# ACEDB User Group Newsletter - February 2002

If you want to have this newsletter mailed to you or you want to make comments/suggestions about the format/content then send an email to acedb@sanger.ac.uk.

In this issue: new builds of acedb for latest SGIs, some useful acedb data processing scripts, acedb incorporates the LGPL licence and some bug fixes.

## General News

This month once again sees us buried deep in the new SMap code, converting the virtual sequence building code to use the new tags while maintaining compatibility with the old Sequence tags. One more time, we hope to have working code sometime soon.

## New Features

### SGI builds of acedb

Acedb now builds on SGI Ultrix 6.5, to compile for this version of the operating system you should set the ACEDB_MACHINE environment variable to SGI_65_GCC.

Thanks to Jeroen van Gastel <Jeroen-van.Gastel@unilever.com> and Stefan Verhoeven <Stefan.Verhoeven@unilever.com> of Unilever for providing the necessary changes to the code and makefile.

### New/old acedb tool - ace2line & line2ace utilities

Dave Matthews recently sent me a couple of useful awk scripts for processing AceDB data prompted by a users question on the acedb newsgroup. Let us know (acedb@sanger.ac.uk) if they prove useful or have bugs or whatever.

Acknowledgements: The scripts were written in awk in 1992 by Cornel Lee at the Lawrence Berkeley Lab. (his address at that time was <clee@genome.lbl.gov>). Dave Matthews (<matthews@greengenes.cit.cornell.edu>) kindly forwarded the scripts to be included with the AceDB CVS repository.

Synopsisace2line.awk converts ACEDB .ace files to tab-delimited tables. line2ace.awk performs the reverse conversion. See also documentation at the top of the scripts.

DescriptionThis is a widely useful functionality and there is a script to do it. It was written for our project by Cornel Lee at LBL some years ago.

It's called ace2line.awk and its purpose is to select fields in arbitrary order from .ace file and create line-records.

The hard part about converting .ace data to CSV/tab-delimited is dealing with 1) multivalued fields and 2) compound (vector) fields. The script seems to do reasonable things for these.

A short example

    INPUT -
      Sequence :
      DNA_homol

      Sequence : "Contig5002"
      DNA_homol BE443570 Phrap 587 1 587 1 587
      DNA_homol BE446512 Phrap 200 1 200 1 200

      Sequence : "Contig5003
      DNA_homol BE492786 Phrap 456 1 456 1 456
      DNA_homol BF473179 Phrap 538 157 692 4 538
      DNA_homol BE444401 Phrap 629 382 1010 1 629

    OUTPUT -
      Sequence        DNA_homol
      Contig5002      BE443570 Phrap 587 1 587 1 587$BE446512 Phrap 200 1 200 1 200
      Contig5003      BE492786 Phrap 456 1 456 1 456$BF473179 Phrap 538 157 692 4 538$BE444401 Phrap 629 382 1010 1 629

and a longer one

    INPUT -
    /* Sample.ace: a sample input file for ace2line.awk */

     // Class Paper
    /***** Specification record for ace2nal.awk *****/

    Paper :

    Title
    Author

    Year

    /***** end of the spec record  *****/

    /************ .ace data ***********/
    Paper : "?Paper"

    Paper : "mazur-1987-aaaqb"
    Title	 "Acetolactate synthase, the target enzyme of the sulfonylurea \
    	herbicides"
    So	 \
    	"NATO-advanced-science-institutes-series-:-Series-A-:-Life-sciences \
    	(USA). (1987). v. 140 p. 339-349"
    DNAL	 "QH301.N32"
    Year	 1987
    Author	 "Mazur-B-J"
    Author	 "Falco-S-C"
    Author	 "Knowlton-S"
    Author	 "Smith-J-K"
    Language	 "English"

    Paper : "knowl-1988-aaauc"
    Title	 "Creation and field testing of sulfonylurea-resistant crops"
    So	 "Fraley,-R.T.; Frey,-N.M.; Schell,-J. (eds.). Genetic \
    	improvements of agriculturally important crops : progress and issues. \
    	Cold Spring Harbor, N.Y. (USA). Cold Spring Harbor Laboratory. 1988. \
    	p. 55-60"
    DNAL	 "QK981.5.G464"
    Year	 1988
    Author	 "Mazur-B-J"
    Author	 "Knowlton-S"
    Author	 "Arntzen-C-J"
    Language	 "English"

    Paper : "mazur-1987-aaadc"
    Title	 "Acetolactate synthase, the target enzyme of the sulfonylurea \
    	herbicides"
    So	 "Plant molecular biology. Proceedings of a NATO Advanced Study \
    	Institute, 10-19 June, 1987, Carlsberg Lab., Copenhagen, Denmark \
    	[edited by Wettstein, D. von; Chua, N. H.]. 1987, 339-349; 18 ref., \
    	in NATO ASI Series A, Life Sciences Vol. 140. New York, USA; Plenum \
    	Press"
    Year	 1987
    Author	 "Mazur-B-J"
    Author	 "Falco-S-C"
    Author	 "Knowlton-S"
    Author	 "Smith-J-K"
    Language	 "English"

