Difference between revisions of "Chembl processing protocol"

From DISI
Jump to navigation Jump to search
Line 1: Line 1:
 
This is intended for internal use for the BKS lab members.  
 
This is intended for internal use for the BKS lab members.  
  
 +
==Overveiw==
 
Everytime a new Chembl comes out we need to process it.   
 
Everytime a new Chembl comes out we need to process it.   
  
* Exstact the following information from MYSQL into files and bins.
+
* Extract the following information from MYSQL into files and bins.
 +
 
 +
==Extract==
 +
 
 +
This is currently done in Bet's Directories:
 +
~bet/ChEMBL/chembl14/
  
  
Line 18: Line 24:
 
   
 
   
 
  >> scripts/mysql_export.sh chembl14 B
 
  >> scripts/mysql_export.sh chembl14 B
 +
 +
== process data==
 +
Next we run the following script to process the data into the correct format:
 +
 +
scripts/run_after_export.py -h
 +
usage: run_after_export.py [options] activities.txt outfile
 +
 +
options:
 +
  -h, --help            show this help message and exit
 +
  -m X, --maxaffinity=X
 +
                        Only include affinities up to X nM (default 10000)
 +
  -f, --funct          Work with functional data (default binding data)

Revision as of 23:02, 19 September 2012

This is intended for internal use for the BKS lab members.

Overveiw

Everytime a new Chembl comes out we need to process it.

  • Extract the following information from MYSQL into files and bins.

Extract

This is currently done in Bet's Directories:

~bet/ChEMBL/chembl14/


The "scripts/mysql_export.sh" is a shell script that calls information that has been loaded in to the MySQL data base on SGEHEAD of the BKSLB cluster.

 syntax: mysql_export.sh chembl_db_name [F|B|A]
 
 chembl_db_name  chemble databas file, for example chembl14 is release 
 F -- Functional Data: for example, cell assays to efficacy ( life span of a mouse). 
 B -- Binding Datd:  ki, kd, 
 A -- Affinity: ??

To do this run the following:

>> scripts/mysql_export.sh chembl14 B

process data

Next we run the following script to process the data into the correct format:

scripts/run_after_export.py -h
usage: run_after_export.py [options] activities.txt outfile

options:
  -h, --help            show this help message and exit
  -m X, --maxaffinity=X
                        Only include affinities up to X nM (default 10000)
  -f, --funct           Work with functional data (default binding data)