在fasta.gz上的SeqIO.parse

Question

编码新手。Pytho /
biopython的新手；这是我有史以来第一个在线问题。如何打开压缩的fasta.gz文件以提取信息并在函数中执行计算。这是我正在尝试做的简化示例（我尝试了不同的方法）以及错误是什么。我正在使用的gzip命令似乎无效。

with gzip.open("practicezip.fasta.gz", "r") as handle:
    for record in SeqIO.parse(handle, "fasta"):
        print(record.id)

Traceback (most recent call last):

  File "<ipython-input-192-a94ad3309a16>", line 2, in <module>
    for record in SeqIO.parse(handle, "fasta"):

  File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\__init__.py", line 600, in parse
    for r in i:

  File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\FastaIO.py", line 122, in FastaIterator
    for title, sequence in SimpleFastaParser(handle):

  File "C:\Users\Anaconda3\lib\site-packages\Bio\SeqIO\FastaIO.py", line 46, in SimpleFastaParser
    if line[0] == ">":

IndexError: index out of range

Answer 1

您在使用python3吗？

这个（“ r”->“ rt”）可以解决您的问题。

import gzip
from Bio import SeqIO

with gzip.open("practicezip.fasta.gz", "rt") as handle:
    for record in SeqIO.parse(handle, "fasta"):
        print(record.id)