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See [[SEA]] | See [[SEA]] | ||
To run [[SEA]] we need three | To run [[SEA]] we need, for both the query and the reference, three files with the same basename and different extensions: | ||
* smiles : The separator between smiles and IDs is a | * <b>smiles</b> (.smi) : The separator between smiles and IDs is a semicolon. Make sure it has the same characteristics than the reference by running the following command: | ||
* fingerprints : Separator is also a | > sea-molecule-clean | ||
* <b>fingerprints</b> (.fp) : Separator is also a semicolon. Can be generated by the following command: | |||
> sea-molecule-fingerprint | > sea-molecule-fingerprint | ||
* set | * <b>sets</b> (.set) : First element (separated by semicolon) is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a colon. | ||
Additionally, we will need the model fit file generated from [[SEA]]. | |||
The actual command is: | The actual command to <b>run SEA</b> is: | ||
> sea-run -f model_fit_file model_set_file query_set_file | > sea-run -f model_fit_file model_set_file query_set_file |
Revision as of 23:16, 11 October 2012
See SEA
To run SEA we need, for both the query and the reference, three files with the same basename and different extensions:
- smiles (.smi) : The separator between smiles and IDs is a semicolon. Make sure it has the same characteristics than the reference by running the following command:
> sea-molecule-clean
- fingerprints (.fp) : Separator is also a semicolon. Can be generated by the following command:
> sea-molecule-fingerprint
- sets (.set) : First element (separated by semicolon) is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a colon.
Additionally, we will need the model fit file generated from SEA.
The actual command to run SEA is:
> sea-run -f model_fit_file model_set_file query_set_file