--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/doc/text/gbasecounter.txt	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,205 @@
+                                  gbasecounter
+Function
+
+   Creates a position weight matrix of oligomers around start codon
+
+Description
+
+   This function creates a position weight matrix (PWM) of
+   oligomers of specified length around the start codon of all
+   genes in the given genome.
+    
+   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 gbasecounter
+
+% gbasecounter refseqn:NC_000913
+Creates a position weight matrix of oligomers around start codon
+Weight matrix output file [nc_000913.gbasecounter]: 
+
+   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    [*.gbasecounter] Weight matrix output file
+
+   Additional (Optional) qualifiers: (none)
+   Advanced (Unprompted) qualifiers:
+   -position           selection  [start] Either 'start' (around start codon)
+                                  or 'end' (around stop codon) to create the
+                                  PWM
+   -patlen             integer    [3] Length of oligomer to count (Any integer
+                                  value)
+   -upstream           integer    [30] Length upstream of specified position
+                                  to create PWM (Any integer value)
+   -downstream         integer    [30] Length downstream of specified position
+                                  to create PWM (Any integer value)
+   -[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
+
+   gbasecounter reads one or more nucleotide sequences.
+
+Output file format
+
+   The output from gbasecounter is to a plain text file.
+
+   File: nc_000913.gbasecounter
+
+Sequence: NC_000913
+Pattern,30,29,28,27,26,25,24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0,-1,-2,-3,-4,-5,-6,-7,-8,-9,-10,-11,-12,-13,-14,-15,-16,-17,-18,-19,-20,-21,-22,-23,-24,-25,-26,-27,-28,-29,-30
+aaa,0,1,199,111,104,139,94,103,99,44,42,26,75,103,107,95,107,103,102,82,91,71,73,81,86,80,74,74,78,65,69,65,31,41,68,51,61,83,55,67,92,55,71,89,60,77,100,59,87,123,97,105,141,83,117,180,154,203,262,2,0
+aac,2,0,0,63,104,56,67,64,28,34,22,12,17,37,43,59,61,71,54,42,62,59,63,52,56,61,48,55,56,52,38,30,34,54,36,42,43,33,49,49,36,43,58,37,53,62,46,47,79,38,52,72,58,52,89,74,83,91,68,2,1
+aag,0,0,17,46,38,57,56,44,25,44,43,170,162,125,92,70,61,50,42,46,21,22,43,39,29,35,39,34,28,26,30,25,9,43,31,12,55,33,13,66,21,21,50,30,21,55,31,21,47,38,16,55,35,23,63,96,31,51,71,0,0
+aat,1,565,4,56,124,45,83,74,63,42,24,24,20,27,59,71,54,74,66,71,67,52,58,77,61,52,57,49,56,71,61,34,33,24,40,38,30,43,46,25,48,56,35,58,51,33,47,71,46,70,77,60,74,74,73,83,69,61,110,0,1
+aca,0,1,92,73,39,69,39,24,31,31,16,19,34,64,61,63,65,56,42,60,45,66,38,45,46,41,49,40,51,43,39,20,34,29,23,26,28,34,35,26,35,39,30,28,48,26,28,53,35,36,59,42,53,46,64,56,62,44,55,0,0
+acc,2,2,0,81,37,19,28,19,15,8,12,7,7,14,22,27,30,24,31,23,30,27,34,27,30,22,25,42,34,29,25,41,23,32,44,19,32,51,21,19,50,23,24,52,30,31,56,25,31,55,30,25,35,30,32,53,20,21,48,0,2
+acg,0,0,21,38,23,38,32,25,13,18,12,15,34,29,34,37,25,31,25,34,30,20,22,24,40,22,24,30,34,29,25,29,25,34,41,23,32,25,36,44,28,32,40,32,23,28,40,30,25,36,39,32,28,40,38,39,45,30,33,0,0
+act,0,0,1,57,35,14,30,29,21,9,6,9,9,10,17,38,28,35,30,37,41,46,38,43,39,31,31,31,30,32,27,18,55,24,20,32,16,25,32,24,31,44,14,33,43,12,35,60,24,40,58,19,36,71,22,44,46,13,45,3,1
+
+   [Part of this file has been deleted for brevity]
+
+tcg,0.000,0.000,0.347,0.255,0.301,0.764,0.347,0.232,0.162,0.093,0.093,0.278,0.347,0.370,0.370,0.440,0.556,0.394,0.486,0.440,0.417,0.347,0.370,0.463,0.417,0.695,0.394,0.671,0.533,0.579,0.602,0.347,0.695,1.598,0.556,0.648,1.366,0.394,0.463,1.505,0.579,0.810,1.320,0.278,0.810,1.065,0.533,0.579,0.972,0.255,0.787,1.158,0.440,0.787,0.602,0.255,0.625,0.463,0.347,0.000,0.000
