--- a/GEMBASSY-1.0.3/doc/text/gentrez.txt	Fri Jun 26 05:20:29 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,182 +0,0 @@
-                                    gentrez
-Function
-
-   Search NCBI Entrez
-
-Description
-
-   gentrez searches NCBI Entrez with keyword through EUtilities. 
-   This is intended for quick lookup through the command line
-   so only top ten hits are reported.
-    
-   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 gentrez
-
-% gentrez genome 'Escherichia coli'
-Search NCBI Entrez
-ASCII text output file [genome.Escherichia coli.gentrez]: 
-
-   Go to the input files for this example
-   Go to the output files for this example
-
-Command line arguments
-
-   Standard (Mandatory) qualifiers:
-  [-database]          string     [pubmed] NCBI database to search (Any
-                                  string)
-  [-query]             string     Query to search (Any string)
-  [-outfile]           outfile    [$(database).$(query).gentrez] ASCII text
-                                  output file
-
-   Additional (Optional) qualifiers: (none)
-   Advanced (Unprompted) qualifiers: (none)
-   Associated qualifiers:
-
-   "-outfile" associated qualifiers
-   -odirectory3        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
-
-   gentrez reads no file input.
-
-Output file format
-
-   The output from gentrez is to a plain text file.
-
-   File: genome.Escherichia coli.gentrez
-
-    53 entries found in NUCLEOTIDE: (Showing up to 10 hits)
-
-     1. Accession Number:   NZ_AKBV01000001
-        Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome
-
-     2. Accession Number:   NC_018658
-        Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome
-
-     3. Accession Number:   NC_012971
-        Escherichia coli BL21(DE3) chromosome, complete genome
-
-     4. Accession Number:   NC_017635
-        Escherichia coli W chromosome, complete genome
-
-     5. Accession Number:   NC_018650
-        Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome
-
-     6. Accession Number:   NC_018661
-        Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome
-
-     7. Accession Number:   NC_017906
-        Escherichia coli Xuzhou21 chromosome, complete genome
-
-     8. Accession Number:   NC_017634
-        Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome
-
-     9. Accession Number:   NC_017656
-        Escherichia coli O55:H7 str. RM12579 chromosome, complete genome
-
-    10. Accession Number:   NC_017664
-        Escherichia coli W chromosome, complete genome
-
-
-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
-
-   None.
-
-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.
-