Biopython

BioPython

• Types to reprisent sequences (Seq and MutableSeq)
• Parsers for several file formats (including GenBank, EMBL, Fasta)
• Sequence alignment
• Population genetics
• Clustering
• BioSQL

Sequences

>>> from Bio.Seq import Seq
>>> seq = Seq("AGTACACTGGT")
>>> seq
Seq('AGTACACTGGT', Alphabet())
>>> print seq
AGTACACTGGT

Sequences

Sequences behave a lot like strings

>>> seq[:2]
Seq('AG', Alphabet())
>>> print seq[:2]
AG
>>> seq.count("A")
3
>>> Seq("ATCCGG") + Seq("TTGGAATC")
Seq('ATCCGGTTGGAATC', Alphabet())

Sequences != Strings

You can specify a specific alphabet:

>>> from Bio.Alphabet import IUPAC
>>> seq = Seq("AGTACACTGGT", IUPAC.unambiguous_dna)
>>> seq
Seq('AGTACACTGGT', IUPACUnambiguousDNA())

Sequence Methods

>>> seq
Seq('AGTACACTGGT', IUPACUnambiguousDNA())
>>> seq.complement()
Seq('TCATGTGACCA', IUPACUnambiguousDNA())
>>> seq.reverse_complement()
Seq('ACCAGTGTACT', IUPACUnambiguousDNA())

Notice that the alphabet does not change

Transcription

>>> seq = Seq('ATGAAGACAG', IUPAC.unambiguous_dna)
>>> seq
Seq('ATGAAGACAG', IUPACUnambiguousDNA())
>>> seq.transcribe()
Seq('AUGAAGACAG', IUPACUnambiguousRNA())

Notice the alphabet changes

Mutable Sequences

>>> seq
Seq('ATGAAGACAG', IUPACUnambiguousDNA())
>>> mseq = seq.tomutable()
>>> mseq
MutableSeq('ATGAAGACAG', IUPACUnambiguousDNA())

>>> mseq.reverse_complement()
>>> mseq
MutableSeq('CTGTCTTCAT', IUPACUnambiguousDNA())

Notice that this behaviour means you cannot substitute Seq and MutableSeq objects.

Parsers

Parsers yield SeqRecord objects:

>>> from Bio import SeqIO
>>> p = SeqIO.parse(open(r"wgs_aacr_pro.dat", "rb"), "embl")
>>> p.next()
SeqRecord(seq=Seq('TG...GCA', IUPACAmbiguousDNA()),
          id='AACR01000001.1',
          name='AACR01000001',
          description='Pasteuria nishizawae str. North American PnPst10, whole genome shotgun sequence.',
          dbxrefs=[])

SeqRecord

>>> rec = p.next()

>>> print rec
ID: AACR01000002.1
Name: AACR01000002
Description: Pasteuria nishizawae str. North American PnEco4A, whole genome shotgun sequence.
Number of features: 1
/taxonomy=['Bacteria', 'Firmicutes', 'Bacillales', 'Pasteuriaceae', 'Pasteuria']
/references=[<Bio.SeqFeature.Reference instance at 0x0155FAA8>]
/accessions=['AACR01000002', 'AACR01000000', 'AACR00000000']
/data_file_division=PRO
/organism=Pasteuria nishizawae str. North American
/sequence_version=1
Seq('AATTCGTGGCGGGGCAAACGGGTTCATTATAAAAATTGTCGGAACGAGTTCAAC...ATT', IUPACAmbiguousDNA())

SeqRecord fields

>>> rec.seq
Seq('AATTCGTGGCGGGGCAAA...ATT', IUPACAmbiguousDNA())
>>> len(rec)
1124
>>> len(rec.seq)
1124

SeqRecord fields

>>> rec.name
'AACR01000002'
>>> len(rec.features)
1
>>> rec.features[0].type
'source'
>>> rec.features[0].strand
1

Annotations

>>> pprint(rec.annotations)
{'accessions': ['AACR01000002', 'AACR01000000', 'AACR00000000'],
 'data_file_division': 'PRO',
 'organism': 'Pasteuria nishizawae str. North American',
 'references': [<Bio.SeqFeature.Reference instance at 0x0155FAA8>],
 'sequence_version': 1,
 'taxonomy': ['Bacteria',
              'Firmicutes',
              'Bacillales',
              'Pasteuriaceae',
              'Pasteuria']}

Writing SeqRecords

from Bio import SeqIO
in_file = SeqIO.parse(open("infile"), "embl")
out_file = open(sys.argv[2], "w")
SeqIO.write(in_file, out_file, "fasta")

write will accept lists or iterators.

Excersizes

See handout