python.md

Python

• Python Library
  • Core, Built-in, import not needed
  • Standard Library, comes installed but needs import
  • Other
    • Pandas
    • BioPython
    • Custom scripts
• Object Oriented Programming
  • Additional layer of code organization
  • Classes create new objects
  • Still have functions under classes
  • self allows access outside defined function
• Spaces, Tabs and Indentation

imports

import os
import pandas as pd
from Bio import SeqIO
from usda_file_setup import Setup

defining a class

class Call_Class():

defining a function

class Call_Class():
    def call_fuction(self,):
        <instructions>

special init function

class Call_Class():
    def __init__(self, FASTA=None, debug=False):
        <instructions>

arguments

if __name__ == "__main__": # execute if directly access by the interpreter
    parser = argparse.ArgumentParser(prog='PROG', formatter_class=argparse.RawDescriptionHelpFormatter,)


    parser.add_argument('-f', '--fasta', action='store', dest='FASTA', help='FASTA file')
    parser.add_argument('-b', '--myboolean', action='store_true', dest='myboolean', help='description')
    args = parser.parse_args()
    
    print(f'\n{os.path.basename(__file__)} SET ARGUMENTS:')
    print(args)
    print("\n")

    myclass = Call_Class()
    myclass.call_fuction(FASTA=args.FASTA)

• Interpreter
  • python
  • ipython
• Jupyter Labs
  • jupyter lab
    • conda install -c conda-forge jupyterlab
  • <shift><enter>
• VS Code
  • Text editor
  • Light weight but extensible
  • File management
  • Git integration
  • Debugging
• Debugging
  • Find errors
  • Breakpoints
  • Check variable and file output
  • Step through loops and logic
• Data Types
  • strings
  • integers
  • floats
  • tuples
  • list
  • dictionaries
  • dataframes

Data type examples:

string

a = "axl"

integer

b = 1

float

c = 1.0

tuple - immutable

d = ("sue", 1, 1.0)

list

e = ["brick", 1.0]
e.append(1)

dictionary

f={}
f["a"] = "frankie"
f["b"] = 1
f["c"] = 1.0
f["c"] = "mike"

Indexing

g = [a, b, c, d, e, f]
g[0]
g[1]
g[5]
g[-1]
h, i, j, k, l, m = g

Loops

n=[]
for i in g:
    n.append(i)

Logic

if n == g:
    print("g and n are the same")
else:
    print("Difference between n and g")
    # list comprehension
    o = [x for x in n if x not in g]
    p = [x for x in g if x not in n]
    q = p + o
    print (q)

n.append("colin_firth")
g.append("doris")

Packages

from Bio import SeqIO

seq_dict=[]
for seq_record in SeqIO.parse('assembly.fasta', "fasta"):
    seq_dict[seq_record.id] = seq_record.seq

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