indexing multiple blast files

[Tim Dudgeon]

Hi,

Here's a question for the icarus gurus amongst you.

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:

% $SRSEXE/srsbuild multi_blast
...processing MULTI_BLAST
SRSICA:icarus.i:77: error: insufficient memory - error during malloc,
could not allocate "library file objects"

Can anyone point out the error of my ways.
My new blast.i is as follows:

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#    $RCSfile: blast.i,v $
#    $Revision: 1.4 $
#    $Date: 1997/03/03 18:33:46 $
#    $Author: srs $
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


BLAST_DB:$library:[BLAST group:@APPLICATION_LIBS 
  comment:"" 
  format:@BLAST_FORMAT maxNameLen:40 ifiles:{"blast.i" "blast.is"}
  type:user
  files:{
    $file:tmp
  }
]


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
#  }
]

BLAST_FORMAT:$libformat:[fileType:@BLAST_FILE syntax:@BLAST_SYNTAX 
  fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_TopMatch code:tmatch
      tableToken:t_tmatch tableFormat:left]
    $field:[@DF_Alignment code:tmatch
      tableToken:t_entry tableFormat:left]
    $field:[@DF_TopScore code:tscore1 index:int indexToken:score
      tableToken:score tableFormat:right]
    $field:[@DF_PercIdent code:tscore2 index:int indexToken:percIdent
      tableToken:percIdent tableFormat:right]
    $field:[@DF_QueryBeg code:tmatch index:int indexToken:queryBeg
      tableToken:queryBeg tableFormat:right]
    $field:[@DF_QueryEnd code:tmatch index:int indexToken:queryEnd
      tableToken:queryEnd tableFormat:right]
    $field:[@DF_MatchLen code:tmatch index:int indexToken:matchLen
      tableToken:matchLen tableFormat:right]
    $field:[@DF_LINK index:link code:link indexToken:link]
  }
]

MULTI_BLAST_FORMAT:$libformat:[fileType:@MULTI_BLAST_FILE
syntax:@BLAST_SYNTAX 
  fields:{
    $field:[@DF_ID code:title index:id indexToken:id]
    $field:[@DF_TopMatch code:tmatch
      tableToken:t_tmatch tableFormat:left]
    $field:[@DF_Alignment code:tmatch
      tableToken:t_entry tableFormat:left]
    $field:[@DF_TopScore code:tscore1 index:int indexToken:score
      tableToken:score tableFormat:right]
    $field:[@DF_PercIdent code:tscore2 index:int indexToken:percIdent
      tableToken:percIdent tableFormat:right]
    $field:[@DF_QueryBeg code:tmatch index:int indexToken:queryBeg
      tableToken:queryBeg tableFormat:right]
    $field:[@DF_QueryEnd code:tmatch index:int indexToken:queryEnd
      tableToken:queryEnd tableFormat:right]
    $field:[@DF_MatchLen code:tmatch index:int indexToken:matchLen
      tableToken:matchLen tableFormat:right]
    $field:[@DF_LINK index:link code:link indexToken:link]
    }
]

DF_TopMatch:$srsfield:[TopMatch short:tma]
DF_TopScore:$srsfield:[TopScore short:tsc]
DF_PercIdent:$srsfield:[PercentIdentity short:pid]
DF_QueryBeg:$srsfield:[QueryMatchBeginPos short:qbp]
DF_QueryEnd:$srsfield:[QueryMatchEndPos short:qep]
DF_MatchLen:$srsfield:[MatchLength short:mtl]


BLAST_SYNTAX:$syntax:[file:"SRSDB:blast.is" ignore:" "]
BLAST_FILE:$filetype:[typename:blast maxline:100]
MULTI_BLAST_FILE:$FileType:[
  singleEntry:n
  maxline:100
  saveName:file saveNameLength:20 
#  searchName:'*.blastp'
   typeName:'blastp'
]

$link:[@BLAST_DB to:@?SWISSPROT_DB token:'link|swiss'
toField:@DF_Accession]



-- 
Dr. Tim Dudgeon                           Phone: 01865 748747
British Biotech Pharmaceuticals Ltd.      FAX:   01865 717598
Watlington Road, Oxford, OX4 5LY, UK      email: dudgeon at britbio.co.uk