Mindy is the Biopython flat-file indexing system. Currently under development, it uses the Martel parsing technology to read a file and find record boundaries, identifiers, keywords and cross-references. This information is stored in a data system that allows simple queries and fast record retrieval. The final product will also include command-line and web based interfaces as well as HTML output and format conversion methods.
Please contact email@example.com if you are interested in being a development partner.
The proof of concept prototype is available. Here is an example of how to use Mindy to first index then search a file in SWISS-PROT format:
% mindy_index.py --format Martel.formats.swissprot38.format \ --dbname swiss --record-tag swissprot38_record \ --identifier entry_name --alias ac_number --progress 100 \ /home/dalke/ftps/swissprot/sprot38.dat % mindy_search --dbname swiss --identifier 100K_RAT ID 100K_RAT STANDARD; PRT; 889 AA. AC Q62671; DT 01-NOV-1997 (Rel. 35, Created) ...
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