问题描述
当我从命令行执行我的 python 脚本时,我没有像这样的问题:
When I execute my python script from the command line I have no problems like so:
[rv@med240-183 db]$ python formatdb.py
[rv@med240-183 分贝]$
[rv@med240-183 db]$ python formatdb.py
[rv@med240-183 db]$
当我每半夜尝试使用 crontab 运行脚本时,我收到一系列错误:
When I try to use crontab to run the script every midnight I get a series of errors:
import: unable to open X server `' @ import.c/ImportImageCommand/367.
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 2: from: command not found
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 3: from: command not found
import: unable to open X server `' @ import.c/ImportImageCommand/367.
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 6: syntax error near
unexpected token `('
/home/rv/ncbi-blast-2.2.23+/db/formatdb.py: line 6: `conx = MySQLdb.connect
(user = 'root', passwd = '******', db = 'vaxijen_antigens')'
我的脚本目录如下:
/home/rv/ncbi-blast-2.2.23+/db/
/home/rv/ncbi-blast-2.2.23+/db/
Crontab 看起来像:
Crontab looks like:
SHELL=/bin/bash
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/bin/python/:/home/rv/ncbi-blast-2.2.23+/database_backup:/home/rv/ncbi-blast-2.2.23+/db/
MAILTO="******"
HOME=/
# For details see man 4 crontabs
# Example of job definition:
# .---------------- minute (0 - 59)
# | .------------- hour (0 - 23)
# | | .---------- day of month (1 - 31)
# | | | .------- month (1 - 12) OR jan,feb,mar,apr ...
# | | | | .---- day of week (0 - 6) (Sunday=0 or 7) OR sun,mon,tue,wed,thu,fri,sat
# | | | | |
# * * * * * command to be executed
0 0 * * * root /home/rv/ncbi-blast-2.2.23+/database_backup/backup.py
0 0 * * * root /home/rv/ncbi-blast-2.2.23+/db/formatdb.py
我的python脚本看起来像:
and my python script looks like:
import MySQLdb
from subprocess import call
from subprocess import Popen
import re
conx = MySQLdb.connect (user = 'root', passwd = '******', db = 'vaxijen_antigens')
cursor = conx.cursor()
cursor.execute('select * from sequence')
row = cursor.fetchall()
f = open('vdatabase.fasta', 'w')
for i in row:
f.write('>'+i[0].strip()+'
')
#f.write(i[1].strip().replace(' ','')+'
')
s = re.sub(r'[^w]','',str(i[1]))
s = ''.join(s)
for k in range(0, len(s), 60):
f.write('%s
' % (s[k:k+60]))
f.write('
')
f.close
Popen(["formatdb", "-p", "T", "-i", "vdatabase.fasta"]).wait()
推荐答案
添加
#!/usr/bin/env python
到脚本的开头 - 现在它正在尝试将脚本作为 bash 执行,该行显示我是 python 脚本,请使用正确的解释器".它也称为 hash-bang 行,但它必须是脚本中的第一行.
to the beginning of your script - right now it's trying to execute your script as a bash, that line says "I'm a python script, please use the right interpreter". It's also called a hash-bang line, but it needs to be the first line in your script.
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