed GTF to stdout.
	"""

BenLangmead / CG_001_StringBasics1.json

Created September 10, 2013 17:26

BenLangmead / CG_002_NaiveMatching1.json

Created September 10, 2013 17:55

BenLangmead / 003_CG_InvertedIndex1

Created September 16, 2013 15:46

BenLangmead / 004_CG_InvertedIndex2.json

Created September 16, 2013 16:14

BenLangmead / CG_InvertedIndex2.json

Created September 16, 2013 18:28