BRAINCL - Unnamed repository; edit this file 'description' to name the repository.

Age	Commit message (Collapse)	Author
2020-02-11	merge_edges.py: use the most recent update date as the merged edge's date.	Hui Lan

2020-02-11	merge_edges.py: add a few comments for function make_new_edge.	Hui Lan

2020-02-11	merge_edges.py: log more information in network.log.	Hui Lan

2020-02-11	merge_edges.py: log number of edge files scanned.	Hui Lan

2020-02-11	merge_edges.py: what is the purpose of variable d.	Hui Lan

2020-02-11	merge_edges.py: make a better key	Hui Lan
	Use a combination of target gene ID and tf gene ID as a key. So if we having the following: Target: AT5G09445 AT5G09445 TF: AT1G53910 RAP2.12 Then the key will be "AT5G09445_AT1G53910". Before it was "AT5G09445 AT5G09445 AT1G53910 RAP2.12". This is OK in most cases, as long a gene ID's corresponding gene name is consistent. But if "AT1G53910" has a different gene name, then we will have a DIFFERENT key, which is not what we want.
2020-02-11	merge_edges.py: why 10?	Hui Lan

2020-02-11	merge_edges.py: consider all files in directory EDGE_POOL whose file name ↵	Hui Lan
	starts with 'edegs'
2020-01-21	merge_edges.py: write all edge information to an SQLite database file called ↵	Hui Lan
	edges.sqlite When I saved a static html page for each edge (e.g., http://118.25.96.118/static/edges/AT1G20910_AT1G30100_0.html), it took 5GB disk space for saving 1 million html pages. Not very disk space efficient. An alternative is to save all edge information in a database table (i.e., edge), and query this database table for a particular edge. The database file edges.sqlite takes less than 200MB for 1 million edges, requiring 10 times smaller space than the static approach. The reason is that we do not have a lot of HTML tags in the database. Quite happy about that, though it seems that filling a database is a bit slower (2 hours??? for 1 million rows). Also updated two files that were affected: update_network.py and update_network_by_force.py. Now instead of copying 1 million static html page to the Webapp, I just need to copy edges.sqlite to static/edges/. Faster. In the Webapp, I updated start_webapp.py and added a file templates/edge.html for handling dynamic page generation. -Hui
2019-12-26	merge_edges.py: save memory by removing the dictionary variable duniq	Hui Lan
	The purpose of duniq is to avoid duplicated edge lines. Now, just make sure we don't insert the same tuple. -Hui
2019-12-04	merge_edges.py: run dos2unix on merge_edges.py to remove ^M characters.	Hui Lan

2019-12-04	merge_edges.py: clean up source code by removing commented lines and editing ↵	Hui Lan
	the head comments.
2019-12-04	brain: add python and R code to local repository.	Hui Lan