indexing multiple blast files

etzold etzold at ebi.ac.uk
Thu Jul 3 07:21:32 EST 1997


Tim Dudgeon wrote:

> I am wanting to set up SRS5 to index multiple blast files (pregenerated
> output, not generating the blast output within SRS).
> 
> I've made what I beleive should be the required changes by including a
> MULTI_BLAST database, based on what is already in blast.i and on how
> hssp.i handles multiple input files, but I'm getting run time errors:
> 
> MULTI_BLAST_DB:$library:[MULTI_BLAST group:@APPLICATION_LIBS
>   comment:""
>   format:@MULTI_BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"}
>   type:user
> #  files:{
> #    $file:tmp
> #  }
> ]

the problem is that at the moment there is the choice between 1) each
entry
is in a separate file and 2) entries are contained in one or more
flatfiles.
in the latter case the file names as attribute "files" of $library MUST
be specified. Searching files with a search expression as for hssp
(*.hssp)
work only for the single entry/file case. That means to fix the problem 
quickly you need to remove the above comments and write something like

   files:{
     $file:tmp1
     $file:tmp2
     ...
   }

...obviously that is not what you want since the names and number fo the
blast output files will probably vary quite a lot. To make that a little
more flexible you could write a script that generates the 'files' part,
inserts
it into blast.i and runs srssection ....sorry about that!

Since I am working on the problem with the multiple directories for pdb
i will probably fix the  multiple blast file problem next since the too
are quite related (at least as seen from SRS's perspective).

regards
Thure
problems




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