question about SRS5.0

Thure etzold at embl-heidelberg.de
Wed Dec 11 09:48:58 EST 1996

Tao Jiang wrote:
> I downloaded the SRS version 5.0, and had a small test
> yesterday. I installed only a very small part of EMBL
> : phg.dat, and try to index it. To my surprising, I
> found it would take me over 12 hours to index it (in fact,
> the indexing hasn't finished yet), and too many index
> files were generated: embl_fts_1.inx, embl_fts_2.inx, ...
> , embl_569.inx, ... (I have modified srsdb.i and embl.i to
> include only phg.dat of EMBL).
> However, if I test it with swissprot, it seems to work well
> (only one index file for every index).
> Any suggestions and help are greatly appreciated.

I found the bug, in fact there were two: 

1) edit file src/icarus.c

after line 670 you find 

    if (!IcaCursorIsInput (job->inCursor, job->cursor)) {
/*      CursorDelete (&job->cursor); */
      job->cursor = NULL;


remove the comments and rebuild srsbuild:

srsmake srsbuild

2) edit icarus/db/embl.is

around line 55 you find

  seq:       ~ (/.*2BIT *Len:/ /[0-9]+/ {$len=$Ct} ln ln 
	       {$s=$SeqGet2Bit:[$s file:$File len:$len]} ('>>>>'{$Not} ln)*|
               /.*ASCII/ ln ln ('>>>>' {$Not} /.*/ {$SeqApp:[$s
s:$Ct]})+) ~

change '$s=$SeqGet2Bit' to '$SeqGet2Bit'


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