+tct,0.000,0.046,0.000,0.671,0.764,0.394,0.278,0.347,0.278,0.116,0.116,0.162,0.255,0.162,0.486,0.648,0.533,0.625,0.741,0.718,0.903,0.834,0.880,0.857,0.741,0.857,0.671,0.648,0.857,0.695,0.625,0.440,0.880,0.463,0.556,1.111,0.509,0.579,1.227,0.556,0.370,1.135,0.671,0.648,1.250,0.834,0.509,1.273,0.440,0.718,0.972,1.042,0.648,0.926,0.533,0.625,0.556,0.185,1.690,0.000,0.000
+tga,0.000,0.000,2.315,0.463,1.227,1.297,1.088,0.949,0.625,0.417,1.065,0.903,1.737,1.667,1.042,1.158,1.366,1.320,1.227,1.158,0.926,1.459,1.181,0.810,1.366,0.972,0.972,1.111,0.764,0.787,1.227,0.000,1.598,1.250,0.000,1.482,1.181,0.000,1.459,1.389,0.000,1.783,1.297,0.000,1.505,1.482,0.023,1.343,1.690,0.000,1.690,1.204,0.000,1.389,0.949,0.000,2.408,0.996,0.000,0.023,24.311
+tgc,0.023,0.000,0.000,0.394,0.996,0.579,0.787,0.556,0.208,0.185,0.208,0.116,0.278,0.324,0.394,0.834,0.486,0.394,0.718,0.556,0.509,0.857,0.509,0.625,0.810,0.741,0.695,0.834,0.625,0.787,1.158,0.347,1.158,1.621,0.394,1.667,1.204,0.347,1.551,1.320,0.417,1.088,1.065,0.232,1.320,1.042,0.139,1.204,0.996,0.208,0.996,0.602,0.139,0.648,0.764,0.069,0.857,0.394,0.023,0.000,7.803
+tgg,0.000,0.023,0.069,0.208,0.370,0.509,0.486,0.417,0.394,0.671,1.343,1.713,1.621,1.482,0.810,0.834,0.718,0.301,0.463,0.509,0.509,0.741,0.579,0.509,0.625,0.486,0.509,0.625,0.625,0.533,0.857,0.996,0.718,1.968,1.042,0.880,1.760,0.671,0.949,1.459,0.556,0.787,0.903,0.718,0.695,1.273,0.533,0.440,0.648,0.880,0.417,0.718,0.648,0.278,0.625,0.463,0.440,0.486,0.116,0.023,11.021
+tgt,0.023,0.880,0.023,0.533,1.135,0.301,0.440,0.602,0.417,0.208,0.232,0.185,0.185,0.278,0.370,0.440,0.533,0.556,0.648,0.764,0.509,0.926,0.579,0.718,0.880,0.695,0.718,0.741,0.741,0.579,0.625,0.278,1.158,0.857,0.278,0.972,0.718,0.324,0.926,0.695,0.463,1.111,0.834,0.162,1.482,0.787,0.278,1.065,0.695,0.278,1.042,0.695,0.208,0.903,0.718,0.139,0.857,0.232,0.093,0.023,7.340
+tta,0.000,0.000,6.506,0.648,0.810,1.829,1.320,0.602,0.486,0.509,0.255,0.347,0.301,0.834,1.320,1.459,1.412,1.667,1.644,1.852,1.667,1.574,1.366,1.042,1.204,1.621,1.505,1.227,1.436,1.088,1.273,1.343,0.486,1.158,1.042,0.440,1.135,1.389,0.370,1.273,1.574,0.486,1.875,1.505,0.463,1.991,1.875,0.533,2.362,2.061,0.324,2.084,2.200,0.509,1.505,1.320,0.463,1.366,0.648,0.000,0.069
+ttc,0.000,0.000,0.000,0.648,0.417,0.695,0.764,0.347,0.301,0.278,0.208,0.023,0.232,0.533,0.718,0.718,0.903,1.042,1.158,0.880,1.158,1.065,0.903,0.834,1.343,0.996,0.926,0.810,0.741,0.834,1.042,0.926,0.579,1.088,0.695,0.695,1.297,0.741,0.741,1.111,0.926,0.787,1.366,0.695,0.857,1.412,0.648,0.834,1.111,0.440,0.602,1.250,1.019,1.135,0.787,0.440,0.880,0.509,0.370,0.000,0.000
+ttg,0.857,0.023,0.255,0.394,0.556,1.111,0.533,0.463,0.417,0.185,0.232,0.533,0.602,1.042,0.718,0.695,1.135,0.972,0.857,0.926,0.787,0.671,1.320,0.695,0.903,1.204,0.880,0.764,0.926,0.741,0.718,1.019,0.347,1.551,1.042,0.370,2.014,0.834,0.463,2.061,0.880,0.278,2.014,0.857,0.208,2.593,0.741,0.278,1.922,0.764,0.417,2.130,0.834,0.208,1.111,0.394,0.093,1.111,0.417,0.000,0.023
+ttt,0.023,0.440,0.093,1.598,1.181,1.320,1.829,1.343,0.648,0.370,0.394,0.278,0.185,0.440,1.135,1.574,1.667,1.945,2.315,2.362,2.431,2.501,2.107,2.362,1.806,2.014,2.292,2.014,1.598,1.760,1.829,1.389,1.505,1.042,1.343,1.297,0.926,1.528,1.574,1.227,1.482,1.737,1.389,1.667,1.922,1.389,1.945,1.922,1.343,1.806,1.760,1.389,2.014,1.760,1.065,0.949,1.111,0.625,1.227,0.023,0.023
+
+
+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
+
+   gbasezvalue Extracts conserved oligomers per position using Z-score
+   gviewcds    Displays a graph of nucleotide contents around start and stop
+               codons
+
+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.
+