
      getloc.txt                                          update 25 Jan 2002


      NAME
            getloc - retrieve database entries listed in namefile to outfile.
      
      SYNOPSIS
            getloc [-asfcgep] namefile [anofile] [seqfile] indfile outfile
      
      DESCRIPTION
            getloc reads a list of names from namefile and recreates
            entries by combining the annotation and sequence portions of each
            entry from anofile and seqfile.  getloc will work most quickly
            when the namefile is in alphabetical order, but it will also
            work on unsorted lists.  The following options affect the output:

            a    Write annotation portions of entries only, terminated by '//'.
                 seqfile is not included on command line.
  
            s    Write sequence data only, in Pearson (.wrp) format.
                 anofile is not included on commandline.

            f    Write each entry to a separate file.  The filename will 
                 consist of the LOCUS name, followed by .ano for annotation 
                 only, .wrp for sequence only, or .gen for complete GenBank 
                 format, and .pir for PIR CODATA format files.

            c    namefile contains accession numbers, rather than names

            The following options identify the type of database being read:

            g    GenBank (default)
            e    EMBL
            p    PIR (NBRF)

                 
            namefile consists of an alphabetically ordered list of LOCUS names, 
            each on a separate line. Indfile could be used to create a 
            namefile by simply editing out some subset of names. (This can also 
            be done using the Unix comm command.)  If the entire indfile was 
            used, the entire database would be recreated, minus the header 
            information that might have been present in the original, but 
            deleted by splitdb.

     NOTE
            Getloc automatically expands leading blanks that have been 
            compressed using splitdb -c. See splitdb.doc for more information.
     
     SEE ALSO
           splitdb, comm(1).

     AUTHOR
       Dr. Brian Fristensky
       Dept. of Plant Science
       University of Manitoba
       Winnipeg, MB  Canada  R3T 2N2
       Phone: 204-474-6085
       FAX: 204-474-7528
       frist@cc.umanitoba.ca

     REFERENCE
       Fristensky, B. (1993) Feature expressions: creating and manipulating
       sequence datasets. Nucleic Acids Research 21:5997-6003.
