run_FLUTE
This page describes the script that accesses the FLUTE database. The functions in this module ground element names and check against the FLUTE database.
Functions
- run_FLUTE.getRelatedPapers(db_user, db_pass, db_host, db_name, prot)[source]
This function retrieves related papers based on a protein name and saves a file of related paper IDs.
- Parameters
db_user (str) – Name of the MySQL user where the FLUTE DB is stored.
db_pass (str) – Password for the MySQL user where the FLUTE DB is stored.
db_host (str) – Host name for the local machine where the coopy of the FLUTE DB is stored.
db_name (str) – Name of the local copy of the FLUTE DB.
prot (str) – Input protein
- run_FLUTE.getRelatedInts(db_user, db_pass, db_host, db_name, f)[source]
This function retrieves interactions from the same papers as
- Parameters
db_user (str) – Name of the MySQL user where the FLUTE DB is stored.
db_pass (str) – Password for the MySQL user where the FLUTE DB is stored.
db_host (str) – Host name for the local machine where the coopy of the FLUTE DB is stored.
db_name (str) – Name of the local copy of the FLUTE DB.
f (str) – File name of the list of papers
- run_FLUTE.getRecentPapers(f)[source]
This function should search the OA file and find all interactions occuring in papers less than X years old
- Parameters
f (str) – Input filename that contains list of interactions
- run_FLUTE.getDups(f)[source]
This function calculates the number of occurences of an interaction in a reading set.
- Parameters
f (str) – Filename of the list of interactions to be counted.
- run_FLUTE.convID(db_user, db_pass, db_host, db_name, X)[source]
This function uses the FLUTE DB to ground interactions
- Parameters
db_user (str) – Name of the MySQL user where the FLUTE DB is stored.
db_pass (str) – Password for the MySQL user where the FLUTE DB is stored.
db_host (str) – Host name for the local machine where the coopy of the FLUTE DB is stored.
db_name (str) – Name of the local copy of the FLUTE DB.
X (numpy array) – Array containing all grounded interactions
- Returns
X – Grounded ineractions
- Return type
numpy array
- run_FLUTE.findInts(db_user, db_pass, db_host, db_name, ints, es, ts, ds)[source]
This function uses the FLUTE DB to filter interactions
- Parameters
db_user (str) – Name of the MySQL user where the FLUTE DB is stored.
db_pass (str) – Password for the MySQL user where the FLUTE DB is stored.
db_host (str) – Host name for the local machine where the coopy of the FLUTE DB is stored.
db_name (str) – Name of the local copy of the FLUTE DB.
X (numpy array) – Array containing all filtered interactions
- Returns
X – Filtered interactions
- Return type
numpy array
- run_FLUTE.uniOnly(allInts)[source]
This function returns only proteins
- Parameters
allInts (numpy array) – All interactions from the input file
- Returns
rel_ints – Protein-protein interactions only
- Return type
numpy array