Ivan Krukov ivan-krukov

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Getting there

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Canada

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ivan-krukov / fastaparse.py

Created May 29, 2013 21:04

Different ways of parsing fasta files. Last one is my favorite - generators and named tuples.

	#load everythin in memory

	#split
	def split_fasta(input_file):
	with open(input_file) as fasta_file:
	text = fasta_file.read().split(">")[1:]
	data = []
	for entry in text:
	header,sequence = entry.split("\n",1)
	sequence = sequence.replace("\n","")

ivan-krukov / time-update.sh

Created May 28, 2013 22:05

time resync and hwclock update (arch)

	sudo ntpd -gq
	sudo hwclock --systohc --utc

ivan-krukov / cons.py

Last active December 17, 2015 15:19

fancy consensus builder

	#!/usr/bin/env python
	#http://rosalind.info/problems/cons/

	import fastaparse

	letters = ["A","C","G","T"]

	sequences = [i.seq for i in fastaparse.sequences("temp2")]

	#create empty profile matrix

ivan-krukov / corr.pl

Created May 15, 2013 21:00

Solution to Rosalind CORR problem

	#!/usr/bin/env perl
	use v5.14;
	use warnings;

	sub hamming {
	my @a = split "", shift;
	my @b = split "", shift;
	my $distance = 0;
	for (my $n = 0; $n < scalar(@a); $n++) {
	unless (($a[$n]) eq ($b[$n])) {

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

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 / gs.vim

Created January 6, 2013 14:27

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

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

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 / 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 / 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

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