# ------------------------------------------------------------------------------------
# configuration files for the program arka, 23 03 2001
# ------------------------------------------------------------------------------------
# FIRST PART: global configuration file

file_history_size=5
command_history_size=20

# ------------------------------------------------------------------------------------
# SECOND PART: global program descriptions
# This part contains descriptions of the command line utilities arka is supposed
# to run. You can create your own descriptions and either put them in this file,
# or in a file in your HOME directory -- $HOME/.arka/programs
# I guess the format is easy enough to figure out.

# rc program options file for create
# just a joke and example
# start(program)(gp_create)(create)(utilities/optional)(create a useful program written in C)
#	start(options)
#	(-a)()()(use pure ANSI C)
#	(-n)(int)(0)(maximal number of bugs. If 0, there is no limit)
#	(-h)()()(print a brief description of a program and exit)
#	(-b)(float)(1)(bugs / 100 lines of code)
#	(-t)()()(use telepathy to determine what program should be written)
#	()(hidden)(%input)(file with specification)(required)
#end(options)
#
#start(description)
#The "create" program takes as input a description of a program and creates
#a program written in C which does the specified task. If you have troubles
#writing a specification, you might want to use the -t option.
#
#Here is an example description:
#--example start here:
#Umm, I need, umm, a program for parsing rcfiles. You know what I mean.
#--end of the example input file
#end(description)
#
#end(program)

start(program)(gp_acc)(acc)(DNA-RNA/statistics)(Encoding and autocrosscorrelating sequences)
	start(options)
		(-e)()()(encode only, do not compute the ACC)
		(-l)(int)()(print a header with variable descriptions for sequence length equal to [value])
		(-p)(int)()(crossterm to position [value])
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_dimer)(dimer)(DNA-RNA/statistics)(count frequencies of nucleotide pairs)
	start(options)
		(-l)(int)(0(distance between nucleotides)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(invisible)(%input) 
	end(options) 

	start(description)
	end(description)
end(program)


