Delila Program: dbpull

dbpull program

Documentation for the dbpull program is below, with links to related programs in the "see also" section.

{version = 2.49; (* of dbpull.p 1998 July 16}

(* begin module describe.dbpull *)
(*
name
      dbpull: database extraction program.

synopsis
      dbpull (fin: in, fout: out,
              dbl1, dbl2, dbl3, dbl4, dbl5, dbl6, dbl7, dbl8: in,
              ecat: in, gcat: in, output: out)

files
      fin:  User requests for extractions from libraries.  Each request
         takes up a single line and consists of a genetic sequence identi-
         fication code followed by either a single special extraction code
         or a series of line code requests.  If an entry request is to be
         found in embl format the request line must have a line containing
         simply 'embl' somewhere above it.  A line containing only 'genb'
         will instruct dbpull to look only for genbank format entries on
         the following request lines.  Important note: the exact form of
         fin instructions is found in delman.use.dbpull.instructions.

         If no request is given, then ALL is assumed.  This means that
         the program will now run using a raw list of entry names.
      fout:  contains fulfilled requests in the same entry order as fin.
         this file may serve, itself, as a database library for dbpull as
         long as 'id ' or 'loc' occur with every request.(one of these two
         line codes identifies the beginning of each entry and holds its id)
      dbl1-dbl8:  same files, in the same order, as dbcat. see delman.
                  describe.dbcat.
      ecat:  same as in dbcat also.
      gcat:  same as in dbcat also.
      output:  messages to the user.

description
      this program uses catalogs generated by the dbcat program to quickly
      extract all or part of embl or genb type entries from data base lib-
      raries. the user may choose one of two special requests('all', which
      pulls out an entire entry or 'raw', which pulls out only the genetic
      sequence) or s-he may simply request a number of line codes. the wild-
      card character '*' represents any number of unspecified characters
      in an id request. this allows one fin line to extract several entries
      whose ids have characters in common. the id 'every' extracts all ids
      it is compared to. dbpull also checks the production dates of all the
      catalogs and libraries to see that they are consistent.

documentation
      dbhelp, delman.describe.dbcat, embl and genbank libaries.

see also
      dbcat.p

author
      matthew yarus

bugs

technical notes
      1:dbpull functions on genbank(tm) release 9 (june 1, 1983). 2: if the
      value of the constant checknum is increased, dbpull will do a more
      complete check of its catalogs.
*)
(* end module describe.dbpull *)
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