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Mindy

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 info@dalkescientific.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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