README:  Gene_tools                       Last modified:  September 7, 2016

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SCOPE:
Documentation for tools of interest to those processing information 
  in Entrez Gene.


Table of Contents:
I.   taxidToGeneNames.pl
       Sample script using E-utilities to extract name information from 
       Entrez Gene for a species 

II.  gene2xml  
       program to process Entrez Gene's binary ASN.1 files into XML

III. geneDocSum.pl
       Sample script using E-utilities to extract GeneIDs and other fields 
       from Entrez Gene using a query

==========================================================================
I. taxidToGeneNames.pl
---------------------------------------------------------------------------
      A representative perl script, using ESearch and ESummary, to extract
GeneIDs, names and names for a species (i.e. by Taxonomy's id). Usage notes 
provide when no arguments are supplied are:

Usage: taxidToGeneNames.pl [option] -t taxonomyId -o xml|tab
    Options:   -h     Display this usage help information
               -v     Verbose
               -o     output options
                        xml  - XML
                        tab  - tab-delimited

Output is written to STDOUT. 

Sample execution statement:

       taxidToGeneNames.pl -t 9615 -o xml > 9615_genes


==========================================================================
II. gene2xml
---------------------------------------------------------------------------
    gene2xml is a standalone program that converts Entrez Gene ASN.1 into XML.
    It also interconverts different formats of Entrez Gene ASN.1.  It is 
    available for multiple platforms.

    You may download this program and view its documentation from:

ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/gene2xml


==========================================================================
III. geneDocSum.pl
---------------------------------------------------------------------------
      A representative perl script, using ESearch and ESummary, to extract
GeneIDs and other fields from the Document Summary (DocSum).  Usage notes
provided when no arguments are supplied are:

Usage: ./geneDocSum.pl [options] -q query -o xml|tab
    Options:   -h     Display this usage help information
               -v     Verbose
               -q     Query to run against Entrez Gene, e.g. "has summary[prop]"
               -o     Output options
                        xml  - XML
                        tab  - tab-delimited
               -t     Tag from eutils xml to extract, e.g. "Summary"
                        - is case sensitive
                        - may be specified multiple times to extract multiple
                              tags & values
                        - used only with "-o tab" option
                        - to see all available xml tags in the DocSum, run first
                              with "-o xml" option


Output is written to STDOUT.

Sample execution statement:

       geneDocSum.pl -q "has_summary[prop] AND chimpanzee[orgn]" -o tab -t Name -t Summary