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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.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ height:90px;width:728px;box-sizing:border-box;
}
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
edited yesterday
Anaksunaman
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
add a comment |
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
edited yesterday
Anaksunaman
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
Create a new python script,import pygorthen 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.csvfile, 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
add a comment |
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
edited yesterday
Anaksunaman
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
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
python
edited yesterday
Anaksunaman
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
edited yesterday
Anaksunaman
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
edited yesterday
Anaksunaman
5,72321423
edited yesterday
Anaksunaman
5,72321423
edited yesterday
Anaksunaman
5,72321423
5,72321423
asked yesterday
qingkai wangqingkai wang
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.
asked yesterday
qingkai wangqingkai wang
12
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 pygorthen 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.csvfile, 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
add a comment |
Create a new python script,import pygorthen 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.csvfile, 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
add a comment |
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Create a new python script,
import pygorthen 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
.csvfile, 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