[ACEDB DOCUMENTATION]

ACEDB Tools

User Guide To Acedb Tools

Originally written by
Ed Griffiths <edgrif@sanger.ac.uk>, March 2000

Background

The ACEDB tools are a collection of shell, perl and python scripts and C executables that are useful for the curating/administration of databases. The tools can all be found in the /wtools directory.

The Tools

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Tools decriptions

Restriction2Motif

#
# awk script to convert ace2 Restriction objects to ace4 Motif
#

aceExtract

# perl script to extract objects from an ace file
#
# usage: aceExtract class:name acefile ...
#
# perl regexp allowed in name (but protect from shell globbing)
#

aceGetVersion

#
# Perl script to read the acedb kernel version from the source file that
# holds the version number:   aceversion.c
#
# The idea is that only the version.c source file will be altered when changing
# the ACEDB version number, then the scripts that produce the public tar files
# will use this script to get that version number.
#
# The script returns the version, release and update read from aceversion.c
# in the form:    _     e.g.  4_6d
#
# it must be given the name of the directory where aceversion.c can be found.
#

ace_perl

#  File: ace_perl.pl
#   Author: Jean Thierry-Mieg, Steve Rosen, Gabor Marth
# -------------------------------------------------------------------
#  This file is part of the client/server interface to
#       the ACEDB genome database package, written by
#  	Richard Durbin (MRC LMB, UK) rd@mrc-lmba.cam.ac.uk, and
#	Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.cnrs-mop.fr
#   Copyright (C) J Thierry-Mieg and R Durbin, 1989-
#
#  Description:
#  Exported functions:
#   ace_in, ace_new, ace_count, ace_table, ace_script
# -------------------------------------------------------------------

acecsplit

# This file is part of the IGD project
#
# Description: split a .ace file into parts according to mapping file
# usage: acecsplit [-c ] [-p ] [...]
# Inputs: .ace data from files or stdin
#         if option -c is given, then
#         split according to config file,
#         else split by class name
# Output: .ace data is distributed into files according to config
#         if  is given then all output files start with it,
#         default for  is "split."

acesplit

# read a .ace file and split it every n objects
# contributed by Detlef Wolf, DKFZ
#
# Fri Feb  3 10:54:04 MET 1995  dok256
# - comments may start anywhere on a line
# Thu Feb  2 10:28:53 MET 1995  dok256; bugs fixed:
# - DNA tags are no longer treated as objects
# - .ace commands -D -R -A are recognized
# - terminates even if last line of last file does not end with a newline

classCount

There is no help...sigh...

embl2ace

# script to process EMBL entry to ACEDB4 .ace file

fmap2_4

# Script to convert Sanger ace files containing Sequence/DNA
#   objects to ACEDB4 models.
# May assume sometimes layout of .ace file dumped from acedb.

homol2match

There is no help...sigh...

homonym

#
# Replacement of old homonym C program
#
# Format of homfile:
#	// any line starting with '//' is ignored
#	Full name 1 =
#	Variant A of 1
#	Variant B_of_1
#	Full_name 2 =
#	Variant of 2
#	etc.
# i.e. the correct names come first, followed by an '=' sign
# all names on subsequent lines up until the next '=' sign are treated 
# as homonyms.  NOTE THAT THIS IS DIFFERENT FROM THE OLD FORMAT.
#
# By default Author lines are substituted, but you can apply to any other 
# tag using option "-T tag"
#
# Option -c will just output information on changes that will be made
#
# Option -2 is like -T, but looks for items 2 in from the tag
#
# Lines ending with '// fix' will not be changed

$usage = "Usage: homonym [-T tag] [-c] [-2 tag] homfile [files]\n" ;

html2txt


Don't be fooled, this doesn't really translate html -> plain text !!

Now read on...


html2txt - decorate an html file with text characters for prettier plain text output.


     html2txt < inputfile > outputfile


This perl module decorates an HTML file in such a way that
when it is saved from Netscape (other browsers untested) as
plain text then headings will be underlined so they still
stand out in the text.

You have some html that you want to translate to text but you have
noticed that when you do this with Netscape ("Save as" menu option)
none of the headers are marked in any way. This script takes an
html file and adds underlining to headers using ordinary text
characters to produce a new decorated html file. View this new
file in Netscape and save it as plain text. If you now look at
the plain text file you will see that all the headings are now
underlined. (The script also marks bold text as well.)

e.g. headings:

<H1> A Heading </H1>

would become:

A Heading
*********

e.g. bold:

<B>Some text</B>

would become:

_Some text_


If you want more details then you can use the perl pod2XXX commands to
extract the man page in the html2txt perl script.

Currently this script is used to prepare a plain text version of
acedb monthly newsletter (which is in html).

modelcheck

To run the program:

> modelcheck models.wrm


Output is written densely to stdout so you will probably want to capture it into a file.

NOTE that you need python version 1.5 or later to run this script.

models2tags

# parse models.wrm and generate
# tags.tmp and classes.tmp from it

parsecode

You are beyond all help...

rm-O

#
# removes -O usersession data and big pointless keysets
# particularly good for dumps
#

rsort

#
# rsort was written to sort ace dump but
# is general enough to be used for
# other purposes.
#

split

 * Description: stand alone, will split big ace files in a naive way
"Usage split prefix, splits stdin into n files of max 10^5 lines called prefix.n

splitdump

#
# script to split up ACEDB dump output into classes
#

tace2table

# tace2table
#
#  tace dumps tables with ; separating the fields.
#
#  Typically : "E77B4";;"95-06-08";;;;
#
# Convert ;; to ;""; so don't lose fields when split
#

tagCount

No help here...

tagsInModel

#
# lists tags and classes used in a model
#

xcl

#-------------------------------------------------------------------
# Usage: xcl host port
#  example: xcl beta 20000100
#-------------------------------------------------------------------
# Description: 
#   Launches a graphic acedb xace working as a client on an ace-server
#

ACEDB Tools

Ed Griffiths <edgrif@sanger.ac.uk>
Last modified: Fri Feb 15 09:50:28 GMT 2002