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Example Integration - Full Database

In the previous example only a few Experiment File line types varied. A more general approach is to allow for flexibility in all fields. A `.pregaprc' file for controlling many more fields follows.

#-----------------------------------------------------------------------------
# Our database hooks

CN_com='pregap_lookup db-long $ID 9'
SF_com='pregap_lookup db-long $ID 1'
SP_com='pregap_lookup db-long $ID 2'
SC_com='pregap_lookup db-long $ID 3'
SI_com='pregap_lookup db-long $ID 4'
CF_com='pregap_lookup db-long $ID 5'
ST_com='pregap_lookup db-long $ID 6'
PR_com='pregap_lookup db-long $ID 7'
TN_com='pregap_lookup db-long $ID 8'

SV_com='echo $SF'
CV_com='echo $CF'

# Constants evaluated as commands are pregap startup
OP=`whoami`
DT=`date`

To simplify things slightly the above defines the sequencing vector name to be the same as the sequencing vector filename. If this vector is copied into the same directory as the readings to be processed then this can easily be made so. Similarly the same is true for the cosmid cloning vector sequence. The database file containing this information is of the same line-by-line format as before, except with many more fields. In this contrived example this has been named `db-long'.

#ID        SF          SP SC   SI         CF           ST PR TN     CN
xa19a1.s1  psC         55 2305 6000..9000 pJB8         1  1  xa19a1 R10E9
wb20a1.r1  m13mp18    -24 6249 1000..1400 lorist2      2  2  wb20a1 F21G4
zf18a1.s1  m13mp18     41 6249 1400..2000 pjB8         1  1  zf18a1 B0334

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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_9.html