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wilkelab / Opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
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Tidy up pipeline before merging code-freeze #96

Closed alexismhill3 closed 4 years ago

alexismhill3 commented 4 years ago

Deleted make_blast_db.py because it wasn't being used, and combined blast_options.py and option_handling.py into a single file.

Also, the pipeline now saves whatever the input data path is (rather than parsing it for the filename, and saving that).

So for example, if in pipeline.run we set data="/path/to/contig.fa", in the last column of the pipeline csv, we are now saving "/path/to/contig.fa" instead of just "contig.fa".