indexing multiple blast files

etzold etzold at
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:
>   comment:""
>   format:@MULTI_BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" ""}
>   type:user
> #  files:{
> #    $file:tmp
> #  }
> ]

the problem is that at the moment there is the choice between 1) each
is in a separate file and 2) entries are contained in one or more
in the latter case the file names as attribute "files" of $library MUST
be specified. Searching files with a search expression as for 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


...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,
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).


More information about the Bio-srs mailing list