| Calling Sequence
| DbToDarwin(inp,outfile,descr,TagsToKeep)
|
| Parameters
| | Name | Type | Description |
|
| inp
| string | the complete input database as a string |
| outfile
| string | name of the output file (database) |
| descr
| string | any commentary |
| TagsToKeep
| list(string) | tags to keep from SwissProt |
|
| Return Type
| NULL |
| Synopsis
| Converts a SwissProt formatted text (inp) into a file
(outfile) usable by Darwin. This program requires a lot of main
memory, (as much the original input file). Make sure that you have
enough memory by using (in unix) "unlimit datasize memoryuse". |
| Once the new database is created, the first time
the command "ReadDb(SwissProt40);" is executed,
the index of the database will be built. Building the index
can take quite a bit of CPU time. This time is spent only once;
future uses of the database will not require any index building.
You will find that Darwin
creates a file named "SwissProt40.tree". This index file is the Pat
tree for all the peptides and is needed for most of the basic
operations of Darwin. You must have write permissions
in the directory in which the database is stored to create the
tree (only the first time the database is loaded).
If an index is not needed (no fast searches will be possible),
creating an empty SwissProt40.tree file will indicate to ReadDb
that the user does not want an index.
|
| Examples
| > DbToDarwin( ReadRawFile('sprot40.dat'), 'SwissProt40',
ReadRawFile('relnotes.txt'), ['AC','DE','OS','KW'] );
|
| See also
| ConsistentGenome, DB, GenomeSummary, ReadDb |