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+++ b/GEMBASSY-1.0.3/doc/text/gentrez.txt	Fri Jun 26 05:19:29 2015 -0400
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+                                    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.
+