allow offline usage

[EricDeveaud]

Hello

I was asked to install FUNGuild on our cluster.

as our cluster does not allow compute nodes to access internet I want to propose a PR that enable FUNGuild to work from local saved databases.

this PR add to FUNGuild 2 new options.
*) --download that downloads the databases to FUNGuild_db directory located at the same level than Guilds_v1.1.py (or any other directory specified by FUNGUILD_DB environnement variable
obviously this step need to be run from a node that can connect to internet

*) --local that turns Guilds_v1.1.py to use local databases previously saved.

see an example of usage

1. download DBs from internet connected node to default db_dir location:

maestro-builder:pull-request/FUNGuild > python Guilds_v1.1.py --download                    
Download DBs to /home/edeveaud/Work/pull-request/FUNGuild/FUNGuild_db
downloading http://www.stbates.org/funguild_db_2.php	 OK
downloading http://www.stbates.org/nemaguild_db.php	 OK

2. download DBs from internet connected node to default db_dir location superseeded by FUNGUILD_DB environnement variable:

maestro-builder:pull-request/FUNGuild > FUNGUILD_DB=/tmp/db python Guilds_v1.1.py --download
Download DBs to /tmp/db
downloading http://www.stbates.org/funguild_db_2.php	 OK
downloading http://www.stbates.org/nemaguild_db.php	 OK

3. work with dowloaded DBs from default db_dir location on non network context. simukated using unshare -n

maestro-builder:pull-request/FUNGuild > sudo unshare -n  python  Guilds_v1.1.py -otu example/otu_table.txt  --local                   
FunGuild v1.1 Beta
Connecting with FUNGuild database ... file:///home/edeveaud/Work/pull-request/FUNGuild/FUNGuild_db/funguild_db_2.php

Reading in the OTU table: 'example/otu_table.txt'

Searching the FUNGuild database...
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%

Found 12 matching taxonomy records in the database.
Dereplicating and sorting the result...
FunGuild tried to assign function to 10 OTUs in 'example/otu_table.txt'.
FUNGuild made assignments on 6 OTUs.
Result saved to 'example/otu_table.guilds.txt'

Total calculating time: 0.15 seconds.

same applies with overwritting db_dir using FUNGUILD_DB environnement varaible.

I have a question regarding the Databases, how regularly are they upsdated ?
is there some notification when they are ?

regards

Eric

[EricDeveaud]

hummmm sorry a small error.

a more robust way of handling the env var will be to change
DB_DIR=os.environ.get('FUNGUILD_DB', os.path.abspath(os.path.join(os.path.dirname(__file__), 'FUNGuild_db')))

to
DB_DIR=os.path.abspath(os.environ.get('FUNGUILD_DB', os.path.join(os.path.dirname(__file__), 'FUNGuild_db')))

this will allow FUNGUILD_DB=<some_relative_path> and avoid an error in such situation.

regards

Eric