Delila Program: bk2seq

bk2seq program

Documentation for the bk2seq program is below, with links to related programs in the "see also" section.

{   version = 1.13; (* of bk2seq.p 2008 Jul 29}

(* begin module describe.bk2seq *)
   bk2seq: takes a book file and makes it a protseq file.

   bk2seq(inst: in, book: in, bk2seqp: in,
          alprop: out, protseq: out, output: out)

   inst: delila instructions of the form 'get from 56 -5 to 56 +10;'
      (This file may be empty, in which case the sequences will be
      aligned by their 5' ends.)
   book: the book generated by delila using inst
   bk2seqp: parameters to control the program.
      If the file is empty, the protseq format is generated.
      If the file begins with the letter 'f', fasta format is generated.
   alprop: parameter file to control the alpro program so that alpro
      uses the correct alignment coordinates.
   protseq: the output file, usable by alpro and other programs.
   output: messages to the user

   This program simply takes a file in book format and converts it to protseq
   format. It was written mainly as an interface between books and those
   progams such as alpro and align that require protseq format.  Fasta
   format can be used by other programs.


   R. Michael Stephens

   User defined range is not yet implemented.

technical notes
   symbolsperline is a constant that determines the maximum
   number of symbols written per line to the protseq.

(* end module describe.bk2seq *)
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