arq5x’s gists

arq5x / test_gemini_query.py

Last active December 15, 2015 09:09

Example script using the Gemini query API for custom analysis.

	#!/usr/bin/env python
	import sys
	from gemini import GeminiQuery

	db = sys.argv[1]

	# create a GeminiQery instance for the requested database
	gq = GeminiQuery(db)

arq5x / test.sh

Last active April 22, 2025 18:31

Compress and then Decompress a string with zlib.

	# compile
	$ g++ zlib-example.cpp -lz -o zlib-example

	# run
	$ ./zlib-example
	Uncompressed size is: 36
	Uncompressed string is: Hello Hello Hello Hello Hello Hello!

	----------

arq5x / grantham-dict.py

Last active January 30, 2025 06:31

Convert Grantham Amino Acid matrix into Python dict.

	#!/usr/bin/env python
	import sys
	import pprint

	def make_grantham_dict(grantham_mat_file):

	"""
	Citation: http://www.ncbi.nlm.nih.gov/pubmed/4843792
	Provenance: http://www.genome.jp/dbget-bin/www_bget?aaindex:GRAR740104

arq5x / test.vcf

Last active December 17, 2015 19:09

CBW 2013 - Structural Variation Practical Session.

	##fileformat=VCFv4.1
	##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
	##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
	##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
	##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
	##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
	##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
	##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
	##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
	##ALT=<ID=DEL,Description="Deletion">

arq5x / gemini-somatic.sh

Last active December 18, 2015 10:29

Example of using GEMINI genotype columns to identify confident somatic mutations in a cancer experiment

	# DOCS:
	# https://gemini.readthedocs.org/en/latest/content/database_schema.html#genotype-information

	# GEMINI SOURCE:
	# https://github.com/arq5x/gemini

	#########################################################################
	# load a VCF for a tumor / normal pair into gemini.
	# - use 4 cores
	# - assume VCF has been annotated with snpEff

arq5x / shuffle-non-overlapping.sh

Created June 18, 2013 13:20

"Strategy" for generating shuffled BED files while preventing overlapping records in the shuffled output.

	tries=0

	while true;
	do
	tries=$((tries+1))
	echo "attempt number $tries"

	# try a shuffle
	bedtools shuffle -i foo.bed -g human.hg19.genome > foo.shuffled.bed

arq5x / workflow.sh

Last active December 21, 2015 01:58

GBM

	export SAMPLES="BLV4 NCH411GBM_CD133high NCH411GBM_CD133low NCH537P54_CD133neg NCH537P54_CD133pos NCH620P55_CD133neg NCH620P55_CD133pos NCH644GBM_CD133high NCH644GBM_CD133low NCH7Md_P43_CD133neg NCH7Md_P43_CD133pos NPC-v"

	######################################
	# Sort the original BAM files by name:
	######################################
	export GBMHOME=/net/midtier18/vol79/cphg-quinlan2/projects/gbm-seq-abounader
	export STEPNAME=gbm-nmsrt
	for sample in `echo $SAMPLES`
	do
	export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=6000m:ncpus=1 -N $STEPNAME -m bea -M arq5x@virginia.edu"

arq5x / acknowledgements.txt

Last active December 21, 2015 09:59

A collection of both popular and lesser known biographies, autobiographies and histories of scientific figures and their discoveries. Focused primarily on biology and genetics. This is largely a collection of responses to a query on twitter.

	Thanks to @Adrian_H, @RoryKirchner, @genetics_blog,
	@leonidkrugliak, @Graham_Coop, @yokofakun,
	@pathogenomenick, @caseybergman, @Jalfoldi,
	@Paul_R_Johnston, @gknoProject, @David_Dobbs,
	@vsbuffalo, @robinhenig, @nccomfort,
	@GholsonLyon, @notSoJunkDNA, @neilfws,
	@rovingpencil, @rtraborn

	In addition, please refer to Casey Bergman's collection of other books:
	http://www.librarything.com/catalog/xylem&tag=genetics&collection=-1

arq5x / rest-example.md

Last active July 23, 2019 00:16

Example use of a RESTful API to GEMINI databases.

Load a GEMINI database from a VCF

$ gemini load -v nobel.vcf -t VEP --cores 23 -p samples.ped nobel.db

Launch the GEMINI web server

(this will run on your local machine on port 8088)

$ gemini browser nobel.db

arq5x / comparo.txt

Created September 11, 2013 03:20

bedtools 2.18 timing comparisons with 2.17 and bedops

	######################################################################################################
	# Version 2.18.0
	######################################################################################################

	# BAM, CHROMSWEEP
	time ./bedtools intersect -a random.20M.sorted.bam -b gencode.v17.exons.sorted.bed -sorted > /dev/null

	real 0m20.153s
	user 0m19.953s
	sys 0m0.192s

Aaron Quinlan arq5x

Load a GEMINI database from a VCF

Launch the GEMINI web server