Cannot execute Python file in IGoR (a immunerepertoire analysis software) The 2019 Stack...

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Cannot execute Python file in IGoR (a immunerepertoire analysis software)



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}







-1















Recently, I've been trying to learn how to use the IGoR software for immunorepertoire analysis. But I encountered a problem in parsing the output file. The author provided the manual, however, I cannot fulfill the function and get the results. Below is the link to the manual and the key words provided by author. Maybe the author is very busy and he cannot respond immediately.




  • github link

  • manual

  • question



The output of this Counter is a semicolon separated values file with one field for each event realization, associated mismatches/errors/mutations indices on the read, the scenario rank, its associated probability and the sequence index. Python functions to parse the output of the Best scenario counter can be found in the pygor.counters.bestscenarios submodule.




Or this is the content in this .py file:



import copy

import pandas

from ...models.genmodel import GenModel
from ...utils import utils
def read_bestscenarios_values(scenarios_file, model_parms_file):
best_scenarios_df = read_bestscenarios_indices(filename=scenarios_file)
gen_model = GenModel(model_parms_file=model_parms_file)
return scenarios_indices2values(best_scenarios=best_scenarios_df,
input_genmodel=gen_model)


and bulalalala!



How can I use the .py file? Thanks a lot!










share|improve this question









New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
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  • Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

    – Anaksunaman
    16 hours ago













  • In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

    – Anaksunaman
    16 hours ago


















-1















Recently, I've been trying to learn how to use the IGoR software for immunorepertoire analysis. But I encountered a problem in parsing the output file. The author provided the manual, however, I cannot fulfill the function and get the results. Below is the link to the manual and the key words provided by author. Maybe the author is very busy and he cannot respond immediately.




  • github link

  • manual

  • question



The output of this Counter is a semicolon separated values file with one field for each event realization, associated mismatches/errors/mutations indices on the read, the scenario rank, its associated probability and the sequence index. Python functions to parse the output of the Best scenario counter can be found in the pygor.counters.bestscenarios submodule.




Or this is the content in this .py file:



import copy

import pandas

from ...models.genmodel import GenModel
from ...utils import utils
def read_bestscenarios_values(scenarios_file, model_parms_file):
best_scenarios_df = read_bestscenarios_indices(filename=scenarios_file)
gen_model = GenModel(model_parms_file=model_parms_file)
return scenarios_indices2values(best_scenarios=best_scenarios_df,
input_genmodel=gen_model)


and bulalalala!



How can I use the .py file? Thanks a lot!










share|improve this question









New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





















  • Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

    – Anaksunaman
    16 hours ago













  • In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

    – Anaksunaman
    16 hours ago














-1












-1








-1








Recently, I've been trying to learn how to use the IGoR software for immunorepertoire analysis. But I encountered a problem in parsing the output file. The author provided the manual, however, I cannot fulfill the function and get the results. Below is the link to the manual and the key words provided by author. Maybe the author is very busy and he cannot respond immediately.




  • github link

  • manual

  • question



The output of this Counter is a semicolon separated values file with one field for each event realization, associated mismatches/errors/mutations indices on the read, the scenario rank, its associated probability and the sequence index. Python functions to parse the output of the Best scenario counter can be found in the pygor.counters.bestscenarios submodule.




Or this is the content in this .py file:



import copy

import pandas

from ...models.genmodel import GenModel
from ...utils import utils
def read_bestscenarios_values(scenarios_file, model_parms_file):
best_scenarios_df = read_bestscenarios_indices(filename=scenarios_file)
gen_model = GenModel(model_parms_file=model_parms_file)
return scenarios_indices2values(best_scenarios=best_scenarios_df,
input_genmodel=gen_model)


and bulalalala!



How can I use the .py file? Thanks a lot!










share|improve this question









New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.












Recently, I've been trying to learn how to use the IGoR software for immunorepertoire analysis. But I encountered a problem in parsing the output file. The author provided the manual, however, I cannot fulfill the function and get the results. Below is the link to the manual and the key words provided by author. Maybe the author is very busy and he cannot respond immediately.




  • github link

  • manual

  • question



The output of this Counter is a semicolon separated values file with one field for each event realization, associated mismatches/errors/mutations indices on the read, the scenario rank, its associated probability and the sequence index. Python functions to parse the output of the Best scenario counter can be found in the pygor.counters.bestscenarios submodule.




Or this is the content in this .py file:



import copy

import pandas

from ...models.genmodel import GenModel
from ...utils import utils
def read_bestscenarios_values(scenarios_file, model_parms_file):
best_scenarios_df = read_bestscenarios_indices(filename=scenarios_file)
gen_model = GenModel(model_parms_file=model_parms_file)
return scenarios_indices2values(best_scenarios=best_scenarios_df,
input_genmodel=gen_model)


and bulalalala!



How can I use the .py file? Thanks a lot!







python






share|improve this question









New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











share|improve this question









New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









share|improve this question




share|improve this question








edited yesterday









Anaksunaman

5,72321423




5,72321423






New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









asked yesterday









qingkai wangqingkai wang

12




12




New contributor




qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





New contributor





qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






qingkai wang is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.













  • Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

    – Anaksunaman
    16 hours ago













  • In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

    – Anaksunaman
    16 hours ago



















  • Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

    – Anaksunaman
    16 hours ago













  • In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

    – Anaksunaman
    16 hours ago

















Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

– Anaksunaman
16 hours ago







Create a new python script, import pygor then call e.g. read_bestscenarios_values('path/to/example_scenarios_file', '/path/to/example_model_parms_file') in your script, perhaps?

– Anaksunaman
16 hours ago















In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

– Anaksunaman
16 hours ago





In any case, you should update your question with a link to your .csv file, any model parameters file and provide the relevant details of any script you've come up with so far by editing these into your question.

– Anaksunaman
16 hours ago










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