Delila Program: fealoc

fealoc program

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

{   version = 1.13; (* of fealoc.p 2018 Mar 07}

(* begin module describe.fealoc *)
   fealoc: feature location in a genome

   fealoc(featab: in, data: in, fealocp: in, fealocreport: out, output: out)


   featab:  feature table from dbinst giving locations of features.
      After an id line beginning with '*', the second line defines
           accession       name    begin   end     orientation
      Remaining lines contain the data, for example:
           NC_000913.3     thrL    190     255     +
           NC_000913.3     thrA    337     2799    +

   data:  data table from scan giving locations of sites
          Lines that begin with '*' are ignored.
          Coordinate data is expected to be in the 6th space
          separated column

   fealocreport:  report of results in a table

   fealocp:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      line 2: Lowest site in bits to identify

      line 3: Maximum number of sites to report.
              For testing set this to a small number.
              For production, set it to -1 (meaning all sites).

   output: messages to the user


   Read in a feature table (featab) created by dbinst and then read
   through data from scan and locate the sites identified by scan in
   the features.



see also

   creates featab: dbinst.p
   creates data: scan.p


   Thomas Dana Schneider


technical notes

(* end module describe.fealoc *)
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