    Paper : "mazur-1987-aaapv"
    Title	 "Isolation and characterization of plant genes coding for \
    	acetolactate synthase, the target enzyme for two classes of \
    	herbicides"
    So	 "Plant-physiology (USA). (Dec 1987). v. 85(4) p. 1110-1117"
    DNAL	 "450 P692"
    Year	 1987
    Author	 "Mazur-B-J"
    Author	 "Smith-J-K"
    Author	 "Chui-C-F"
    Language	 "English"

    Paper : "smith-1989-aaauz"
    Title	 "Functional expression of plant acetolactate synthase genes in \
    	Escherichia coli"
    So	 \
    	"Proceedings-of-the-National-Academy-of-Sciences-of-the-United-States-o\
    	f-America (USA). (Jun 1989). v. 86(11) p. 4179-4183"
    DNAL	 "500 N21P"
    Year	 1989
    Institution	 "Agric. Prod. Dep., E.I. du Pont de Nemours & Co., Exp. \
    	Stn. E402,Wilmington, DE 19880-0402, USA"
    Author	 "Mazur-B-J"
    Author	 "Smith-J-K"
    Author	 "Schloss-J-V"
    Type	 "Journal Article"
    Language	 "English"
    Keyword	 "algae"
    Keyword	 "Escherichia coli"
    Keyword	 "expression of cloned genes"
    Keyword	 "gene expression"
    Keyword	 "Gene manipulation"
    Keyword	 "Genetic engineering"
    Keyword	 "acetolactate synthase"

    Paper : "haugh-1987-aabsb"
    Title	 "AN ARABIDOPSIS ACETOLACTATE SYNTHASE GENE IN TOBACCO CONFERS \
    	RESISTANCE TO SULFONYLUREA HERBICIDES"
    Journal	 "INTERNATIONAL BOTANICAL CONGRESS ABSTRACTS"
    So	 "XIVTH INTERNATIONAL BOTANICAL CONGRESS, BERLIN, WEST GERMANY, \
    	JULY  24-AUGUST 1, 1987. INT BOT CONGR ABSTR 17. 1987. 71"
    Year	 1987
    Author	 "Mazur-B-J"
    Author	 "Smith-J-K"
    Author	 "Somerville-C-R"
    Author	 "Haughn-G-W"
    Keyword	 "selectable marker"
    Keyword	 "plant transformation"

    Paper : "chui--1987-aadad"
    Title	 "ISOLATION AND CHARACTERIZATION OF PLANT GENES CODING FOR \
    	ACETOLACTATE SYNTHASE THE TARGET ENZYME FOR TWO CLASSES OF HERBICIDES"
    Journal	 "PLANT PHYSIOLOGY (BETHESDA)"
    Year	 1987
    Volume	 85
    Page	 1110 1117
    Author	 "Mazur-B-J"
    Author	 "Smith-J-K"
    Author	 "Chui-C-F"
    Keyword	 "Nicotiana tabacum"
    Keyword	 "yeast"
    Keyword	 "bacterial isozymes"
    Keyword	 "homology"
    Keyword	 "valine"
    Keyword	 "isoleucine"
    Keyword	 "leucine"
    Keyword	 "sulfonyl urea"
    Keyword	 "imidazolinones"
    Keyword	 "amino acid sequences"

    Paper : "mazur-1989-aadew"
    Title	 "FUNCTIONAL EXPRESSION OF PLANT ACETOLACTATE SYNTHASE GENES IN \
    	ESCHERICHIA-COLI"
    Journal	 "PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE \
    	UNITED STATES OF AMERICA"
    Year	 1989
    Volume	 86
    Page	 4179 4183
    Author	 "Mazur-B-J"
    Author	 "Smith-J-K"
    Author	 "Schloss-J-V"
    Keyword	 "EC 4.1.3.18"
    Keyword	 "chloroplast"
    Keyword	 "transit peptide"
    Keyword	 "herbicide"
    Keyword	 "amino acid biosynthesis"

    Paper : "marti-1987-aabrk"
    Title	 "TRANSCRIPTION OF ACETOLACTATE SYNTHASE GENES IN HIGHER PLANTS"
    Journal	 "PLANT PHYSIOLOGY (BETHESDA)"
    So	 "ANNUAL MEETING OF THE AMERICAN SOCIETY OF PLANT PHYSIOLOGISTS, \
    	ST.  LOUIS, MISSOURI, USA, JULY 19-23, 1987. PLANT PHYSIOL (BETHESDA) \
    	83 (4  SUPPL.). 1987. 16"
    Year	 1987
    Author	 "Smith-J-K"
    Author	 "Martin-S-J"
    Keyword	 "Nicotiana tabacum"
    Keyword	 "regulation"

