设置输出Biopython后未找到ValueError文件

Question

from Bio.Blast.Applications import NcbiblastpCommandline

blastp_cline = NcbiblastpCommandline(cmd="~ncbi-blast.2.10.1+bin/blastp", query="human.fa", db="mouse.fa", evalue=.0001, out="output.xml", outputfmt=5)
blastp_cline

from Bio.Blast import NCBIXML


result_handle = open(homoutput.xml)
blast_records - NCBIXML.parse(results_handle)

for br in blast_records:
    for alignments in br.alignments:
        for hsp in alignments.hsps:
            if hsp.expect < 1e-107:
                print (alignments.title)
                print (alignments.length)
                print (hsp.expect)

                print (hsp.query)

                print (hsp.match)

这就是我得到的全部错误：

Traceback (most recent call last):
  File "parseBlast.py", line 5, in <module>
    blastp_cline = NcbiblastpCommandline(cmd="~ncbi-blast.2.10.1+bin/blastp", query="human.fa", db="mouse.fa", evalue=.0001, out="output.xml", outputfmt=5)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Blast/Applications.py", line 512, in __init__
    _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Blast/Applications.py", line 438, in __init__
    _Ncbiblast2SeqCommandline.__init__(self, cmd, **kwargs)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Blast/Applications.py", line 392, in __init__
    _NcbiblastCommandline.__init__(self, cmd, **kwargs)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Blast/Applications.py", line 308, in __init__
    _NcbibaseblastCommandline.__init__(self, cmd, **kwargs)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Blast/Applications.py", line 115, in __init__
    AbstractCommandline.__init__(self, cmd, **kwargs)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Application/__init__.py", line 295, in __init__
    self.set_parameter(key, value)
  File "/home/minhlam/.local/lib/python3.8/site-packages/Bio/Application/__init__.py", line 410, in set_parameter
    raise ValueError("Option name %s was not found." % name)

**ValueError: Option name outputfmt was not found.**

我正在检查我的目录，但没有输出，所以第二个blast部分甚至不工作。我正在处理两个本地文件：human.fa和mouse.fa。我假设通过human.fa进行解析，用Blast在mouse.fa数据库中找到同系物，并打印出人类序列ID、小鼠ID、类似同系物和相应的比对

Answer 1

您似乎已经发现，参数outputfmt需要更正为outfmt。然而，这里似乎还有一些问题：

你好像想把两个fasta文件互相攻击？ 首先，需要使用makeblastdb为引用序列创建blast数据库。然后，您就可以对该数据库进行快速查询

B.）似乎你正试图使用blastp（用于蛋白质序列）来根据核苷酸参考来爆破核苷酸序列。如果blastp找到的是核苷酸数据库而不是蛋白质数据库，它会尝试查找引用相应蛋白质序列的别名文件（因此在注释中会出现错误）。确保选择了正确的爆破工具：

• blastn：用于针对核苷酸引用的核苷酸查询
• blastp：用于针对蛋白质引用的蛋白质查询
• blastx：用于针对蛋白质参考的核苷酸查询
• tblastn：用于针对核苷酸参考的蛋白质查询