Ivan Krukov ivan-krukov

🗃️

Getting there

ivan-krukov / splitter.sh

Created August 17, 2012 18:28

This atrocious shell script prints the first 1/nth (half, third, etc) part of a file

	#!/bin/sh
	#get the command line arguments
	input_file=$1
	divisor=$2
	#run wc on the file in argv[1]
	size=`wc -l $input_file`
	#split the return on whitespace - first word is now in
	set $size
	#get the intiger division of wc/divisor
	part=$(($1/$divisor))

ivan-krukov / fastaparse.py

Created August 9, 2012 18:20

Another quick FASTA parser

	#Read a fasta file and only keep the sequences with correct headers (id_pattern regex)

	import re
	import sys

	seq_pattern = re.compile(r">[^>]+\n",re.MULTILINE)
	id_pattern = re.compile(r"protein_id:(?P<id>[.\w]+)")

	with open(sys.argv[1]) as f:
	text = f.read()

ivan-krukov / kyles_script.py

Created August 9, 2012 17:19

Header remover

	import argparse
	from Bio import SeqIO
	parser=argparse.ArgumentParser()

	parser.add_argument("inputFile", help="input fasta file")
	parser.add_argument("outputFile",help="output file name")
	parser.add_argument("sampleName",help="sample name to be removed")

	args = parser.parse_args()

ivan-krukov / volume

Created August 2, 2012 23:18

Change the OS X sound volume from the command line