Question

我正在尝试阅读通过多个序列提交生成的XML文件列表到NCBI爆炸网站。从每个文件，我想打印某些信息行。我想要阅读的文件都给出了后缀"_recombination.xml"。

for file in glob.glob("*_recombination.xml"):
    result_handle= open(file)
    blast_record=NCBIXML.read(result_handle)
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            print "*****Alignment****"
            print "sequence:", alignment.title
            print "length:", alignment.length
            print "e-value:", hsp.expect
            print hsp.query
            print hsp.match
            print hsp.sbjct

该脚本首先找到所有带有"_recombination.xml"后缀的文件，然后我希望它读取每个文件，然后打印某些行（这几乎是BioPython烹饪书中的直接副本），它似乎去做。但是我收到以下错误：

Traceback (most recent call last):
File "Scripts/blast_test.py", line 202, in <module>
blast_record=NCBIXML.read(result_handle)
File "/Library/Python/2.7/site-packages/Bio/Blast/NCBIXML.py", line 576, in read
first = iterator.next()
File "/Library/Python/2.7/site-packages/Bio/Blast/NCBIXML.py", line 643, in parse
expat_parser.Parse("", True) # End of XML record
xml.parsers.expat.ExpatError: no element found: line 3106, column 7594

我不确定问题是什么。我不确定它是否试图循环回读它已经读过的文件 - 例如，关闭文件似乎有帮助：

for file in glob.glob("*_recombination.xml"):
    result_handle= open(file)
    blast_record=NCBIXML.read(result_handle)
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            print "*****Alignment****"
            print "sequence:", alignment.title
            print "length:", alignment.length
            print "e-value:", hsp.expect
            print hsp.query
            print hsp.match
            print hsp.sbjct
    result_handle.close()
    blast_record.close()

但它也给了我另一个错误：

Traceback (most recent call last): 
File "Scripts/blast_test.py", line 213, in <module> blast_record.close() 
AttributeError: 'Blast' object has no attribute 'close'

Answer 1

我通常使用解析方法而不是读取，也许它可以帮助您：

for blast_record in NCBIXML.parse(open(input_xml)):
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            print "*****Alignment****"
            print "sequence:", alignment.title
            print "length:", alignment.length
            print "e-value:", hsp.expect
            print hsp.query
            print hsp.match
            print hsp.sbjct

并确保在查询文件中使用 -outfmt 5 生成xml

Answer 2

我会对Biogeek的答案添加评论，但我不能（还没有足够的声誉）。他是对的，你应该使用

NCBIXML.parse(open(input_xml))

而不是NCBIXML.read（open（input_xml）），因为您“正在尝试读取XML文件列表”，而对于XML文件列表，您需要解析而不是读取即可。它解决了你的问题吗？

读取多个blast文件（biopython）

2 个答案: