这就是我一直在尝试的
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])
但是我被抓住了,我真的搞不懂
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
有人能帮忙吗?谢谢
最佳答案
我猜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)
换言之,将astaseq = subprocess.call(["fastacmd","-i", file1, "-o",foutname])
更改为astaseq = subprocess.call(["fastacmd","-i", sys.argv[1], "-o",foutname])