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. | ||
* | * 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)