Difference between revisions of "Basic Tutorial"

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See [[SEA]]
 
See [[SEA]]
  
To run [[SEA]] we need three query files:
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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 semicolumn
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* <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 semicolumn. Can be generated by the following command:
+
  > 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 file : First element is the set code, the second is the set description, the third is the list of compound IDs in the set separated by a coumn.
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* <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.
 
+
  
For the reference sets we need the same three files plus the model file, generated from [[SEA]].
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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 16:16, 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