Principles and Applications of Modern DNA Sequencing

EEEB GU4055

Session 2: Introduction to Python, Genomic Data, and Text

Learning objectives


Learn to design, conduct, and analyze genomic experiments. By the end of class you should be able to:


1. Describe the structure of genomes and how information is represented in them.
2. Choose appropriate sequencing techniques for genomic experiments.
3. Analyze genomic data using computational methods.

THE SYLLABUS

Today's topics:



Genome Structure

A Brief History of Genomics

An introduction to Codio

Hierarchical File System

Always know where you are and where your files are.


    # format of unix command line toold
     [-arg -arg -arg] 

    # where am I now?
    pwd

    # what is here
    ls

    # what is that folder
    ls folder/

    # move me into that folder
    cd folder/
        
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def get_ref_locus_idxs(self):
    idxs = []

    with open(self.data) as indata:
        liter = (indata.read().strip().split("|\n"))

    for idx, loc in enumerate(liter):
        lines = loc.split("\n")
        snpline = loc[-1]
        locidx, chidx, pos = snpline.split("|")[1].split(":")            
        names = [i.split()[0] for i in lines[:-1]]

    

Eaton Lab China expedition 2018

Limits on the application of genomics to phylogeny

Hello world

def wat(x, y):
    for i in range(x):
        y += x
        return y
    
Vertical slide 1
Vertical slide 2

Slide 1

2018 sampling in Yunnan and Sichuan provinces, China

P. integrifolia

return

when curried, will become

a chain of functions, each

with a single argument

function(x) {

return function(y) {

return x + y;

};

}

Pedicularis

Fading

hello

heereree

YEEP