    Paper : "hepbu-1987-aaaqc"
    Title	 "DNA methylation in plants"
    So	 "Developmental-genetics (USA). (1987). v. 8(5/6) p. 475-493"
    DNAL	 "QH426.D32"
    Year	 1987
    Author	 "Hepburn-A-G"
    Author	 "Belanger-F-C"
    Author	 "Mattheis-J-R"
    Language	 "English"

    Paper : "belan-1987-aadaj"
    Title	 "DNA methylation in plants"
    Journal	 "DEVELOPMENTAL GENETICS"
    Year	 1987
    Volume	 8
    Page	 475 494
    Author	 "Hepburn-A-G"
    Author	 "Belander-F-C"
    Author	 "Mattheis-J-B"
    Keyword	 "Zea sp"

     /*#########################*/

    OUTPUT -
    Paper	Title	Author	Year

    ?Paper
    mazur-1987-aaaqb	Acetolactate synthase, the target enzyme of the sulfonylurea herbicides	Mazur-B-J$Falco-S-C$Knowlton-S$Smith-J-K	1987
    knowl-1988-aaauc	Creation and field testing of sulfonylurea-resistant crops	Mazur-B-J$Knowlton-S$Arntzen-C-J	1988
    mazur-1987-aaadc	Acetolactate synthase, the target enzyme of the sulfonylurea herbicides	Mazur-B-J$Falco-S-C$Knowlton-S$Smith-J-K	1987
    mazur-1987-aaapv	Isolation and characterization of plant genes coding for acetolactate synthase, the target enzyme for two classes of herbicides	Mazur-B-J$Smith-J-K$Chui-C-F	1987
    smith-1989-aaauz	Functional expression of plant acetolactate synthase genes in Escherichia coli	Mazur-B-J$Smith-J-K$Schloss-J-V	1989
    haugh-1987-aabsb	AN ARABIDOPSIS ACETOLACTATE SYNTHASE GENE IN TOBACCO CONFERS RESISTANCE TO SULFONYLUREA HERBICIDES	Mazur-B-J$Smith-J-K$Somerville-C-R$Haughn-G-W	1987
    chui--1987-aadad	ISOLATION AND CHARACTERIZATION OF PLANT GENES CODING FOR ACETOLACTATE SYNTHASE THE TARGET ENZYME FOR TWO CLASSES OF HERBICIDES	Mazur-B-J$Smith-J-K$Chui-C-F	1987
    mazur-1989-aadew	FUNCTIONAL EXPRESSION OF PLANT ACETOLACTATE SYNTHASE GENES IN ESCHERICHIA-COLI	Mazur-B-J$Smith-J-K$Schloss-J-V	1989
    marti-1987-aabrk	TRANSCRIPTION OF ACETOLACTATE SYNTHASE GENES IN HIGHER PLANTS	Smith-J-K$Martin-S-J	1987
    hepbu-1987-aaaqc	DNA methylation in plants	Hepburn-A-G$Belanger-F-C$Mattheis-J-R	1987
    belan-1987-aadaj	DNA methylation in plants	Hepburn-A-G$Belander-F-C$Mattheis-J-B	1987

## Articles

### File permissions for wscripts scripts

If you are a database administrator or you are involved in the setting up of a wscripts directory within a database then you should read this note.

The scripts in wscripts are called from various parts of the acedb code, for this to work the scripts themselves must be executable by the user running the script. A recent user problem turned out to be caused by a script not having the execute flag turned on (you can see this using the "ls-l" command). You will probably want to make sure that anyone can execute the script and you can do this by:

``

    cd wscripts
    chmod ugo+x the_script_name

This will allow anyone to run the script, if you want to restrict the script to the user and group for the script you should specify just "ug" instead of "ugo" in the above example.

### AceDB changes its license

Acedb has been licensed under the Gnu Public License (GPL) for some years now which means that the code is freely available to all but cannot be filched for commercial gain and that authors must be acknowledged. This license has a major drawback however in that it effectively prevents the use of the licensed code in any form in commercial software. As this was restricting the spread of GPL code (synonymous with "open source software"), a new less restrictive license was produced which meant libraries consisting of GPL code could be incorporated into programs sold for profit provided the inclusion of GPL code was acknowledged.

Acedb has now moved on to this less restrictive form of licensing allowing greater use of the code for commercial programs.

## Bugs Fixed

### Tablemake bug in batch mode.

There was a bug in tablemaker which caused the first line of the table to clash with the prompt in batch mode.

### Bug in flags to "dna" command in tace.

The bug in tace that caused the "-mismatch" flag to be interpreted as a filename has been fixed.

### Crash in gene finder.

A bug in genefinder caused it to crash if used on objects where no dna was available, now an error message is displayed.

### Grim CYGWIN bug.

Set a registry key to increase available cygwin heap space from the deafult 128MB. currently tp 256MB, which is enough for wormbase.

## February monthly build not available.

Apologies, once again there was no build this month due to the major SMap development work.

Last modified: Thu May 16 11:51:56 2002