Ivan Krukov ivan-krukov

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ivan-krukov / volume

Created August 2, 2012 23:18

Change the OS X sound volume from the command line

	! /usr/bin/osascript
	on run argv
	set Volume (item 1 of argv)
	end run

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 / 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 / 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 / oggle.sh

Created November 10, 2012 01:20

A little output logging tool

	#!/bin/sh
	cmd=$*
	pid=$$

	echo "$cmd @ `pwd`; Started at `date`" > $pid.out
	echo "[$pid] $cmd"
	eval $cmd >> $pid.out 2>> $pid.err

	echo "$cmd @ `pwd`; Finished at `date`" >> $pid.out

ivan-krukov / fastq_sample.py

Created November 21, 2012 20:04

Random sample of a FASTQ file

	#Take a fraction of random sequence reads from a fastq file
	from sh import wc
	import argparse
	import random

	def first_word(string):
	return string.strip().split()[0]

	#read a file in chunks of deflines
	def read_segments(filename,deflines):

ivan-krukov / blosum62.txt

Last active December 10, 2015 04:48

A little utility to read scoring matrices, like blosum62. Creates a dict of dicts for the scoring matrix, uses two implementations of the head-tail pattern.

	# blosum62
	# * column uses minimum score
	# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
	# Blocks Database = /data/blocks_5.0/blocks.dat
	# Cluster Percentage: >= 62
	# Entropy = 0.6979, Expected = -0.5209
	A R N D C Q E G H I L K M F P S T W Y V B Z X *
	A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4
	R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4
	N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4

ivan-krukov / gs.vim

Created January 6, 2013 14:27

Vim regex that matches a "Genus species" name on a line

^\<\u\l\{-}\> \<\l\{-}\>$

ivan-krukov / mul_print.sh

Created January 6, 2013 18:08

Printing multiple tab delimited files while skipping a few lines in the beginning

tail -n+4 -q results/* | less -S

ivan-krukov / descriptive_join.sh

Created January 14, 2013 17:54

This is a nice join snippet that you can use for a descriptive join that will include NAs in the proper columns for each file. Input: A and B, with two columns (tabs) that give an attribute to a name (eg object count) <obj_1> <count_1> <obj_2> <count_2>

join -a 1 -a2 -e 'NA' -o '0,1.2,2.2' ce hc > join.count

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