Biopython跑不了了

Question

所以我一直在试着和Biopython合作，我还是个新手。我的代码：

fasta_string = open("C:\\Users\\saeed\\Desktop\\dna2.fasta").read()
print('1')
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
print('2')


blast_record = NCBIXML.read(result_handle)

len(blast_record.alignments)

E_VALUE_THRESH = 0.01
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.expect < E_VALUE_THRESH:
            print('*Alignment*')
            print('sequence', alignment.title)
            print('length', alignment.length)
            print(' e value', hsp.expect)
            print(hsp.query)
            print(hsp.match)
            print(hsp.sbjct)

每当我运行这段代码，它就会输出1并停止运行。不是像在出口那样停止，而是继续运行，不打印任何其他内容。我试着把dna2.fasta文件替换为myseq.fa公司“，但这似乎也没用。它只是说文件不存在。我想知道我做错了什么，以及如何解决它。有什么帮助吗？在

Answer 1

这就是我要做的，通过Bioython对序列进行qblast：

import ssl  # monkey patch for BioPython 1.68 & 1.69
ssl._create_default_https_context = ssl._create_unverified_context

from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from Bio import SeqIO

E_VALUE_THRESH = 0.01

input_file_name = "C:\\Users\\saeed\\Desktop\\dna2.fasta"

fasta_object = SeqIO.read(input_file_name, format='fasta')

result_handle = NCBIWWW.qblast("blastn", "nt", fasta_object.seq)

blast_record = NCBIXML.read(result_handle)

for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.expect < E_VALUE_THRESH:
            print('*Alignment*')
            print('sequence', alignment.title)
            print('length', alignment.length)
            print('e value', hsp.expect)
            print(hsp.query)
            print(hsp.match)
            print(hsp.sbjct)

我很想知道是否有更好的方法来处理SSL/证书问题。在

Answer 2

下面是我在一个请求中包含多个查询的示例。在

import timeit # Not necessary; just for timing the blast request.

from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML

fasta_string = open("dna2.fasta").read()
# In "dna2.fasta":
# >test1
# CGCTCATGCTAAAACCACGGAGGAATGTTTGGCCTATTTTGGGGTGAGTG
# >test2
# GCCAAGTCTGCAGGAAGCTTTGAGTTCTGACATCCTTAATGACATGGAGT
#
# Or you can make a string for this simple example.
# fasta_string = ">test1\nCGCTCATGCTAAAACCACGGAGGAATGTTTGGCCTATTTTGGGGTGAGTG\n>test2\nGCCAAGTCTGCAGGAAGCTTTGAGTTCTGACATCCTTAATGACATGGAGT\n"
print(fasta_string)

a = timeit.default_timer() # Not necessary; just for timing the blast request.
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
print(timeit.default_timer() - a) # Not necessary; just for timing the blast request.
# This takes me ~ 40 sec in one test.

# Use "parse" instead of "read" because you have lots of results (i.e., multiple query sequences)
blast_records = NCBIXML.parse(result_handle)
for blast_record in blast_records:
    print(blast_record.alignments[0].hsps[0])

“cdlane”是正确的。您可能还想使用Bio.SeqIO模块读入FASTA文件。我相信你已经读过了，但以防万一，相关文件在这里：http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc87