fomightez

""" Usage: python diff.py FILE1 FILE2

A primitive `diff` in 50 lines of Python.
Explained here: http://pynash.org/2013/02/26/diff-in-50-lines.html
"""

def longest_matching_slice(a, a0, a1, b, b0, b1):
    sa, sb, n = a0, b0, 0

    runs = {}

fomightez

#! /usr/bin/env python

# extract_conserved_from_alignments.py by Damian Menning and Wayne Decatur
# ver 0.1
#
#*******************************************************************************
# USES Python 2.7
# PURPOSE: Takes a file of aligned sequences in FASTA format and extracts the
# residues that are 100% conserved in all sequences. As it scans the sequences,
# it writes to a file the residue if it is the same or a blank line if it is not.

fomightez

> p4339 natMX plasmid from Boone Lab as described at http://sites.utoronto.ca/boonelab/sga_technology/index.shtml 339-1460 are natMX amplicon insert made from primers 5'-ACATGGAGGCCCAGAATACCC-3' and 5'-CAGTATAGCGACCAGCATTCAC-3' according to Boone Lab
AGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGG
AAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCC
GGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCTAT
TTAGGTGACACTATAGAATACTCAAGCTATGCATCAAGCTTGGTACCGAGCTCGGATCCACTAGTAACGGCCGCCAGTGT
GCTGGAATTCGCCCttaaACATGGAGGCCCAGAATACCCtccttgacagtcttgacgtgcgcagctcaggggcatgatgt
gactgtcgcccgtacatttagcccatacatccccatgtataatcatttgcatccatacattttgatggccgcacggcgcg
aagcaaaaattacggctcctcgctgcagacctgcgagcagggaaacgctcccctcacagacgcgttgaattgtccccacg
ccgcgcccctgtagagaaatataaaaggttaggatttgccactgaggttcttctttcatatacttccttttaaaatcttg
ctaggatacagttctcacatcacatccgaacataaacaaccatgggtaccactcttgacgacacggcttaccggtaccgc

fomightez

#!/usr/bin/env python

"""
Sequence-based structural alignment of two proteins.
"""

from __future__ import print_function, division

import argparse
import os

fomightez

here is an example of what the code will make when you add your plot credentials and run

UPDATE: The former plot.ly site for the plots shas been moved to https://chart-studio.plot.ly/ , see here, but for some reason this plot no longer shows there?!? That's okay because now seems to work in Jupyter without credentials and that was why I originally didn't post the code where it worked. Now it has been added back in to https://github.com/fomightez/methods_in_yeast_genetics/blob/master/cell_density_estimator/cell_density_estimator_for_multiple_samples.ipynb and https://github.com/fomightez/methods_in_yeast_genetics/blob/master/cell_density_estimator/cell_density_estimator_for_single_sample.ipynb. (Although I need to see if resulting plot show in nbviewer still.)

fomightez

Resources used in making Launching VPython Binder.md simply for Wayne's own reference

Bottom of here for how to add a bunch of images quickly to a gist.

the question here illustrates a way that works always to place images into markdown gists, follow the link through to here to see it in action. Note that the full link extracted from the url seen when viewing the 'raw' image for a gist, a.k.a., "the hard way" on that page, is the only way that really works.

For adding small icons and symbols use advice here to add things like play button [►], etc. and [here](http://jrgraphix.net/r/Unicode/25A0

fomightez

• Go to VPython.org in your browser. The landing page will look like below.

• Click on Binder package link on that page. That link is near the very bottom of the part of the page that is showing above; it is just below Demo Programs.

• A notebook will then launch. (Sometimes first times they hang, just hit reload in your browser.)
  After it loads fully it will look like below with a URL different from what you see but similar.
  

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fomightez

• Go to my fork of the VPython Binder repository in your browser.

• Click on the on the bottom of that page.

• That will take you to a new page and trigger deploying version of the jupyter notebook environment from the correct repository. You shouldn't need to do anything as this takes place; you can watch the progress bar roughly in the middle of the screen, just below the Launch button. It may take about a minute. After it boots up, it should bring you to the dashboard that will look like below

fomightez

%matplotlib notebook
from matplotlib import pyplot as plt
from matplotlib_venn import venn3, venn3_circles
#**REQUIRES `matplotlib_venn` ADDED TO `REQUIREMENTS.TXT` FOR BINDER, or run `%pip install matplotlib_venn` first**
#**One already set like that can be launched from https://github.com/fomightez/vpython-jupyter ***
# NOTE: I corrected the Subset labels according to info I posted at
# http://matthiaseisen.com/pp/patterns/p0145/ , which is
# where this code was adapted from

# Subset sizes