python - 如何从 python 中调用安装在 linux 上的程序？

Question

这是我一直在尝试的

def test():
    import sys
    import subprocess
    file1 = open(sys.argv[1],"r") #this is the input to fastacmd
    idx = file1.readlines()
    outname = idx[0].split("\r\n")[0]
    foutname = outname + "_f_output"
    astaseq = subprocess.call(["fastacmd","-i", file1, "-o",foutname])
    blastresult = subprocess.call(["blastp", "-db", "db1.faa", "-query", foutname, "-out", outname])

但是我被这个捕获了，我无法真正理解它

File "test.py", line 16, in <module>
    fastacmd_blastp()
  File "test.py", line 11, in test
    fastaseq = subprocess.call(["fastacmd","-i", file1, "-o",fastaoutname])
  File "/usr/local/lib/python2.7/subprocess.py", line 486, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/local/lib/python2.7/subprocess.py", line 672, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1202, in _execute_child
    raise child_exception
TypeError: execv() arg 2 must contain only strings

有人可以帮忙吗？谢谢

Answer 1

猜测输入文件应该是文件名 sys.argv[1] 而不是文件的 python 句柄。 ( http://nebc.nerc.ac.uk/bioinformatics/documentation/blast/fastacmd.html )

换句话说，将 astaseq = subprocess.call(["fastacmd","-i", file1, "-o",foutname]) 更改为 astaseq = subprocess.call (["fastacmd","-i", sys.argv[1], "-o",foutname])