************************  GFA2    ********************************************

usage:./gfa -seq <input_fasta_filename> -out <output_file_prefix> [optional_switches]
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 GFA2 takes in a DNA sequence in fasta format and returns Gene Feature Format
 (.gff) and Tab Separated Value (.tsv) files containing the location and details of potential non-B DNA forming motifs. 
 
Required Switches:
	-seq <string>; The filename for the input DNA fasta file.
	-out <string>; The output filename prefix.
	Motif abbreviations and file extension are automatically appended.
 
Optional Integer Switches:  Each switch is followed by its default value.
		All values refer to sequential nucleotides.
		Note: if an integer switch is given, its associated value is required.
	-minGQrep <3>; The minimum number of consecutive G's to form a G run (no max).
	-maxGQspacer <7>; The maximum allowed distance between G runs (min of 1).
	-minMRrep <10>; The minimum length of half of a mirror repeat (no max).
	-maxMRspacer <100>; The c mirror repeat halves (min = 0).
	-minIRrep <6>; The minimum length of half of an inverted repeat (no max).
	-maxIRspacer <100>; The maximum allowed distance between inverted repeat halves (min = 0).
	-shortIRcut <9>; The maximum length of half of an inverted repeat for it to be considered "short".
	-shortIRspacer <4>; The maximum allowed distance between short inverted repeat halves (min = 0).
	-minDRrep <10>; The minimum length of half of a direct repeat.
	-maxDRrep <300>; The maximum length of half of a direct repeat.
	-maxDRspacer <100>; The maximum allowed distance between direct repeat halves (min = 0).
	-minATracts <3>; The minimum number of consecutive A Tracts to form an A-Phased Repeat.
	-minATractSep <10>; The minimum separation between A Tracts centers.
	-maxATractSep <11>; The maximum separation between A Tracts centers.
	-maxAPRlen <9>; The maximum number of consecutive As allowed in an A tract.
	-minAPRlen <3>; The minimum number of consecutive As allowed in an A tract.
	-minZlen <10>; The minimum length of Z-DNA alternating purine/pyramadine run (no max).
	-minSTR <1>; The minimum length of repeating element in short tandem repeats.
	-maxSTR <9>; The maximum length of repeating element in short tandem repeats.
	-minSTRbp <8>; The minimum overall length for qualification as a short tandem repeat.
	-minCruciformRep <6>; The minimum repeat length for IR to qualify as cruciform.
	-maxCruciformSpacer <4>; The maximum spacer length for IR to qualify as cruciform.
	-minTriplexYRpercent <10>; The minimum purine/pyramadine percent contend for MR to qualify as triplex.
	-maxTriplexSpacer <8>; The maximum spacer length for MR to qualify as triplex.
	-maxSlippedSpacer <0>; The maximum spacer length for DR to qualify as slipped.
 
Other Optional Switches: (not followed by values)
	-chrom <string>; An identifier for the input sequence, "chr1" for example.
	   If not given, the first word of the fasta title string is used
	-skipAPR; Do not search for A-Phased Repeats (bent DNA). 
	-skipSTR; Do not search for Short Tandem Repeats. 
	-skipDR; Do not search for Direct Repeats (slipped DNA). 
	-skipMR; Do not search for Mirror Repeats (triplex DNA). 
	-skipIR; Do not search for Inverted Repeats (cruciform DNA). 
	-skipGQ; Do not search for G-Quadruplexe motifs. 
	-skipZ; Do not search for Z DNA motifs. 
	-skipSlipped; Do not search for slipped subset of DRs. 
	-skipCruciform; Do not search for cruciform subset of IRs. 
	-skipTriplex; Do not search for triplex subset of MRs. 
	-skipWGET; Do not make wget call to php scripts to signify completion. 
	-doCHMOD; Run a system call to chomd command (664) on output files. 
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         EXAMPLE:
./gfa -skipWGET -seq gfa_test.fasta -out gfa_test
	The input sequence file is gfa_test.fasta
	There should be 14 output files (included in test_files.tar for comparison) using the default values
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 Author: Duncan E. Donohue, Ph.D.
 Expansion of work by Jack R. Collins, Ph.D.