@(#)client.doc	1.2 3/6/96
###################

aceclient command line parser
recognises in this order

host [-time_out time] [ -ace_out ] [ ace_in ] [-f filename args ]

ace_out and -f filenmae implies no banner etc

######################################
This is the aceserver menu:

static FREEOPT qmenu[] = 
{ 
  20,  "acedb",
  'x', "Quit :   Exits the program.       Any command can be abbreviated, $starts a subshell",
  'h', "Help : for further help",
  '?', "? : List of commands",
  'c', "Classes : Give a list of all the visible class names and how many  objects they contain.",
  'n', "Find class [name]: Creates a new current list with all objects from class, optionally matching name",
  'z', "Model class: Shows the model of the given class, useful before Follow or Where commands",
  'g', "Grep template: searches for *template* everywhere in the database",
  'u', "Undo : returns the current list to its previous state",
  'l', "List [template]: lists names of items in current list [matching template]",
  's', "Show [tag] : shows the [branch tag of] objects of current list",
  'i', "Is template : keeps in the active list only those objects whose name match the template",
  'r', "Remove template : removes from the active list only those objects whose name match the template",
  't', "Follow Tag : i.e. Tag Author gives the list of authors of the papers of the current list", 
  'q', "Where query_string : performs a complex query - 'help query_syntax' for further info",
  'w', "Write filename : acedump current list to file",
  'b', "Biblio : shows the associated bibliography",
  'd', "Dna : Fasta dump of related sequences",
  'a', "Array class:name format : formatted acedummp of A class object",
  'p', "Parse file : parses an aceFile, or stdio,  until \000 or EOF",
  'T', "Table-Maker file outputfile : Executes the file as a table-maker.def command file, outputs ",
} ;

static FREEOPT helpmenu[] =	/* no \n inside FREEOPT text (else rethink) */
{ 5, "helpmenu",
  1, "Tacedb : copyright etc", 
  2, "Query_syntax for the find command",
  3, "Useful_sequences : SL1 etc",
  4, "Clone_types used in the physical map (vector etc)",
  5, "DNA_and_amino_acids_nomenclature : codes for bases/amino acids and translation table",
} ;


######################################
This is a valid file for import:

// Hoping that my computer is running try the following
// that i develloped with Danielle
// ftp from ncbi my executable
// sparc.aceclient.Z

// uncompres it and type on your commnad line
// usage:
// "usage : aceclient host  [-time_out nn_in_seconds] [-ace_out] [-f reportfile parameters]\n",
// if filename is omitted, you run interactivelly
//
// for example try:
// aceclient 193.49.111.71 -f thisfilename genename

// 193.49.111.71 is my dec alpha in montpellier

// you will get a developped form of the gene
// embedded in the non // lines

// are pure comments
// %nn announces a parameter
// 
// %(command text) invokes the ace_server
// 
%(Find Gene %1) 

This is what we know on gene %1 // %1 represente le nom du gene


These are the known papers:%(Show Reference)

Or in a more standard blibliographic format:
%(Biblio)

These are the alleles %(Show Allele)
that's all, folks


All I know on tata box:
%(Grep tata) %(List)
# Bonsoir

// fin

######################################

this transmitted to the server the following orders:

(running in France:)

% bin.ALPHA_GCC/aceserver /home1/cele3
**** acedb network server: Version 3.4 en developement ****
Authors: Richard Durbin (MRC, UK) rd@mrc-lmb.cam.ac.uk
         Jean Thierry-Mieg (CNRS, France) mieg@kaa.cnrs-mop.fr
You may redistribute this program and database subject to the
conditions in the accompanying copyright file.  Anyone interested in
maintaining an up to date version should contact one of the authors
at the above email addresses.

 Database directory: /home1/cele3


 Find Gene unc-116
 Show Reference
 Biblio
 Show Allele
 Grep tata
 List

 Find Gene unc-116
 Show Reference
 Biblio
 Show Allele
 Grep tata
 List

######################################
Giving out here the following anser:


This is what we know on gene unc-116 


These are the known papers:


Locus : "unc-116"






Or in a more standard blibliographic format:


[wbg10.1p99]
a little uncoordinated genetics.

Thierry-Mieg D.
Worm Breeder's Gazette
[wm91p66]

MUTATIONS AFFECIING DEVELOPMENT OF THE EXCRETORY CANALS.

Buechner M, Plenefisch JD.



[wm91p130]

UNC-104: A NOVEL KINESIN FAMILY MEMBER?
Otsuka AJ, Tang LZ, Boontrakulpoontatwee P, Zhang YY, Whiteaker K, Allikian MJ.


[wbg11.4p68]
Unc-116 shares sequence homology with the C-terminal domain of the Drosophila Kinesin heavy chain

Patel N, Mancillas JR.
Worm Breeder's Gazette


These are the alleles 


Locus : "unc-116"





that's all, folks


All I know on tata box:

tata* 

Sequence : "CAL1"
Sequence : "COL"
Sequence : "GAPDH"
Sequence : "GSCYSP"
Sequence : "HIS10"
Sequence : "HIS12"
Sequence : "HSP3"
Sequence : "HSP16C"
Sequence : "METAL1A"
Sequence : "METAL2B"
Sequence : "MSP3L4"
Sequence : "MYOD"
Sequence : "MYUNC"
Sequence : "PGPAG"
Sequence : "PGPCG"
Sequence : "PIR:A47212"
Sequence : "SP:TF2D_DROME"
Sequence : "SP:TF2D_HUMAN"
Sequence : "SP:TF2D_MOUSE"
Sequence : "SP:TF2D_SCHPO"
Sequence : "SP:TF2D_XENLA"
Sequence : "SP:TF2D_YEAST"
Sequence : "TBP"
Sequence : "TC1"
Sequence : "UNC33G"
Sequence : "VIT1"
Sequence : "VIT1P"
Sequence : "VIT2"
Sequence : "VIT4"
Sequence : "VIT5"
Sequence : "VIT6"
Sequence : "VIT51"
Sequence : "VIT201"
Sequence : "VIT401"
Sequence : "VIT601"
Sequence : "VITELB"
Paper : "[cgc1535]"
Paper : "[cgc1621]"
Paper : "[cgc1823]"
Paper : "[medline120]"
System : "TATA_signal"



# Bonsoir