Question

我正在尝试使用EMBOSS的biopython包装器在本地对齐一组约100个非常长（> 8000个序列）的序列。

基本上我需要将fasta文件中的每个序列与该fasta文件中的每个其他序列进行局部对齐。到目前为止，我试图运行下面的基本代码：

from Bio.Emboss.Applications import NeedleCommandline
from Bio import AlignIO

seq_fname1 = 'gross-alignment.fasta'
seq_fname2 = 'gross-alignment.fasta'
needle_fname = 'pairwise_output.txt'
needle_cli = NeedleCommandline(asequence=seq_fname1, \
                               bsequence=seq_fname2, \
                               gapopen=10, \
                               gapextend=0.5, \
                               outfile=needle_fname)

"""This generates the needle file"""
needle_cli() 
"""That parses the needle file, aln[0] and aln[1] contain the aligned
first and second sequence in the usual format (e.g. - for a gap)"""
aln = AlignIO.read(needle_file, "emboss") 
print aln

但是当我这样做时出现以下错误：

C:\WINDOWS\system32\cmd.exe /c (python ^<C:\Users\User\AppData\Local\Temp\VIiAAD1.tmp) Traceback (most recent call last): File "<stdin>", line 14, in <module> File "C:\Python27\lib\site-packages\Bio\Application\__init__.py", line 495, in __call__ shell=use_shell) File "C:\Python27\Lib\subprocess.py", line 711, in __init__ errread, errwrite) File "C:\Python27\Lib\subprocess.py", line 959, in _execute_child startupinfo) WindowsError: [Error 2] The system cannot find the file specified shell returned 1 Hit any key to close this window...

我无法弄清楚这个错误的原因是什么，非常感谢任何帮助。

Answer 1

你可以尝试seq_fname1，seq_fname2的绝对路径吗？另外，我希望你在提升的命令提示符下尝试这个

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Biopython / EMBOSS WindowsError [错误2]

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