Biopython – 序列输入/输出

Biopython 有一个内置的Bio.SeqIO模块，它提供了分别从文件读取和写入序列的功能。 Bio.SeqIO支持几乎所有生物信息学中使用的文件处理格式。 Biopython 严格遵循单一方法用SeqRecord对象向用户表示解析的数据序列。

序列记录

Bio.SeqRecord模块提供的SeqRecord对象包含序列的元数据以及有关序列的信息。下面列出了一些主要数据信息：

Record	Description
seq	An actual sequence to be parsed.
id	Primary identity of the sequence, by default it is string type
name	The name of the sequence, by default it is string type.
description	Displays the information about the sequence in human-readable format.
annotations	Dictionary containing additional information related to the sequence.

阅读顺序：

Biopython Seq模块有一个内置的read()方法，该方法获取一个序列文件，并根据文件格式将其转换为单个SeqRecord 。它能够解析只有一条记录的序列文件，如果文件没有记录或多于一条记录，则会引发异常。 read()方法的语法和参数如下：

Bio.SeqIO.read(handle, format, alphabet=None)

Arguments	Description
handle	Handle to file or takes filename as string(older versions only take handle)
format	File; format as a string
alphabet	Optional parameter, used when sequence type is not automatically inferred from file(ex. format = “fasta”).

Python3

# Import libraries
from Bio import SeqIO
  
# Reading file
record = SeqIO.read("sequence.gb", "genbank")
  
# Showing records
print("ID: %s" % record.id)
print("Sequence length: %i" % len(record))
print("Sequence description: %s" % record.description)

输出：

诵经顺序：

当我们必须从句柄中读取多条记录时，使用Bio.Seq模块提供的Parse()方法。它基本上将序列文件转换为返回SeqRecords的迭代器。如果文件包含字符串数据，则必须将其转换为句柄来解析它。无法确定字母表的文件格式，明确指定字母表（例如 FASTA）很有用。 parse()方法的语法和参数如下：

Bio.SeqIO.parse(handle, format, alphabet=None)

Arguments	Description
handle	Handle to file or takes filename as string(older versions only take handle)
format	File format as a string
alphabet	The optional parameter, used when sequence type is not automatically inferred from file(ex. format = “fasta”).

蟒蛇3

# Import libraries
from Bio import SeqIO
  
# Parsing file
filename = "sequence.fasta"
for record in SeqIO.parse(filename, "fasta"):
  
    # Showing records
    print("ID: %s" % record.id)
    print("Sequence length: %i" % len(record))
    print("Sequence description: %s" % record.description)

输出 ：

写入序列：

为了写入文件Bio.Seq模块有一个write()方法，它将序列集写入文件并返回一个表示写入记录数的整数。确保在调用句柄后关闭句柄，否则数据会刷新到磁盘。 write()方法的语法和参数如下：

Bio.SeqIO.write(sequences, handle, format)

Arguments	Description
sequences	List or iterator of SeqRecord object(or single SeqRecord in Biopython version 1.54 or later)
handle	Handle to file or takes filename as string(older versions only take handle)
format	File format to write as a lowercase string

注意：要下载文件，请单击此处

蟒蛇3

# Import libraries
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
  
rec1 = SeqRecord(Seq("MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD"
                     + "GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK"
                     + "NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM"),
                 id="gi|14150838|gb|AAK54648.1|AF376133_1",
                 description="chalcone synthase [Cucumis sativus]")
  
rec2 = SeqRecord(Seq("MVTVEEFRRAQCAEGPATVMAIGTATPSNCVDQSTYPDYYFRITNSEHKVELKEKFKRMC"
                     + "EKSMIKKRYMHLTEEILKENPNICAYMAPSLDARQDIVVVEVPKLGKEAAQKAIKEWGQP"
                     + "KSKITHLVFCTTSGVDMPGCDYQLTKLLGLRPSVKRFMMYQQGCFAGGTVLRMAKDLAEN"
                     + "NKGARVLVVCSEITAVTFRGPNDTHLDSLVGQALFGDGAAAVIIGSDPIPEVERPLFELV"
                     + "SAAQTLLPDSEGAIDGHLREVGLTFHLLKDVPGLISKNIEKSLVEAFQPLGISDWNSLFW"
                     + "IAHPGGPAILDQVELKLGLKQEKLKATRKVLSNYGNMSSACVLFILDEMRKASAKEGLGT"
                     + "TGEGLEWGVLFGFGPGLTVETVVLHSVAT"),
                 id="gi|13925890|gb|AAK49457.1|",
                 description="chalcone synthase [Nicotiana tabacum]")
sequences = [rec1, rec2]
  
# Writing to file
with open("example.fasta", "w") as output_handle:
    SeqIO.write(sequences, output_handle, "fasta")
  
for record in SeqIO.parse("example.fasta", "fasta"):
    print("ID %s" % record.id)
    print("Sequence length %i" % len(record))

输出：