sxv’s gists

sxv / catan_boards.py

Last active May 14, 2018 17:51

script to run simulations of settlers of catan board tile setups to find the average number of games played before encountering a duplicate arrangement.

	import sys, random

	# board is defined as list of 19 land tiles: Forest (4), Sheep (4), Wheat (4), Brick (3), Rocks (3), Desert (1)
	def new_board(board=''):
	available = list('ffffsssswwwwbbbrrrd')
	for i in range(19):
	random.shuffle(available)
	board += available.pop()
	return board

sxv / combine_raw_reads.py

Created November 18, 2017 08:30

take ENS gene id and gene name and append col[2:] from input files

	import sys

	rows = []

	for line in open('gene_names.csv'):
	a,b,c = line.replace('\n','').split(',')
	rows.append([a,c])

	for file in sys.argv[1:]:
	for i, line in enumerate(open(file)):

sxv / 3reads.py

Created November 18, 2017 08:29

make fastq; align; make expression table;

	# usage:
	# python 3reads.py /batch/dir1/ /batch/dir2/ # run all steps on two batches
	# python 3reads.py -2 -3 -loadAndKeep /batch/dir # run steps 2 and 3 and use STAR --loadAndKeep
	# python 3reads.py /batch/dir1 /batch/dir2/ -13 # run steps 1 and 3 on two batches
	import sys, os

	base_dir = '/home/sxv/code/s7s/'
	MAKE_FASTQ = '%s/make_fastq.sh' % base_dir
	ALIGN = '%s/align_smart-3seq.sh' % base_dir
	MAKE_EXPRESSION_TABLE = '%s/make_expression_table.R' % base_dir

sxv / pzzl.awk

Created December 2, 2016 01:53

gawk '//{x=tolower($0); gsub(/[aeiou]/,"",x); a[x]++; b[x]=$0;}END{for(i in a){ if(a[i]==1){print i, b[i]} }}' /usr/share/dict/words

sxv / fumble.py

Created October 18, 2016 08:02

	import sys

	opts = {
	'window': 100000,
	'intrachrom': False
	}
	args = sys.argv[1:]
	for a, arg in enumerate(args):
	if arg.startswith('-'):
	if arg.startswith('-w') or arg.startswith('--window'):

sxv / rna_runner.py

Last active October 11, 2016 20:53

	# define input cases via master_key.txt
	# for each run, align fastq -> bam
	# if GATK specified, run GATK, variant calling, and annovar
	# run matricizer2 on tab output
	# todo: add R clustering scripts

	## usage
	# python rnarunner.py --input-dir /path/to/fastqs
	## NOTES: input-dir must contain master_key.txt, input fastq.gz files, matricizer2.py, UCSC_GENE_NAME3.txt

sxv / rna_runner.py

Created August 10, 2016 18:57

	# define input cases via master_key.txt
	# for each run, align fastq -> bam
	# if GATK specified, run GATK, variant calling, and annovar
	# run matricizer2 on tab output
	# todo: add R clustering scripts

	## usage
	# python rnarunner.py --input-dir /path/to/fastqs
	## NOTES: input-dir must contain master_key.txt, input fastq.gz files, matricizer2.py, UCSC_GENE_NAME3.txt

sxv / index.html

Created June 12, 2016 04:34

dots1

	<canvas id="canvas"></canvas>
	<script src="https://d3js.org/d3.v3.min.js"></script>
	<script>
	var num = 2000;
	var canvas = document.getElementById("canvas");
	var width = canvas.width = window.innerWidth;
	var height = canvas.height = window.innerHeight;
	var ctx = canvas.getContext("2d");
	var particles = d3.range(num).map(function(i) {
	return [Math.round(widthMath.random()), Math.round(heightMath.random()), 2];

sxv / genesort.py

Last active August 10, 2016 20:01

	import sys
	from glob import glob

	if (len(sys.argv)<=1): match = 'n0'
	else: match = sys.argv[1]
	file = glob(match)[0]

	counts = {}
	with open(file) as f:
	print f.readline()

sxv / vcfgenie.sh

Last active August 10, 2016 20:01

	#!/usr/bin/env bash

	for f in *.vcf; do \
	gawk 'BEGIN{FS="\t"; OFS="\t"; } # separator=tab
	/CHROM/{
	## for(i=0; i<NF; i++){ if($i=="FORMAT"){ samples=(NF-i) } } # todo
	if($(NF-2)~/FORMAT/){
	samples=2; # two samples?
	if($(NF)~/[nN]$/ \|\| $(NF)~/normal$/){ swap=1 } # is order t/n?
	}

sujay sxv