Basic Tutorial: Difference between revisions

Revision as of 23:16, 11 October 2012

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

@@ Line 1: / Line 1: @@
 See [[SEA]]
-To run [[SEA]] we need three query files:
+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
+* <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
-* 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.
+* <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]].
+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