#nextcalde.py
- nextclade_runner()
- Calls combine_nextclade_output, nextclade_data_obj, run_nextclade
- This function runs nextcalde and pushes results to Influenza DB
#nextcalde_helper.py
-
run_nextclade()
- Runs nextcalde from resources path
- Returns Dictionary of postive hits
-
concat_fasta()
- Concates all fasta files per samples to be passed on to nextcalde
-
combine_nextclade_output()
- combines nextcalde output into one file
-
nextclade_data_obj() CLASS
-
Initialize class
-
Requires path to data directory to import sql db credentials
-
get_nextclade_dfs() -Read in combined nextcalde file and create DF
-
database_push()
- Pushes nextcalde DF to Influenza DB
-
setup_db()
- Sets up Influenza DB connection
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