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{ version = 2.74; (* of makebk.p 2017 Oct 11}
(* begin module describe.makebk *)
(*
name
makebk: make a book from a file of sequences.
synopsis
makebk(sequ: in, book: out, changes: out, output: out, input: intty)
files
sequ: file of raw sequences, each ending in a '.'; no characters are
allowed in this file except the bases (a,c,g,t,u) and period and blank.
Characters other than these will be converted to 'a' and the change
will be noted in the changes file. The bases can also be in capital
letters.
book: the output file containing the sequences and the necessary
information for it to be a proper book. the user types in the
required information after prompts from the program.
changes: Delila programs cannot handle sequences that have ambiguities
because Delila was designed on the assumption that people would
finish their sequences. Unfortunately this is not true, and the
databases contain bases other than acgt to indicate ambiguity.
These are converted to "a" and the cases are reported in this file.
NOTE: "u" is converted to "t".
output: for messages and queries to the user
input: interactive input.
Type a carriage return to start; this is (unfortunately) ignored.
Then the program asks:
Is this an insertion module (m), an independent book (b),
or an automatically generated book (a, z, g), using default values?
Choose the kind of output you want. An 'a' will give you an
automatically generated book, while 'z' will do the same but
it will first ask you which base is to be the zero coordinate
of each sequence. This allows one to shift the alignment.
If you do not chose the automatic route, you will be prompted
for all the parts of the book.
New as of 2005 Feb 7:
In the automatic route, names of pieces may follow the title.
On each line:
The key name is given.
a space is given
the rest of the line is the long name.
New as of 2011 Dec 01:
The option 'g' means that the user gives the:
title
organism
chromosome
piece
names and everything else is automatic.
description
Makebk takes a file of raw sequences (sequ) separated by periods
(.) and converts that into a proper delila book format, getting
the required information from the user. The user may also have
makebk fill in the piece information automatically, using
default values.
see also
Another program to convert a single sequence to a Delila book: rawbk.p
A program to list the contents of your new book: lister.p
This program evolved as an interactive one, but can be used
under Unix as if it had a parameter file. To do this, execute it
in this form:
makebk < makebkp
where makebkp is an example parameter file that will read
all sequences and give a simple title. It consists of three or
more lines:
this line is ignored.
a this line triggers automatic book generation
title This is the title
name1 first sequence name
name2 second sequence name
examples
makebkp for completely automatic generation (all lines between dashs):
-----
a
title
name1 first sequence name
name2 second sequence name
-----
makebkp for some user defined parts (all lines between dashs):
-----
g
hg19-chr1-TITLE
hg19-ORG
chr1-CHR
hg19-chr1-PIECE
-----
author
Gary Stormo and Tom Schneider
bugs
The delila system requires complete sequence. To handle sequences
with unknown bases, they are replaced with constant chreplace.
technical notes
The constant chreplace replaces all unidentified characters in the
sequence.
The constant maxnumberofchanges limits the maximum number of
changes reported. This avoids generation of huge files for
chromosomes with many changes. For example, human chromosome 1
in hg19 has over 23 million n's (23,970,002)! (That doesn't
seem "finished" to me!)
2016 Oct 06 On the p2c compiler the first piece was not getting a
name and then catal would object. The solution was to do some
extra readlns in Procedure autopiece. A longer term solution would
be to remove the 'input' file and replace it with direct reading of
makebkp. Scripts that use
makebk < makebkp
would then ignore the input file and use the makebkp file directly.
We never input data to makebk by hand and instead edit the makebkp
file. This would work except when one wants to make a more
sophisticated makebkp (instead of automatic piece names) the
question guidance would be lost.
*)
(* end module describe.makebk *)
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