biopython.org/DIST/docs/api/Bio.SeqIO-module.html

http://biopython.org/wiki/SeqIO

解析/读取序列：
Bio.SeqIO.parse()
用于读取序列文件生成 SeqRecord 对象，包含两个参数：
第一个参数是一个文件名或者一个句柄（ handle ）。
第二个参数是一个小写字母字符串，用于指定序列格式。
如SeqIO.parse("ls_orchid.fasta", "fasta")

需要处理只包含一个序列条目的文件，请使用函数 Bio.SeqIO.read() 。它使用与函数 Bio.SeqIO.parse() 相同的参数，当文件有且仅有一个序列条目时返回一个 SeqRecord 对象，否则触发异常。

从文件中提取序列ID列表：
>>> from Bio import SeqIO
>>> identifiers = [seq_record.id for seq_record in SeqIO.parse("ls_orchid.gbk", "genbank")]
>>> identifiers
['Z78533.1', 'Z78532.1', 'Z78531.1', 'Z78530.1', 'Z78529.1', 'Z78527.1', ..., 'Z78439.1']

遍历序列文件：
from Bio import SeqIO
record_iterator = SeqIO.parse("ls_orchid.fasta", "fasta")
first_record = record_iterator.next()
print first_record.id
print first_record.description
second_record = record_iterator.next()
print second_record.id
print second_record.description

只需要第一个条目：
from Bio import SeqIOfirst_record = SeqIO.parse("ls_orchid.gbk", "genbank").next()

获得序列文件中序列条目列表：
from Bio import SeqIO
records = list(SeqIO.parse("ls_orchid.gbk", "genbank"))
print "Found %i records" % len(records)
print "The last record"
last_record = records[-1] #using Python's list tricks
print last_record.id
print repr(last_record.seq)
print len(last_record)
print "The first record"
first_record = records[0] #remember, Python counts from zero
print first_record.id
print repr(first_record.seq)
print len(first_record

运行结果:
Found 94 records
The last record
Z78439.1
Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC', IUPACAmbiguousDNA())
592
The first record
Z78533.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC', IUPACAmbiguousDNA())
740

提取数据：
from Bio import SeqIO
record_iterator = SeqIO.parse("ls_orchid.gbk", "genbank")
first_record = record_iterator.next()
print first_record
ID: Z78533.1
Name: Z78533
Description: C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA.
Number of features: 5
/sequence_version=1
/source=Cypripedium irapeanum
/taxonomy=['Eukaryota', 'Viridiplantae', 'Streptophyta', ..., 'Cypripedium']
/keywords=['5.8S ribosomal RNA', '5.8S rRNA gene', ..., 'ITS1', 'ITS2']
/references=[...]
/accessions=['Z78533']
/data_file_division=PLN
/date=30-NOV-2006
/organism=Cypripedium irapeanum
/gi=2765658
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC', IUPACAmbiguousDNA())

可以直接输出：
print first_record.annotations
与其他Python字典一样，你可以轻松地获得键列表：
print first_record.annotations.keys()
或者值列表:
print first_record.annotations.values()
>>> print first_record.annotations["source"]
Cypripedium irapeanum
>>> print first_record.annotations["organism"]
Cypripedium irapeanum
from Bio import SeqIO
all_species = []
for seq_record in SeqIO.parse("ls_orchid.gbk", "genbank"):
all_species.append(seq_record.annotations["organism"])
print all_species
from Bio import SeqIO
all_species = [seq_record.annotations["organism"] for seq_record in SeqIO.parse("ls_orchid.gbk", "genbank")]
print all_species

你需要从一个FASTA文件提取出物种列表：
>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA
CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAACGATCGAGTG
AATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGTGACCCTGATTTGTTGTTGGG
...
from Bio import SeqIO
all_species = []
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
all_species.append(seq_record.description.split()[1])
print all_species

from Bio import SeqIO
all_species == [seq_record.description.split()[1] for seq_record in \
SeqIO.parse("ls_orchid.fasta", "fasta")]
print all_species

计算GenBank文件中多条序列条目的总长：
>>> from Bio import SeqIO
>>> print sum(len(r) for r in SeqIO.parse("ls_orchid.gbk", "gb"))
67518
使用 with 语句（Python 2.5及以上版本）自动关闭句柄：
>>> from __future__ import with_statement #Needed on Python 2.5
>>> from Bio import SeqIO
>>> with open("ls_orchid.gbk") as handle:
... print sum(len(r) for r in SeqIO.parse(handle, "gb"))
67518
或者，用旧版本的方式，手动关闭句柄：
>>> from Bio import SeqIO
>>> handle = open("ls_orchid.gbk")
>>> print sum(len(r) for r in SeqIO.parse(handle, "gb"))
67518
>>> handle.close()