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Advanced Python Concepts: Modules

BCHB5242013

Lecture 14

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Modules

We've already used these from the python standard library and from BioPython

import sysfilename = sys.argv[1]file_handle = open(filename)

import Bio.SeqIOseq_records = Bio.SeqIO.parse(file_handle, "swiss")

import gzipfile_handle = gzip.open(filename)

import urllibfile_handle = urllib.urlopen(url)

import mathx = math.sqrt(y)

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Modules

Modules contain previously defined functions, variables, and (soon!) classes.

Store useful code for re-use in many programs

Structurerelated codetogether

import sysimport MyNucStuff

seqfilename = sys.argv[1]

seq   = MyNucStuff.read_seq_from_filename(seqfilename)cseq  = MyNucStuff.complement(seq)rcseq = MyNucStuff.reverseComplement(seq)

print "   Sequence:",seqprint " C sequence:",cseqprint "RC sequence:",rcseq

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Modules

In MyNucStuff.pydef read_seq_from_filename(seq_filename):    seq_file = open(seq_filename)    dna_seq = ''.join(seq_file.read().split())    dna_seq = dna_seq.upper()    seq_file.close()    return dna_seq

compl_dict = {'A':'T', 'T':'A', 'C':'G', 'G':'C'}

def complement(seq):    return ''.join(map(compl_dict.get,seq))

def revseq(seq):    return ''.join(reversed(seq))

def reverseComplement(seq):    return complement(revseq(seq))                   # plus anything else you like...

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Modules

We can import specific functions directly… And reference them without the module name

import sysfrom MyNucStuff import read_seq_from_filenamefrom MyNucStuff import complementfrom MyNucStuff import reverseComplement

seqfilename = sys.argv[1]

seq   = read_seq_from_filename(seqfilename)cseq  = complement(seq)rcseq = reverseComplement(seq)

print "   Sequence:",seqprint " C sequence:",cseqprint "RC sequence:",rcseq

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Modules

We can even import all the functions from a module…

import sysfrom MyNucStuff import *

seqfilename = sys.argv[1]

seq   = read_seq_from_filename(seqfilename)cseq  = complement(seq)rcseq = reverseComplement(seq)

print "   Sequence:",seqprint " C sequence:",cseqprint "RC sequence:",rcseq

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Packages

Packages are collections of modules, grouped together. All equivalent:

Implemented using files and folders/directories.

import Bio.SeqIOBio.SeqIO.parse(handle, "swiss")

from Bio import SeqIOSeqIO.parse(handle, "swiss")

from Bio.SeqIO import parseparse(handle, "swiss")

What can go wrong?

Sometimes our own .py files can "collide" with Python's packages.

Test what happens with an "empty" module in files: xml.py (and then try to import ElementTree) Bio.py (and then try to import SeqIO) etc…

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A module for codon tables Module is called: codon_table Functions:

read_codons_from_filename(filename) returns dictionary of codons –

value is pair: (amino-acid symbol, initiation codon true/false) amino_acid(codon_table,codon)

returns amino-acid symbol for codon is_init(codon_table,codon)

returns true if codon is an initiation codon, false, otherwise get_ambig_aa (codon_table,codon)

Returns the single amino-acid consistent with ambiguous codon (containing N's), or X.

translate(codon_table,seq,frame) returns amino-acid sequence for DNA sequence seq

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A module for codon tables

from MyNucStuff import *from codon_table import *import sys

if len(sys.argv) < 3:    print "Require codon table and DNA sequence on command-line."    sys.exit(1)

table = read_codons_from_filename(sys.argv[1])seq = read_seq_from_filename(sys.argv[2])

if is_init(table,seq[:3]):    print "Initial codon is an initiation codon"

for frame in (1,2,3):  print "Frame",frame,"(forward):",translate(table,seq,frame)

A module for codons

In codon_table.py:

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def read_codons_from_filename(codonfile):    # magic    return codon_table

def amino_acid(table,codon):    # magic    return aa

def is_init(table,codon):    # magic    return init

def get_ambig_aa(table,codon):    # magic    return aa

def translate(table,seq,frame):    # magic    return aaseq

A module for codons

In codon_table.py:

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def read_codons_from_filename(codonfile):    f = open(codonfile)    data = {}    for l in f:        sl = l.split()        key = sl[0]        value = sl[2]        data[key] = value        f.close()

    b1 = data['Base1']    b2 = data['Base2']    b3 = data['Base3']    aa = data['AAs']    st = data['Starts']

    codon_table = {}    n = len(aa)    for i in range(n):        codon = b1[i] + b2[i] + b3[i]        isInit = (st[i] == 'M')        codon_table[codon] = (aa[i],isInit)    return codon_table

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Lab exercises Rework the lecture, and your solutions (or mine) from the

homework exercises #1 through #3, to make a MyDNAStuff module. Put as many useful nucleotide functions as possible into

the module...

Rework the lecture, and your solutions (or mine) from homework exercises #4 and #5, to make the codon_table module with functions specified in this lecture.

Demonstrate the use of these modules to translate an amino-acid sequence in all six-frames with just a few lines of code. The final result should look similar to Slide 10. Your program should handle DNA sequence with N’s in it.

Class Project: Expectations

40% of your grade!

Project Report Long version of your homework write-up

Project Presentation Demo your program Describe your project solution

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Class Project: Blast Database

1. Write a program that computes all pairwise blast alignments for two species' proteomes and stores the alignments in a relational database.

2. Write a program that retrieves the blast alignment for two proteins (specified by their accessions) from the relational database.

3. Write a program that finds pairs of orthologous proteins that are mutually best hits in the species' proteomes.

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Class Project: MS/MS Viewer

Write a program to display peptide fragmentation spectra from an mzXML file. The program will take an mzXML file, a scan

number, and a peptide sequence as input. The peptide's b-ion and y-ion m/z values should

be computed, and peaks matching these m/z values annotated with appropriate labels.

The output figure/plot should aid the user in determining whether or not the peptide is a good match to the spectrum.

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Class Project: Protein Digest

Write a simple web-server application using TurboGears to carry out an in silico enzymatic digest of a user-provided protein sequence. Users should be able to specify min and max

length, min and max molecular weight, # of missed cleavages, and specific enzyme.

Output should be a table of peptides, with their length, molecular weight, # of missed cleavages, and amino-acids to left and right of each peptide in the protein sequence.