ivan-krukov

#!/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

#!/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

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

ivan-krukov

#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

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

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

#!/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

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

#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

#!/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__