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SRS templates

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Thu Apr 30 03:52:51 EST 1998


[Request for SRS templates for OWL]

I have one for OWL.  I added the following lines to the top of
GenSRSSDLSource:pir.sdl

#library /id=%OWL_DB 
    /group=@SEQUENCE_LIBS /name=OWL /logicname=OWL /format=@OWL_FORMAT
    /help="pir" /comment="OWL"
    /oddfile="pir.sdl" /cachesize=1024  /maxIndexSizeKb=1500 /datatype=protein
{
    #file /name=owl /logicname=OWL
}

#libformat /id=%OWL_FORMAT /parser=@PIR_PARSER
!           /file_type=@EMPIRREF_FILE, @EMPIRSEQ_FILE
           /file_type=@PIRREF_FILE, @PIRSEQ_FILE
{
    !
    !title
    #field /gblid=%OWL_ID_FIELD
           /itype=ID /ftype=@DF_ID /idtype=@SRSxSEQID
           /begstr=">" /find=id /maxlines=1 

    #field /gblid=%OWL_ACC_FIELD
           /itype=key /ftype=@DF_ACCESSION /idtype=@SRSxSEQID           
           /begstr="C;ACCESSION:","A;ACCESSION:" /find=accession 
           /nextstr=" " !/maxlines=1 

    #field /itype=key /ftype=@DF_DEFINITION /idtype=@SRSxSEQID
           /after=@OWL_ID_FIELD /find=definition /maxlines=1   

    #field /itype=key /ftype=@DF_ORGANISM /idtype=@SRSxSEQID           
           /begstr="C;SPECIES:" /find=species 
           /nextstr=" " !/maxlines=1 

    #field /gblid=%OWL_AUT /itype=key /ftype=@DF_AUTHORS /idtype=@SRSxSEQID
           /begstr="R;" /find=authors 
           /nextstr=" "
    !reference
!    #field /itype=key /ftype=@DF_REF /idtype=@SRSxSEQID /suppress_error=yes
!           /find=reference /after=@PIR_AUT /maxlines=1 

    #field /itype=key /ftype=@DF_TITLE  /idtype=@SRSxSEQID
           /begstr="A;TITLE:" /maxlines=1 /find=title 
                                                                              
    #field /itype=key /ftype=@DF_KEYWORDS /idtype=@SRSxSEQID
           /begstr="C;HOST:", "A;MOLECULE TYPE:", "C;SUPERFAMILY:",     
                   "C;KEYWORDS:", "C;GENE NAME:" /find=keywords 
           /nextstr=" "
    !feature
    #field /itype=key /ftype=@DF_FEATURES /idtype=@SRSxSFTID
           /begstr="F;" /begleft=1 /begright=1 /find=feature         
           /nextstr=" " !/maxlines=1 

    #field /itype=num /ftype=@DF_SEQLENGTH /idtype=@SRSxSEQID
           /find="" 
} 

I then added the following lines to gensrssdlsource:srsdb.sdl


   #libenv /lib=@OWL_DB        /dir="OwlDir:"

in the #environment block.  Obviously you need to have defined the
name OwlDir in gendbconfigure:dblogicals.

Also in srsdb.sdl:

    #libid /n=12 /library=@OWL_DB

in the #srsdb block

Then I edited gendbconfigure:srsnames.map, and added the lines:

!
name owl
sdl pir
id 12
divisions owl
!

My entry for OWL in gendbconfigure:dbnames.map is:

owl             OWLDir          owl             owl     OWL

Hope this lot makes sense to you and helps!


Tim.



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