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Biostumblematic

A biophysicist teaches himself how to code

Yeah, I’ve heard of it. Biopython is A python module package (thanks Chris) that’s written to help with doing computational biology. To my utter dismay I somewhat ignored it, being the “ll just brew it myself” type. What a mistake.

Today I was trying to wrangle some DNA and protein sequences and realized that this might be something covered by Biopython. It’s even better than that. You want tasty yum yums? How about a reverse complementer in 3 lines of code? I even formatted it so it looks nice on the terminal:

from Bio.Seq import Seq
sequence = Seq(raw_input('Paste your DNA sequence >> '))
print '\nReverse Complement\n------------------\n'+sequence.reverse_complement()

The very next bit of code in the tutorial replaced a ~50 line program I had cobbled together (and which still wasn’t working exactly the way I wanted) into this beauty:

#! /usr/bin/env python

# Biopython can automatically parse FASTA
# as well as many other "standard" biological formats

from Bio import SeqIO
inputfile = open('myproteins_fasta.txt')

for seq_record in SeqIO.parse(inputfile, 'fasta'):
    print seq_record.id
    print repr(seq_record.seq)
    print len(seq_record)
inputfile.close

BOOM, FASTA reader.

I’m just getting started on reading the documentation, but so far I’m really impressed (and not a little bit sheepish at my previous obstinance). Expect to see some Biopython examples in the coming days

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