1) Added -wd/--working_directory flags for specifying working directory for outputs
2) Added pyarrow to enviroment files. Prevents pandas futurewarning.
3) Fixed downcasting in fillna() commands in python/pandas
4) Fixed paths so that hhsuite databases are download and referred to correctly
5) Added --genbank flag which allows users to disable genbank outputs
6) Fixed taxonomy lineage parsing in vote_taxonomy.py in certain cases.
7) Fixed hhpred_to_table.py parsing of hhsuite output files to correctly hand CDD and PDB accessions/descriptions.
9) Updated scripts so that in annotation mode -am True (unless flag --caller adaptive) to skip unnecessary initial pyhmmer steps. This reduced runtime by about 25%.
Changes:
1) Added
-wd/--working_directoryflags for specifying working directory for outputs 2) Added pyarrow to enviroment files. Prevents pandas futurewarning. 3) Fixed downcasting infillna()commands in python/pandas 4) Fixed paths so that hhsuite databases are download and referred to correctly 5) Added--genbankflag which allows users to disable genbank outputs 6) Fixed taxonomy lineage parsing invote_taxonomy.pyin certain cases. 7) Fixedhhpred_to_table.pyparsing of hhsuite output files to correctly hand CDD and PDB accessions/descriptions. 9) Updated scripts so that in annotation mode-am True(unless flag--caller adaptive) to skip unnecessary initialpyhmmersteps. This reduced runtime by about 25%.