CPC2安装报错-------解决过程

1.首先我目前的python版本是3.7的
按照网上（http://cpc2.gao-lab.org/download.php）标准流程安装了CPC2

pip install biopython   #首先需要安装这个
剩下的按下面的步骤
wget http://cpc2.gao-lab.org/data/CPC2-beta.tar.gz              
gzip -dc CPC2-beta.tar.gz | tar xf -
cd CPC2-beta
export CPC_HOME="$PWD"
cd libs/libsvm
gzip -dc libsvm-3.18.tar.gz | tar xf -
cd libsvm-3.18
make clean && make

2.尝试运行CPC2

python CPC2-beta/bin/CPC2.py

第一次报错

(base) [jychu@localhost soft]$ python CPC2-beta/bin/CPC2.py
Traceback (most recent call last):
  File "CPC2-beta/bin/CPC2.py", line 8, in <module>
    import commands
ModuleNotFoundError: No module named 'commands'

起初不知道是什么意思，思考了一下它说的是“没有commands"这个模块，在网上搜了一下，说是python3中commands模块已经被subprocess取代了，所以接下来我就试了一下在CPC2-beta/bin/CPC2.py文件中把commands替换为subprocess

2.第二次运行

python CPC2-beta/bin/CPC2.py

结果又报错

(base) [jychu@localhost soft]$ python CPC2-beta/bin/CPC2.py
Traceback (most recent call last):
  File "CPC2-beta/bin/CPC2.py", line 16, in <module>
    import seqio
  File "/public/jychu/soft/CPC2-beta/bin/seqio.py", line 165
    print a
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(a)?

这次一定要看清楚，报错的文件是/public/jychu/soft/CPC2-beta/bin/seqio.py，进入该文件，确实有print a 这一行，百度一下发现python3 的print语法相对于python2的改变了一下，把print a 改为 print(a)就行了。

3.再次运行

(base) [jychu@localhost soft]$ python CPC2-beta/bin/CPC2.py
Traceback (most recent call last):
  File "CPC2-beta/bin/CPC2.py", line 16, in <module>
    import seqio
  File "/public/jychu/soft/CPC2-beta/bin/seqio.py", line 166
    print merge_region(a)
                     ^
SyntaxError: invalid syntax

其实这次报错和上次是一样的问题，也是在print后面加（)即可

4.再次运行，运行成功！

(base) [jychu@localhost soft]$ python CPC2-beta/bin/CPC2.py
Usage: CPC2.py [options] -i input.fasta -o output_file

Contact: Kang Yujian <kangyj@mail.cbi.pku.edu.cn>

Options:
  --version   show program's version number and exit
  -h, --help  show this help message and exit

  Common Options:
    -i FILE   input sequence in fasta format [Required]
    -o FILE   output file [Default: cpc2output.txt]
    -r        also check the reverse strand [Default: FALSE]
    --ORF     output the start position of longest ORF [Default: FALSE]

运行命令

python /public/jychu/soft/CPC2-beta/bin/CPC2.py -i iux200LFPKM0.1.fa -o CPC.txt

又报错了

Traceback (most recent call last):
  File "/public/jychu/soft/CPC2-beta/bin/CPC2.py", line 363, in <module>
    sys.exit(__main())
  File "/public/jychu/soft/CPC2-beta/bin/CPC2.py", line 45, in __main
    if calculate_potential(options.fasta,strand,output_orf,options.outfile):
  File "/public/jychu/soft/CPC2-beta/bin/CPC2.py", line 255, in calculate_potential
    ftmp_feat = file(outfile + ".feat","w")
NameError: name 'file' is not defined

上网查说是python版本升级file函数改为open
又运行了一下出现下面结果

[INFO] read file 'u.fa'
Error: Fail to IO file: u.fa

看不懂了，不知有大佬可否解答
当然之前我也用python2版本试了运行该软件，里面报错的是有些模块适合python3.0以上的版本，所以安装不了，因此就没往下折腾。

最后编辑于：2021.03.19 00:51:40