Chembl processing protocol: Difference between revisions

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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/




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  >> 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)