tycheleturner

---
title: "AlphaFold Viewer Final"
author: "Tychele N. Turner, Ph.D."
date: "Created on October 30, 2022"
output:
  html_document: default
  pdf_document: default
abstract: This document contains the documentation for making the AlphaFold html. 
---

whitead

tranches = pd.read_csv('https://gist.githubusercontent.com/whitead/f47887e45bbd2f38332182d2d422da6b/raw/a3948beac9b9034dab432b697c5ec238503ac5d0/tranches.txt')
def get_mol_batch(batch_size = 32):
  for t in tranches.values:
    d = pd.read_csv(t[0], sep=' ')    
    for i in range(len(d) // batch_size):
      yield d.iloc[i * batch_size:(i + 1) * batch_size, 0].values

deannachurch

##Mar 13, 2015
##Some 'date-names' are aliases and map to more than one gene
#symbol date name
SEPT1 1-Sep
SEPT2	2-Sep
SEPT3	3-Sep
SEPT4	4-Sep
SEPT5	5-Sep
SEPT6	6-Sep
SEPT7	7-Sep

ctokheim

Cython

Cython has two major benefits:

1. Making python code faster, particularly things that can't be done in scipy/numpy
2. Wrapping/interfacing with C/C++ code

Cython gains most of it's benefit from statically typing arguments. However, statically typing is not required, in fact, regular python code is valid cython (but don't expect much of a speed up). By incrementally adding more type information, the code can speed up by several factors. This gist just provides a very basic usage of cython.