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nCov-group Data

Code to generate tables for web page and document

The programs create_dataset_table_1.py and create_dataset_table_2.py generate Markdown and Latex content for the two tables on the nCoV web site.

Create table 1

To run:

python create_dataset_table_1.py

This reads content from two files:

  • DEFINITIONS.csv: A KEY,DESCRIPTION line for each dataset. Manually created.

  • UNIQUES.csv: A KEY,NUM-LINES,NUM-UNIQUES line for each dataset, where NUM-UNIQUES is the number of records that occur in no other dataset. Created via query to PostGres database.

It writes two files, table1.md and table1.tex, in the outputs directory.

Its optional -o, -D, and `-U’ arguments allows you to change the name of the output directory and the two input files.

Create table 2

To run:

python create_dataset_table_2.py

This program reads contents from four files that should previously have been generated via Globus commands as follows:

globus ls -F unix -l -r a386b552-6086-11ea-9688-0e56c063f437:data/smiles > smiles-ls.tsv
globus ls -F unix -l -r a386b552-6086-11ea-9688-0e56c063f437:data/descriptors > descriptors-ls.tsv
globus ls -F unix -l -r a386b552-6086-11ea-9688-0e56c063f437:data/fingerprints > fingerprints-ls.tsv
globus ls -F unix -l -r a386b552-6086-11ea-9688-0e56c063f437:data/images > images-ls.tsv

It writes two files, table2.md and table2.tex, in the outputs directory.

Its optional -o argument allows you to change the name of the output directory.