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 *)
(*
name
   bk2seq: takes a book file and makes it a protseq file.

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

files
   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

description
   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.

documentation
   none

author
   R. Michael Stephens

bugs
   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 *)
{This manual page was created by makman 1.44}
{created by htmlink 1.55}
National Cancer Institute    National Institutes of Health    Health and Human Services    USA Gov - Official Web Portal    Viewing Files    Accessibility