User Guide To ACEDB ace2line & line2ace utilities

> ### ACEDB Version 4_9

> # User Guide To ACEDB ace2line & line2ace utilities

> ## Acknowledgements

> The scripts were written in 1992 by Cornel Lee at the Lawrence Berkeley Lab. His address at that time was clee@genome.lbl.gov.

> Dave Matthews kindly forwarded the scripts to be included with the AceDB CVS repository.

> ## Synopsis

> ace2line.awk converts ACEDB .ace files to tab-delimited tables. line2ace.awk performs the reverse conversion.

> Documentation is at the top of the scripts.

> ## Description

> This 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

> ### ACEDB Version 4_8

> Last modified: Fri Feb 15 09:45:15 GMT 2002