MDU-PHL / ngmaster

In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
GNU General Public License v3.0
6 stars 5 forks source link

Updated function to handle update_db #20

Closed andersgs closed 8 years ago

andersgs commented 8 years ago

Moved the process of updating the DB to a function.

Using requests and BeautifulSoup, making it unnecessary to use the sed functions, and temp files --- unless they are used someplace else, we can delete them.

This should fix the unwanted temp files that kept showing up.

No old file is kept. So, if overwritten and something has gone wrong, the person has to download a new copy. But, it won't be overwritten until we are certain the DB has downloaded, and parsed.

This branch includes new versions of all three database files.

Note that allele DB file is now CSV and TSV. Just scrapping it off the webpage, and doing no transforms. The appropriate change was made in the function that reads the allele DB file.

Updated setup.py to include bs4 and requests dependencies.

Moved the DB URL strings to the top of the main file.