https://biopython.org https://biopython.org/DIST/docs/api/Bio-module.html

SeqIO

• https://biopython.org/wiki/SeqIO
• https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec51
• https://biopython.org/DIST/docs/api/Bio.SeqIO-module.html

read(file, format, alphabet=None)

1配列しか含まないファイルを読んで SeqRecord を返す

parse(file, format, alphabet=None)

複数の配列を含むファイルを読んで SeqRecord のイテレータを返す

index(filename, format, alphabet=None, key_function=None)

id をキーとした辞書likeオブジェクトを返す

write(sequences, file, format)

to_dict(sequences, key_function=None)

convert(in_file, in_format, out_file, out_format, alphabet=None)

from Bio import SeqIO

with open('beer.fasta', 'r') as fin:
    for record in SeqIO.parse(fin, 'fasta'):
        print(record.id)
        print(record.seq)

SeqRecord

• https://biopython.org/wiki/SeqRecord
• https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec32
• https://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html

Seq とそのほかの情報をひとまとまりにしたクラス。

id
seq

name
description
dbxrefs
features
annotations
letter_annotations

>>> for record in SeqIO.parse(fin, 'fasta'):
...     print(record)
...
ID: gi|186972394|gb|EU490707.1|
Name: gi|186972394|gb|EU490707.1|
Description: gi|186972394|gb|EU490707.1| Selenipedium aequinoctiale maturase K (matK) gene, partial cds; chloroplast
Number of features: 0
Seq('ATTTTTTACGAACCTGTGGAAATTTTTGGTTATGACAATAAATCTAGTTTAGTA...GAA', SingleLetterAlphabet())
ID: gi|186972391|gb|ACC99454.1|
Name: gi|186972391|gb|ACC99454.1|
Description: gi|186972391|gb|ACC99454.1| maturase K [Scaphosepalum rapax]
Number of features: 0
Seq('IFYEPVEILGYDNKSSLVLVKRLITRMYQQKSLISSLNDSNQNEFWGHKNSFSS...EEE', SingleLetterAlphabet())

Seq

• https://biopython.org/wiki/Seq
• https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec17
• https://biopython.org/DIST/docs/api/Bio.Seq.Seq-class.html

塩基配列・アミノ酸配列のクラス。 標準 str とほとんど同じように扱えるほか、 相補鎖とかなんとかを簡単に扱えるメソッドが備わっている。

• complement(self)
• reverse_complement(self)
• transcribe(self)
• back_transcribe(self)
• translate(self, table="Standard", stop_symbol="*", to_stop=False, cds=False)
• ungap(self, gap=None)

GenomeDiagram

https://biopython.org/DIST/docs/tutorial/Tutorial.html#sec328 https://biopython.org/DIST/docs/GenomeDiagram/userguide.pdf

Entrez

• https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc90

esearch

• NCBI ESearch Utility

• https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc93

  >>> from Bio import Entrez
  >>> handle = Entrez.esearch(db="nucleotide", retmax=10, term="Opuntia")
  >>> record = Entrez.read(handle)
  >>> for item in record.items():
  ...     print(item)
  ...
  (u'Count', '390')
  (u'RetMax', '10')
  (u'IdList', ['257359511', '283467266', '246905625', '246905624', '246655205', '246655204', '240253899', '240253897', '240253576', '240253574'])
  (u'TranslationStack', [{u'Count': '200', u'Field': 'Organism', u'Term': '"Opuntia"[Organism]', u'Explode': 'Y'}, {u'Count': '390', u'Field': 'All Fields', u'Term': 'Opuntia[All Fields]', u'Explode': 'Y'}, 'OR', 'GROUP'])
  (u'TranslationSet', [{u'To': '"Opuntia"[Organism] OR Opuntia[All Fields]', u'From': 'Opuntia'}])
  (u'RetStart', '0')
  (u'QueryTranslation', '"Opuntia"[Organism] OR Opuntia[All Fields]')
  

efetch

• NCBI EFetch Utility
• https://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc96

返り値は結果(XML)へのハンドル。:

from Bio import Entrez

handle = Entrez.efetch(db="nucleotide", id="186972394,186972394", rettype="fasta")
record = SeqIO.parse(handle, "fasta")
for x in record:
    print(i)

Installation

pip で一発:

pip install biopython