start(program)(gp_pattern)(pattern)(DNA-RNA/statistics)(count frequencies of patterns in DNA/RNA sequences)
	start(options)
		(-l)(int)(3)(length of the pattern)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_scan)(scan)(DNA-RNA/statistics)(Compute auto-cross-correlation profiles)
	start(options)
		(-l)(int)()(set lag to value)
		(-w)(int)()(set window width)
		(-s)()()(print also the sequence)
		(-p)()()(print also the lagged parameters)
		(-z)(int)()(value is the number of the first variable descriptor)
		(-Z)(int)()(value is the number of the second variable descriptor)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_tm)(tm)(DNA-RNA/properties)(Determine the Tm of a sequence)
	start(options)
		(-t)()()(use the 4*GC+2*AT thumb rule)
		(-s)()()(use symmetry correction for self complementary molecules)
		(-M)(float)()(set nucleic acid concentration to [value] mM)
		(-c)(float)()(set salt concentration to [value] M)
		(-N)()()(show sequence names)
		(-H)()()(run in HTML mode)
		(-q)()()(run in quiet mode)
		(-d)()()(turn on debugging)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_cusage)(cusage)(proteins)(Print out codon usage of sequence/s)
	start(options)
		(-c)(file)()(read the optional codon usage table)
		(-o)()()(print only the codon table)
		(-n)()()(output is a *N*icely formated codon table)
		(-u)()()(output is an *U*gly list of codons)
		(-H)()()(run in HTML mode (see manual))
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_findorf)(findorf)(proteins)(Print ORFs found in a sequence)
	start(options)
		(-m)(int)(100)(set minimal ORF length to value)
		(-M)(int)()(set maximal ORF length to value [default - unlimited])
		(-o)(string)()(s: print the ORF protein sequences; n: show the ORF positions)
		(-c)(file)()(read the optional codon usage table)
		(-p)(string)()(n: will print out a formated codon table & exit; u: will print out the codon table & exit)
		(-H)()()(run in HTML mode)
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_matrix)(matrix)(DNA-RNA/search)(Search for promoters using the Hertz matrix)
	start(options)
		(-M)()()(computate a new matrix)
		(-m)(file)()(take the matrix values from file m_file)
		(-G)(float)()(adjust matrix to GC contents of [value] %)
		(-g)()()(ignore gap penalties)
		(-t)()()(assume that the transcription start is experimentally defined)
		(-T)(float)()(set the treshold value (default -99))
		(-X)(string)()(limit=value. Set gap limits. 'limit' can be 'min1', 'max1', 'min10', 'max10'.)
		(-D)(file)()(read GC distribution from a file)
		(-H)()()(format output in HTML)
		(-N)()()(sequence names will be shown)
		(-S)()()(do not show the sequences)
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-e)()()(suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_primer)(primer)(DNA-RNA/properties)(Calculate stem/loop and dimere structures of a primer)
	start(options)
		(-i)()()(print only the parameters for the single strongest structure [for each sequence, you will get the kcal/mol for both the strongest dimere and the strongest stem & loop structure])
		(-m)(int)()(set the maximal number of shown structures (0 for all))
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_seq2prot)(seq2prot)(DNA-RNA)(Convert DNA sequence to protein sequence)
	start(options)
		(-c)(file)()(read the optional codon usage table)
		(-l)()()(be liberal about stop / start codons)
		(-p)(string)()(n: will print out a nicely formated codon table & exit; u: will print out a simple codon table & exit)
		(-H)()()(run in HTML mode)
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_dimer)(dimer)(DNA-RNA/statistics)(count frequencies of nucleotide triplets)
	start(options)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_deform)(deform)(DNA-RNA/properties)(deformability scan)
	start(options)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_gc)(gc)(DNA-RNA/properties)(Determine the gc contents of sequence(s))
	start(options)
		(-t)()()(will calculate the total GC% of all read sequences)
		(-m)()()(will show only mean GC% of all read sequences)
		(-D)(int)()(for each sequence, a distribution of GC with window size equal to value is printed.)
		(-H)()()(run in HTML mode)
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_mkmtx)(mkmtx)(DNA-RNA/statistics)(Computate a nucleotide frequency matrix)
	start(options)
		(-a)()()(Instead of frequencies, print just the numbers of occurences)
		(-d)()()(print print lots of debugging information)
		(-g)(float)()(divide each frequency by the expected frequecy of the given nucleotide at the GC% [value])
		(-h)()()(print this help screen & exit)
		(-l)()()(do not apply a logarythmic scaling of the frequencies)
		(-v)()()(print version information & exit)
		(-H)()()(Use an output format suitable for embedding in HTML)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_qs)(qs)()(Quick sequence search)
	start(options)
		(-i)()()(query sequences are read from standard input)
		(-n)()()(allow not exact binding)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet; suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_shift)(shift)(DNA-RNA)(Printing shifted gene positions)
	start(options)
		(-3)()()(shift relative to sequence 3' end)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_digest)(digest)(DNA-RNA/properties)(Restriction site analysis)
	start(options)
		(-e)(file)()(use alternate enzyme file)
		(-o)(string)()(output type: a: ascii; p: position; s: sequences; f: fragments; l: lengths; n: number)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(string)()(enzyme name)(required)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_getseq)(getseq)(DNA-RNA)(Get a sequence fragment)
	start(options)
		(-r)()()(only reverse the sequence)
#		(-l)(file)()(take a list of sequences from file [name] (use '-' for standard input))
		(-n)(string)()(use alternate name for the sequence)
#		(-H)()()(run in HTML mode (see man page))
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)

		()(int)()(from...)(required)
		()(int)()(...to)(required)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_randseq)(randseq)(DNA-RNA)(Generate random sequences)
	start(options)
		(-l)(int)()(random sequence length)
		(-n)(int)()(number of generated sequences)
		(-q)()()(run in quiet mode)
		(-v)()()(print version information & exit)
		(-h)()()(print this help screen & exit)
		(-H)()()(output in HTML)
		(-d)()()(turn on debugging)


		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)


start(program)(gp_slen)(slen)(DNA-RNA/statistics)(Print out sequence length/s)
	start(options)
		(-m)()()(print mean length and SE)
		(-v)()()(print version information & exit)
		(-H)()()(run in HTML mode)
		(-d)()()(print lots of debugging info)
		(-h)()()(print this help screen & exit)
		(-q)()()(quiet, suppress error messages)
		()(invisible)(%input) 
	end(options)

	start(description)
	end(description)
end(program)

