从Url地址读取Fasta文件

时间:2015-04-17 04:24:12

标签: url fasta

我使用的是Python 3.4 我写了一些代码来读取Fasta文件来自网站,但它没有用。 http://www.uniprot.org/uniprot/B5ZC00.fasta
(我可以下载并将其作为文本文件阅读,但我计划从给定的站点读取多个Fasta文件。)

(1)第一次尝试

# read FASTA file

def read_fasta(filename_as_string):
    """
    open text file with FASTA format
    read it and convert it into string list
    convert the list to dictionary
    >>> read_fasta('sample.txt')
        {'Rosalind_0000':'GTAT....ATGA', ... }
    """
    f = open(filename_as_string,'r')
    content = [line.strip() for line in f]
    f.close()

    new_content = []
    for line in content:
        if '>Rosalind' in line:
            new_content.append(line.strip('>'))
            new_content.append('')
        else:
            new_content[-1] += line

    dict = {}
    for i in range(len(new_content)-1):
        if i % 2 == 0:
            dict[new_content[i]] = new_content[i+1]

    return dict

此代码可以读取我桌面计算机中的任何Fasta文件,但无法从Internet站点读取相同的Fasta文件。

>>> from urllib.request import urlopen
>>> html = urlopen("http://www.uniprot.org/uniprot/B5ZC00.fasta")
>>> print (read_fasta(html))
TypeError: invalid file: <http.client.HTTPResponse object at 0x02A62EF0>

(2)第二次尝试

>>> from urllib.request import urlopen
>>> html = urlopen("http://www.uniprot.org/uniprot/B5ZC00.fasta")
>>> lines = [x.strip() for x in html.readlines()]
>>> print (lines)
[b'>sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase OS=Ureaplasma urealyticum serovar 10 (strain ATCC 33699 / Western) GN=glyQS PE=3 SV=1', b'MKNKFKTQEELVNHLKTVGFVFANSEIYNGLANAWDYGPLGVLLKNNLKNLWWKEFVTKQ', b'KDVVGLDSAIILNPLVWKASGHLDNFSDPLIDCKNCKARYRADKLIESFDENIHIAENSS', b'NEEFAKVLNDYEISCPTCKQFNWTEIRHFNLMFKTYQGVIEDAKNVVYLRPETAQGIFVN', b'FKNVQRSMRLHLPFGIAQIGKSFRNEITPGNFIFRTREFEQMEIEFFLKEESAYDIFDKY', b'LNQIENWLVSACGLSLNNLRKHEHPKEELSHYSKKTIDFEYNFLHGFSELYGIAYRTNYD', b'LSVHMNLSKKDLTYFDEQTKEKYVPHVIEPSVGVERLLYAILTEATFIEKLENDDERILM', b'DLKYDLAPYKIAVMPLVNKLKDKAEEIYGKILDLNISATFDNSGSIGKRYRRQDAIGTIY', b'CLTIDFDSLDDQQDPSFTIRERNSMAQKRIKLSELPLYLNQKAHEDFQRQCQK']

我认为我可以修改我的代码以将在线Fasta文件作为字符串列表阅读,但很快我意识到这并不容易。

>>> print (type(lines[0]))
<class 'bytes'>

我无法移除肮脏的&#39; b&#39;列表中每个元素的头部中的字符。

>>> print (lines[0])
b'>sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase ...
>>> print (lines[0][1:])
b'sp|B5ZC00|SYG_UREU1 Glycine--tRNA ligase ...

(3)问题

如何清除肮脏的&#39; b&#39;人物?
有没有更好的方法从给定的Url读取Fasta文件?

在一些帮助下,我想我可以修改并完成我的代码。 谢谢。

2 个答案:

答案 0 :(得分:1)

如果您只对一级氨基酸序列感兴趣(想要忽略标题),请尝试以下方法:

link = str(sys.argv[1]) #fasta file URL provided as command line argument
FASTA = urllib.urlopen(link).readlines()[1:] # as list without header (">...")
FASTA = "".join(FASTA).replace("\n","") # as a string free of new line markers
print FASTA

答案 1 :(得分:0)

聚会晚了一点,但是尝试Jose的Biopython答案不再适用于Python3。这是一种替代方法:

from Bio import SeqIO
import requests
from io import StringIO

link = "http://www.uniprot.org/uniprot/B5ZC00.fasta"
data = requests.get(link).text

fasta_iterator = SeqIO.parse(StringIO(data), "fasta")

# Pretty print the fasta info
for seq in fasta_iterator:
  print(seq.format("fasta"))