Right now, the -d option has a different usage in index_default_ssu_rrna_db.py + matam_db_preprocessing.py vs. matam_assembly.py.
In the first case, the user has to provide the path to a directory where the database will be written, and the database name/prefix will be automatically and implicitely defined based on the reference fasta filename.
In the second case, the -d option is expecting the path to the prefixed database. This is the way most popular bioinformatic programs using indexes are designed (BLAST, bowtie, ...). This is also the most user friendly way of doing and it doesn't leave place to implicit option/naming.
Therefore, the -d option should be changed in the db creation/indexing scripts. Instead of a directory, the user should be passing a prefix. By default it could be a prefix based on the input file and written in the current working directory, but the user need to be able to explicitly specify another PATH/prefix.
Right now, the
-doption has a different usage inindex_default_ssu_rrna_db.py+matam_db_preprocessing.pyvs.matam_assembly.py. In the first case, the user has to provide the path to a directory where the database will be written, and the database name/prefix will be automatically and implicitely defined based on the reference fasta filename. In the second case, the-doption is expecting the path to the prefixed database. This is the way most popular bioinformatic programs using indexes are designed (BLAST, bowtie, ...). This is also the most user friendly way of doing and it doesn't leave place to implicit option/naming.Therefore, the
-doption should be changed in the db creation/indexing scripts. Instead of a directory, the user should be passing a prefix. By default it could be a prefix based on the input file and written in the current working directory, but the user need to be able to explicitly specify another PATH/prefix.