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.