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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

#!/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
'''Description here'''

import logging
import argparse

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

mgalardini

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

#!/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 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
# Copyright (C) <2015> EMBL-European Bioinformatics Institute

# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of

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