SyntaxError

[Ci-TJ]

I just install the seekr by pip, but I found SyntaxError when I use it.

(base) user_li@WangLab:~/linqin_tmp$ pip install seekr
Defaulting to user installation because normal site-packages is not writeable
Collecting seekr
  Using cached seekr-1.4.2-py3-none-any.whl (32 kB)
Requirement already satisfied: numpy in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (1.18.2)
Requirement already satisfied: cython in /usr/local/lib/python3.5/dist-packages (from seekr) (0.29.2)
Requirement already satisfied: requests in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (2.23.0)
Requirement already satisfied: louvain in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (0.7.0)
Requirement already satisfied: leidenalg in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (0.8.0)
Requirement already satisfied: tqdm in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (4.46.0)
Requirement already satisfied: ushuffle in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (1.1.2)
Requirement already satisfied: pandas in /usr/local/lib/python3.5/dist-packages (from seekr) (0.23.4)
Requirement already satisfied: matplotlib in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (3.0.3)
Requirement already satisfied: seaborn in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (0.9.1)
Requirement already satisfied: networkx in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (2.4)
Requirement already satisfied: python-igraph in /home/user_li/.local/lib/python3.5/site-packages (from seekr) (0.8.2)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/user_li/.local/lib/python3.5/site-packages (from requests->seekr) (1.25.8)
Requirement already satisfied: idna<3,>=2.5 in /home/user_li/.local/lib/python3.5/site-packages (from requests->seekr) (2.9)
Requirement already satisfied: certifi>=2017.4.17 in /home/user_li/.local/lib/python3.5/site-packages (from requests->seekr) (2020.4.5.1)
Requirement already satisfied: chardet<4,>=3.0.2 in /home/user_li/.local/lib/python3.5/site-packages (from requests->seekr) (3.0.4)
Requirement already satisfied: python-dateutil>=2.5.0 in /usr/local/lib/python3.5/dist-packages (from pandas->seekr) (2.7.5)
Requirement already satisfied: pytz>=2011k in /usr/lib/python3/dist-packages (from pandas->seekr) (2014.10)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/user_li/.local/lib/python3.5/site-packages (from matplotlib->seekr) (1.1.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/lib/python3/dist-packages (from matplotlib->seekr) (2.0.3)
Requirement already satisfied: cycler>=0.10 in /home/user_li/.local/lib/python3.5/site-packages (from matplotlib->seekr) (0.10.0)
Requirement already satisfied: scipy>=0.17.1 in /home/user_li/.local/lib/python3.5/site-packages (from seaborn->seekr) (1.4.1)
Requirement already satisfied: decorator>=4.3.0 in /home/user_li/.local/lib/python3.5/site-packages (from networkx->seekr) (4.4.2)
Requirement already satisfied: texttable>=1.6.2 in /home/user_li/.local/lib/python3.5/site-packages (from python-igraph->seekr) (1.6.2)
Requirement already satisfied: six>=1.5 in /home/user_li/.local/lib/python3.5/site-packages (from python-dateutil>=2.5.0->pandas->seekr) (1.14.0)
Requirement already satisfied: setuptools in /home/user_li/.local/lib/python3.5/site-packages (from kiwisolver>=1.0.1->matplotlib->seekr) (39.1.0)
Installing collected packages: seekr
Successfully installed seekr-1.4.2
(base) user_li@WangLab:~/linqin_tmp$ seekr
Traceback (most recent call last):
  File "/home/user_li/.local/bin/seekr", line 5, in <module>
    from seekr.console_scripts import console_seekr_help
  File "/home/user_li/.local/lib/python3.5/site-packages/seekr/console_scripts.py", line 648
    print(f"{'='*25}\n{c}\n{'='*25}\n{d}")
                                        ^
SyntaxError: invalid syntax
(base) user_li@WangLab:~/linqin_tmp$ pip -V
pip 20.1.1 from /home/user_li/.local/lib/python3.5/site-packages/pip (python 3.5)
(base) user_li@WangLab:~/linqin_tmp$

(base) user_li@WangLab:~/linqin_tmp$ seekr_download_gencode lncRNA -s mouse
Traceback (most recent call last):
  File "/home/user_li/.local/bin/seekr_download_gencode", line 5, in <module>
    from seekr.console_scripts import console_download_gencode
  File "/home/user_li/.local/lib/python3.5/site-packages/seekr/console_scripts.py", line 648
    print(f"{'='*25}\n{c}\n{'='*25}\n{d}")
                                        ^
SyntaxError: invalid syntax
(base) user_li@WangLab:~/linqin_tmp$

I'm not familiar with python, what's the problem? Best, Ci

[Jessime]

Hi Ci,

Do you know what version of python you're using? This looks like you're using something <3.6. You can do python --version to find the version.

[Ci-TJ]

I use python3.5.2，but you didn't mention that python need => 3.6.

[Jessime]

You're right. I've just pushed a new commit clarifying this.

[Ci-TJ]

I have used seekr in http://seekr.org, but I found I couldn't download the results after running, which I have nearly 1.7w lncRNA sequences.