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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 to <b>run SEA</b> is: | |||
> sea-run -f model_fit_file model_set_file query_set_file | |||
Export the results | |||
> sea-export -t 0.5 -o sea_output 9 | |||
[[Category:SEA]] | |||
[[Category:Tutorials]] | |||
[[Category:Internal]] |
Latest revision as of 06:46, 13 March 2014
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
Export the results
> sea-export -t 0.5 -o sea_output 9