ivan-krukov

numbers.so: numbers.c
	gcc --std=c99 -fPIC -c numbers.c
	gcc -shared numbers.o -o numbers.so
clean:
	rm -f numbers.o numbers.so

ivan-krukov

#this is a simple way to plot a matrix from a txt file

mat_data_frame=read.table("data.txt",header=F)

#rev is there to start plotting M(0,0) in the upper left corner
#col=rainbow(10) uses the rainbow color palette. You can find other ones here:
#http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/palettes.html

image(as.matrix(rev(mat_data_frame)),col=rainbow(10))

ivan-krukov

#include "mkl.h"
#include <math.h>
#include <float.h>
#include <ctime>
#include <stdio.h>

/* Auxiliary routine: printing a matrix */
void print_matrix(double * matrix, int nrow, int ncol) {
  for (int i = 0; i < nrow; i++) {
    for (int j = 0; j < ncol; j++) {

ivan-krukov

#include "mkl.h"
#include <math.h>
#include <float.h>
#include <stdio.h>

/* Auxiliary routine: printing a matrix */
void print_matrix(float * matrix, int nrow, int ncol) {
  for (int i = 0; i < nrow; i++) {
    for (int j = 0; j < ncol; j++) {
      printf("%.*e\t",FLT_DIG, matrix[i * ncol + j]);

ivan-krukov

#!/usr/bin/perl
use warnings;
#not sure how to use strict here - does not allow bareword in "Inline CPP"
use Inline CPP;
my @data = (0..10);
my $result_ref = do_stuff(\@data);
my @result = @$result_ref;
print "@result\n";
__END__
__CPP__

ivan-krukov

#get sequences by regex match from a fasta file

from argparse import ArgumentParser
import re


parser = ArgumentParser(description="grep for fasta IDs")
group = parser.add_mutually_exclusive_group()
group.add_argument("--query_string","-q")
group.add_argument("--query_file","-f")

ivan-krukov

import inspect

def render(string,variables=None):
	"""Wrapper method for String Template:
		name="Jeff"
		render("Hello, $name")
		>>Hello, Jeff
	"""
	t = Template(string)
	if not variables:

ivan-krukov

#!/usr/bin/env python3

from ftplib import FTP

def ftp_download(server,remote_path,local_path,username="anonymous",password="",verbose=True):
        #new ft object
        ftp = FTP(server) 
        if verbose: print("Connected to %s"%server)
        
        #notice that default login is "anonymous" with no password. works on most public servers

ivan-krukov

#!/usr/bin/env python

import fastaparse
import sys

sequences = [i.seq for i in fastaparse.parse_fasta(sys.argv[1])]

def substrings(string):
	n = len(string)
	for length in range(n,0,-1):

ivan-krukov

def qw(s,t=str):
    return list(map(t,s.split()))