s-boardman

# How to use the ModelMultipleChoiceField widget outside the Django admin interface
# when processing forms with Crispy-forms

## Prerequisites

django-crispy-forms installed and included in settings (as per crispy docs)

## Edited files:

### urls.py (root, not app/urls.py)

s-boardman

import numpy as np
from scipy import stats
from itertools import combinations
from statsmodels.stats.multitest import multipletests
from statsmodels.stats.libqsturng import psturng
import warnings


def kw_dunn(groups, to_compare=None, alpha=0.05, method='bonf'):
    """

s-boardman

import os
import subprocess

import numpy as np
import pandas as pd

from sample_class import Sample
from custom_parser import Parser
from pipeline_tools import file_checker

s-boardman

The [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/)  Unix package is extremely well regarded for RNA-seq analysis.  Yet it is widely acknowledged that installation is difficult, not least by the [Cufflinks authors themselves](http://cole-trapnell-lab.github.io/cufflinks/getting_started/#installing-a-pre-compiled-binary-release)! Whilst the authors provide precompiled binaries to make the installation process easier [the instructions aren't very explicit](http://cole-trapnell-lab.github.io/cufflinks/getting_started/). Having spent a good hour on Google and StackOverflow I've put together an instruction list for the less experienced Unix user like myself.

Note this guide is for Unix distributions.

1. Download the Cufflinks tar from http://cole-trapnell-lab.github.io/cufflinks/install/
'''shell
wget http://cole-trapnell-lab.github.io/cufflinks/install/
'''
2. Untar the downloaded file
'''shell

s-boardman

# argparse section
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-l","--list", help="pass a list", nargs="*")
parser.add_argument("-b","--boolean", action="store_true", default=False, help="use this flag to turn on an option")


# grab the options here from the command line, console overrides email
args = parser.parse_args()

s-boardman

"""Plots a Pandas dataframe as a heatmap"""
import matplotlib as mpl
import matplotlib.pyplot as plt

def heatmap(df,
            edgecolors='w',
            cmap=mpl.cm.RdBu,
            log=False,vmin=0,vmax=500):    
    width = len(df.columns)/4
    height = len(df.index)/4