Delila Program: tod

tod program

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

{   version = 3.01; (* of tod.p 2016 Jan 24}

(* begin module describe.tod *)
   tod: to database format for sites program

   tod(abi: in, thedate: in, ssb: in, todp: in,
       results: out, summary: out, db: out, output: out)

   abi: Raw sequences from the ABI sequencing machine.  The
      files called *_??.Seq.txt are manipulated under Unix by:

      more *_??.Seq.txt | cat > abi
      echo "" >> abi

      The more program puts each name followed by the contents, and it is smart
      enough to pipe it to cat which joins the results together.  Thus the abi
      file contains the sample names followed by the sequences.  The echo puts
      a single carriage return at the end of the file so that it ends cleanly.

   thedate:  Date that the sequences were run, output of makedate program.

   ssb:  This must be a copy of the "Sample_Sheet.bin" file from the ABI
      machine.  It contains:
           lane number
           plasmid name
           primer name
      in a funny non-ASCII format which this program extracts from.  (The
      program extracts the data from their known rigid locations.)  The sample
      name column of the sample sheet must contain the plasmid name.  Any
      number of spaces, slashes (/) or null characters are then skipped and the
      next non null word (ending in null or space) is taken as the primer
      name.  Thus the format is "plasmid/primer".  For example:  pTS421/pTS37f1

      There is a bug in the ABI code which will replace the first letter
      of the 24th lane with a null character sometimes.  To get around
      the bug, we will try to rewrite the sample sheet if this appears.

   todp: parameters to control the program
      first line:  a string of characters, called R1, which represents
         a restriction site or other sequence.
         NOTE: it should be self complementary.
      second line:  a string of characters, called R2, which represents
         a restriction site or other sequence.
         NOTE: it should be self complementary.
      following lines: Editing commands for sequences.  There is one editing
  command per line, and each consists of three integers (called N, P1
  and P2) followed by a string (S).  N is the lane number to edit.
  The P1 and P2 define two positions in the sequence.  The sequence
  between these positions is deleted and replaced by the string S.  The
  string must contain only the letters 'acgt' or the single letter 'd'.
  This allows one to insert sequence (make the P1 = P2 + 1, string is
  'acgt' form), to delete (P1 > P2 + 1, string is 'd') and to replace
  (make P1 = P2 + 1 + length of string in 'acgt' form).  Lines that
  begin with '*' are comments, copied to the results file.  Comments
         for each edit must be placed just below the edit command line.

   results: running commentary of the processing of the sequences.

      The following changes are made:
      1.  Each sequence is edited according to instructions in todp.
      2.  Each sequence is converted to lower case.
      3.  The letter 'n' is converted to 'x'.
      4.  When there is exactly one copy of R1 and one copy of R2,
          the region between R1 and R2 is printed (including R1 and R2).
          Otherwise, the entire original sequence is printed.
      5.  The sequence complement is printed if necessary to assure that R1
          is printed before R2.  The program will print the original
          sequence if R1 and R2 cannot be found on the complement.

      The sequence is then joined to the data from ssb, and the results printed.

   summary: summary of the results.

   db: The sequences from abi are reformed into the database format needed
      by the sites program.

   output: messages to the user

   Convert output sequence from ABI sequencing machine into format usable
   by the sites program.



see also
   sites.p, makedate.p, dotod

   Thomas Dana Schneider


technical notes

(* end module describe.tod *)
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