mgalardini

#!/usr/bin/env python2
'''
skeleton for parallel python 2 scripts

Marco Galardini 2015
GPL v3.0
'''
import sys
from multiprocessing.queues import Queue
import multiprocessing

mgalardini

#!/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

mgalardini

#!/usr/bin/env python
'''
Run and save a jupyter notebook by providing arguments from the command line

Uses the nbparameterise package, and requires the first cell to have variables
definitions.

Command line parsing based on this Stack Overflow answer:
https://stackoverflow.com/a/42355279/1237531
'''

mgalardini

mgalardini

#!/usr/bin/env python
'''Description here'''

import logging
import argparse

def get_options():
    description = ''
    parser = argparse.ArgumentParser(description=description)

mgalardini

#!/usr/bin/env python

if __name__ == "__main__":
    import sys
    
    if len(sys.argv) < 2:
        print('USAGE: python nwk2mat.py TREE.nwk')
        sys.exit(1)
    
    import pandas as pd

mgalardini

#!/usr/bin/env python

def get_options():
    import argparse

    parser = argparse.ArgumentParser()

    parser.add_argument('reference',
                        help='Reference fasta file')
    parser.add_argument('reads',

mgalardini