--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/doc/text/gcodoncompiler.txt	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,213 @@
+                                 gcodoncompiler
+Function
+
+   Calculate various kinds of amino acid and codon usage data
+
+Description
+
+   gcodoncompiler calculates various kinds of amino acid and codon usage data.
+   The following values are calculable:
+      A0: Absolute amino acid frequency
+      A1: Relative amino acid frequency
+      C0: Absolute codon frequency
+      C1: Relative codon frequency in a complete sequence
+      C2: Relative codon frequency in each amino acid
+      C3: Relative synonymous codon usage
+      C4: Relative adaptiveness
+      C5: Maximum or minor codon
+
+   For amino acids unpresent in a gene, C2-C3 does not calculate the values.
+   By using R* in place, such values are hypothesized that alternative
+   synonymous codons are used with equal frequency.
+    
+   G-language SOAP service is provided by the
+   Institute for Advanced Biosciences, Keio University.
+   The original web service is located at the following URL:
+
+   http://www.g-language.org/wiki/soap
+
+   WSDL(RPC/Encoded) file is located at:
+
+   http://soap.g-language.org/g-language.wsdl
+
+   Documentation on G-language Genome Analysis Environment methods are
+   provided at the Document Center
+
+   http://ws.g-language.org/gdoc/
+
+Usage
+
+Here is a sample session with gcodoncompiler
+
+% gcodoncompiler refseqn:NC_000913
+Calculate various kinds of amino acid and codon usage data
+Codon usage output file [nc_000913.gcodoncompiler]: 
+
+   Go to the input files for this example
+   Go to the output files for this example
+
+Command line arguments
+
+   Standard (Mandatory) qualifiers:
+  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
+                                  format, or reference (input USA)
+  [-outfile]           outfile    [*.gcodoncompiler] Codon usage output file
+
+   Additional (Optional) qualifiers: (none)
+   Advanced (Unprompted) qualifiers:
+   -translate          boolean    [N] Include to translate using standard
+                                  codon table
+   -startcodon         boolean    [N] Include to include start codon
+   -stopcodon          boolean    [N] Include to include stop codon
+   -delkey             string     [[^ACDEFGHIKLMNPQRSTVWYacgtU]] Regular
+                                  expression to delete key (i.e. amino acids
+                                  and nucleotides) (Any string)
+   -data               menu       [R0] Kinds of codon usage data. R*
+                                  hypothesizes amino acids which are not
+                                  present in the gene (Values: A0 (Absolute
+                                  amino acid frequency ('AA')); A1 (Relative
+                                  amino acid frequency ('RAAU')); C0 (Absolute
+                                  codon frequency ('AF')); C1 (Relative codon
+                                  frequency in a complete sequence); C2
+                                  (Relative codon frequency in each amino acid
+                                  ('RF')); C3 (Relative synonymous codon
+                                  usage ('RSCU')); C4 (Relative adaptiveness);
+                                  i.e., ratio to maximum of minor codon ('W')
+                                  C5 (Maximum (1) or minor (0) codon); R0
+                                  (Absolute codon frequency ('AF')); R1
+                                  (Relative codon frequency in a complete
+                                  sequence); R2 (Relative codon frequency in
+                                  each amino acid ('RF')); R3 (Relative
+                                  synonymous codon usage ('RSCU')); R4
+                                  (Relative adaptiveness); i.e., ratio to
+                                  maximum of minor codon ('W') R5 (Maximum (1)
+                                  or minor (0) codon))
+   -[no]accid          boolean    [Y] Include to use sequence accession ID as
+                                  query
+
+   Associated qualifiers:
+
+   "-sequence" associated qualifiers
+   -sbegin1            integer    Start of each sequence to be used
+   -send1              integer    End of each sequence to be used
+   -sreverse1          boolean    Reverse (if DNA)
+   -sask1              boolean    Ask for begin/end/reverse
+   -snucleotide1       boolean    Sequence is nucleotide
+   -sprotein1          boolean    Sequence is protein
+   -slower1            boolean    Make lower case
+   -supper1            boolean    Make upper case
+   -scircular1         boolean    Sequence is circular
+   -sformat1           string     Input sequence format
+   -iquery1            string     Input query fields or ID list
+   -ioffset1           integer    Input start position offset
+   -sdbname1           string     Database name
+   -sid1               string     Entryname
+   -ufo1               string     UFO features
+   -fformat1           string     Features format
+   -fopenfile1         string     Features file name
+
+   "-outfile" associated qualifiers
+   -odirectory2        string     Output directory
+
+   General qualifiers:
+   -auto               boolean    Turn off prompts
+   -stdout             boolean    Write first file to standard output
+   -filter             boolean    Read first file from standard input, write
+                                  first file to standard output
+   -options            boolean    Prompt for standard and additional values
+   -debug              boolean    Write debug output to program.dbg
+   -verbose            boolean    Report some/full command line options
+   -help               boolean    Report command line options and exit. More
+                                  information on associated and general
+                                  qualifiers can be found with -help -verbose
+   -warning            boolean    Report warnings
+   -error              boolean    Report errors
+   -fatal              boolean    Report fatal errors
+   -die                boolean    Report dying program messages
+   -version            boolean    Report version number and exit
+
+Input file format
+
+   The database definitions for following commands are available at
+   http://soap.g-language.org/kbws/embossrc
+
+   gcodoncompiler reads one or more nucleotide sequences.
+
+Output file format
+
+   The output from gcodoncompiler is to a plain text file.
+
+   File: nc_000913.gcodoncompiler
+
+Sequence: NC_000913
+Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag
+26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,
+
+
+Data files
+
+   None.
+
+Notes
+
+   None.
+
+References
+
+   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
+      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
+      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
+
+   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
+      large-scale analysis of high-throughput omics data, J. Pest Sci.,
+      31, 7.
+
+   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
+      Analysis Environment with REST and SOAP Web Service Interfaces,
+      Nucleic Acids Res., 38, W700-W705.
+
+Warnings
+
+   None.
+
+Diagnostic Error Messages
+
+   None.
+
+Exit status
+
+   It always exits with a status of 0.
+
+Known bugs
+
+   None.
+
+See also
+
+   gaminoinfo Prints out basic amino acid sequence statistics
+   gaaui      Calculates various indece of amino acid usage
+
+Author(s)
+
+   Hidetoshi Itaya (celery@g-language.org)
+   Institute for Advanced Biosciences, Keio University
+   252-0882 Japan
+
+   Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
+   Institute for Advanced Biosciences, Keio University
+   252-0882 Japan
+
+History
+
+   2012 - Written by Hidetoshi Itaya
+   2013 - Fixed by Hidetoshi Itaya
+
+Target users
+
+   This program is intended to be used by everyone and everything, from
+   naive users to embedded scripts.
+
+Comments
+
+   None.
+