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qmarcou / IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
https://qmarcou.github.io/IGoR/
GNU General Public License v3.0
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Errors: python to parse the output results? #48

Closed decenwang closed 4 years ago

decenwang commented 5 years ago

Hi @qmarcou

I have installed the pygor by your command line. when I tried to use the submodule: pygor to dispaly the result. igor reported an error: decen@bio:~/Downloads/seq/igor/foo3_output$ igor -pygor best_scenarios_counts.csv [IGoR] ERROR: Unknown IGoR command line argument "-pygor" [IGoR] ERROR: Use "man igor", "igor -help" or visit https://github.com/qmarcou/IGoR to see available commands and their effects. [IGoR] ERROR: Please report any bug by opening an issue on https://github.com/qmarcou/IGoR or email: quentin.marcou@lpt.ens.fr [IGoR] ERROR: Terminating IGoR... the "-pygor" cannot be recognized. If I run independently as the below command: . /home/decen/packages/igor_1-3-0/pygor/pygor/counters/bestscenarios/bestscenarios.py csv.file it also show errors: from: can't read /var/mail/...models.genmodel from: can't read /var/mail/...utils bash: /home/decen/packages/igor_1-3-0/pygor/pygor/counters/bestscenarios/bestscenarios.py: line 32: syntax error near unexpected token(' bash: /home/decen/packages/igor_1-3-0/pygor/pygor/counters/bestscenarios/bestscenarios.py: line 32: def read_bestscenarios_values(scenarios_file, model_parms_file):'

Could you please help this ?

Thanks a lot!

Best,

Decen

decenwang commented 5 years ago

decen@bio:~/packages/igor_1-3-0/pygor/pygor/counters/bestscenarios$ /home/decen/software/miniconda/bin/python3.7 bestscenarios.py Traceback (most recent call last): File "bestscenarios.py", line 28, in <module> from ...models.genmodel import GenModel ValueError: attempted relative import beyond top-level package

qmarcou commented 5 years ago

Dear @decenwang , The pygor module is here to help you deal with IGoR I/O in your own python scripts or within an interactive Python interpreter session, it cannot be directly executed as a Python script. You can import the module once installed via pip, and use it within Python. I invite you to read a short Python tutorial in order to use pygor. We might supply an easier interface in a short while but for now this is it.

I would also kindly ask you to refrain from multi-posting since maintaining the software and answering users question is already time consuming and duplicating your posts is only distracting and making us waste time. I have thus deleted your duplicated questions within the various unrelated issues, in order to keep clear answers for other users. I would also like to remind you that IGoR's under GNU-GPLv3 license, and although we are happy to provide as much help as we can to IGoR users, IGoR comes without any warranty nor obligated 'customer' service.

Best regards,