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Example Integration - Squirrel Database

Notice that in the full external database example described above that there is a significant amount of repetition. When many readings are stored in such a text file it may seem redundant to have to specify the sequencing vector primer and cloning sites for each reading. The earlier Squirrel program kept the information spread over several database files. One file specified the template information (including reading names, sequencing vector name, insert size and database name). The vector name was then used to look up vector information (the primer and cloning sites used) from a separate database. Such a database is generally referred to as a "relational database".

For brevity, the example Squirrel database file aren't listed here. The `.pregaprc' file used is shown below as it serves as a good example of linking a relational database to Pregap. This actual .pregaprc file itself should not be used as it does not determine the primer information correctly (Squirrel used to derive this from local read naming conventions).

_pregap_lookup() {
    pregap_lookup -r $SQUIRREL/tables/$2 "$1" "$3"
}

# NB: We make assumptions on the order of evaluation of the experiment
# file identifiers used in pregap. 
CN_com='_pregap_lookup "$ID" subclones 1'
CV_com='_pregap_lookup "$CN" clone-types 1'
SV_com='_pregap_lookup "$ID" subclones 4'

SF_com='_pregap_lookup "$SV" vector-seqfiles 1'
CF_com='_pregap_lookup "$CV" vector-seqfiles 1'
SC_com='_pregap_lookup "$SV" seqclone-sites 1'
SP_com='_pregap_lookup "$SV" seqclone-sites 2'

DR='+'
DT_com='date'
MT_com='echo $file_type'
OP_com='_pregap_lookup "$CN" databases 5'
SI_com='_pregap_lookup "$ID" subclones 2'

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap_10.html