Biopython Examples

1. Getting started

import Bio
from Bio.Seq import Seq
dna = Seq("ACGTTGCAC")
print(dna)

(alternative)

from Bio.Alphabet import IUPAC
dna = Seq("AGTACACTGGT", IUPAC.unambiguous_dna)

2. Reverse complement, transcribing & translating

dna.reverse_complement()
rna = dna.transcribe()
rna.translate()

(alternative)

from Bio.Seq import reverse_complement, transcribe, translate
reverse_complement("GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCT")

3. Calculating GC-content

from Bio.SeqUtils import GC
GC(dna)

4. Caculating molecular weight (DNA only)

from Bio.SeqUtils import molecular_weight
molecular_weight("ACCCGT")

5. Loading sequences from a FASTA file

from Bio import SeqIO
for record in SeqIO.parse("ls_orchid.fasta", "fasta"):
    print record.seq, len(record.seq)

6. Plotting a histogram of seq lengths with pylab

pylab aka matplotlib needs to be installed separately.

import pylab
sizes=[len(r.seq) for r in SeqIO.parse("ls_orchid.fasta","fasta")]
pylab.hist(sizes, bins=20)
pylab.title("%i orchid sequences\nLengths %i to %i" \
            % (len(sizes), min(sizes), max(sizes)))
pylab.xlabel("Sequence length (bp)")
pylab.ylabel("Count")
pylab.show()