![[ACEDB 4_9 DOCUMENTATION]](../acedb-logo.gif){kind=logo}
ACEDB Version 4_9
User Guide To ACEDB ace2line & line2ace utilities
Originally written byCornel Lee & Dave Matthews <matthews@greengenes.cit.cornell.edu>, 1992
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
Ed Griffiths <edgrif@sanger.ac.uk> Last modified: Fri Feb 15 09:45:15 GMT 2002