ferrolad

#!/usr/bin/env python
doc = """
Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
Author: Rayan Chikhi         

short usage: <reference> <*.fastq> 

example: 
         estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq

ferrolad

#!/usr/bin/env python
'''
Automatically estimate insert size of the paired-end reads for a given SAM/BAM file.
Usage: getinsertsize.py <SAM file> or samtools view <BAM file> | getinsertsize.py -
Author: Wei Li

Copyright (c) <2015> <Wei Li>

ferrolad

#! /usr/bin/env python

"""
extract_reads.py
Created by Tim Stuart
"""

import pysam

ferrolad

#! /usr/local/bin/python2.7
"""
mean_size.py
Created by Tim Stuart
"""

import numpy as np


def get_data(inp):

ferrolad

#!/bin/bash
set -eo pipefail

# A small script to generate artemis comparison files (nucleic acid comparison)
# since all the webservers are apparently defunct!

# Script requires blastn (NOT LEGACY BLAST) and makeblastdb in path - check for existence:

command -v makeblastdb >/dev/null 2>&1 || { echo >&2 "makeblastdb doesn't appear to be installed. Aborting."; exit 1; }
command -v blastn >/dev/null 2>&1 || { echo >&2 "BLAST+ doesn't appear to be installed. Aborting."; exit 1; }

ferrolad

# This script will calculate Shannon entropy from a MSA.

# Dependencies:

# Biopython, Matplotlib [optionally], Math

"""
Shannon's entropy equation (latex format):
    H=-\sum_{i=1}^{M} P_i\,log_2\,P_i
    Entropy is a measure of the uncertainty of a probability distribution (p1, ..... , pM)

ferrolad

#!/bin/bash

###
# Backup Script
###

# Toggle debug mode for CLI output - "YES" or "NO"
DEBUG="YES"

ferrolad

# coding=UTF-8
import nltk
from nltk.corpus import brown

# This is a fast and simple noun phrase extractor (based on NLTK)
# Feel free to use it, just keep a link back to this post
# http://thetokenizer.com/2013/05/09/efficient-way-to-extract-the-main-topics-of-a-sentence/
# Create by Shlomi Babluki
# May, 2013