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|
GENE2XML CONVERTER PROGRAM
gene2xml is a stand-alone program that converts Entrez Gene ASN.1 into XML.
It is available for several computer platforms (Alpha, Linux, Macintosh,
Solaris, and Windows) and is distributed in the asn1-converters area of the
NCBI public ftp site. From asn1-converters, navigate into by_program and
then gene2xml, and download and extract the appropriate file.
The following versions of gene2xml have been made available:
Version 1.5 March 23, 2015
Added RNA-ref field to Gene-commentary
Version 1.4 September 16, 2013
Removed Gene-track.status value 'newentry'
Version 1.3 March 1, 2010
Report write failures
Version 1.2 February 1, 2010
Adds new choices with these values:
ncRNA (8)
tmRNA (9)
miscRNA (10)
Adds elements RNA-gen, RNA-qual, RNA-qual-set
Entrez Gene data are stored as compressed binary Entrezgene-Set ASN.1 files
on the NCBI ftp site, and have the suffix .ags.gz. These are several-fold
smaller than compressed XML files, resulting in a significant savings of
disk storage and network bandwidth. Normal processing by gene2xml produces
text XML files with the same name but with .xgs as the suffix.
The command-line arguments to gene2xml are described below.
- Version and Argument Display
Displays the version of the gene2xml program and its arguments and their
descriptions.
-p Path to Files [String] Optional
Use -p if you want to process a entire directory of files. In this case,
gene2xml ignores the -i and -o arguments. Otherwise it takes -a as the
single input file, regardless of suffix.
-r Path for Results [String] Optional
If -p is given but no -r results path is provided, results are written in
the same directory as the input file. The -p argument recursively explores
any subdirectories, so there can be multiple places where output is written.
-i Single Input File [File In] Optional
default = stdin
-o Single Output File [File Out] Optional
default = stdout
If -p is not given, -i is used for the input file, and -o is used for the
output file. Suffix conventions are ignored in this case.
-b File is Binary [T/F] Optional
default = F
-c File is Compressed [T/F] Optional
default = F
On UNIX platforms you can decompress .ags.gz files on-the-fly by using both
-b and -c. On the PC you will need to manually decompress into .ags files
and then only use the -b flag.
-t Taxon ID to Filter [Integer] Optional
default = 0
If you want to extract only records for a particular organism, pass the
NCBI taxon database number with the -t argument. For example
gene2xml -i All_Mammalia.ags.gz -b -c -t 9685 -o cats.xgs
will only send gene records for cats (taxonomy ID 9685) to the file
cats.xgs.
-l Log Processing [T/F] Optional
default = F
When you are processing an entire directory of files, passing -l on the
command-line causes gene2xml to print the current file name as it
progresses through the directory.
The following arguments, -x, -y, and -z, are normally not used, and
gene2xml will default to writing Entrezgene-Set XML, which is the normal
situation.
-x Extract .ags -> text .agc [T/F] Optional
default = F
To accommodate existing programs, the -x argument will convert .ags files
to the catenated Entrezgene text ASN.1 files that were previously
distributed.
-y Combine .agc -> text .ags (for testing) [T/F] Optional
default = F
-z Combine .agc -> binary .ags, then gzip [T/F] Optional
default = F
NCBI uses gene2xml with the -y or -z arguments to process internal data
into the compressed binary Entrezgene-Set ASN.1 files that are placed on
the NCBI ftp site. It is not expected that anyone outside of NCBI would use
these arguments.
A sample record that illustrates the structure of Entrezgene-Set XML is
shown below. Ellipses (...) are used where blocks of text have been removed
for brevity in this documentation.
<?xml version="1.0"?>
<!DOCTYPE Entrezgene-Set PUBLIC "-//NCBI//NCBI Entrezgene/EN"
"http://www.ncbi.nlm.nih.gov/dtd/NCBI_Entrezgene.dtd">
<Entrezgene-Set>
<Entrezgene>
<Entrezgene_track-info>
<Gene-track>
<Gene-track_geneid>2652</Gene-track_geneid>
<Gene-track_status value="live">0</Gene-track_status>
<Gene-track_create-date>
<Date>
<Date_std>
<Date-std>
<Date-std_year>2003</Date-std_year>
<Date-std_month>8</Date-std_month>
<Date-std_day>28</Date-std_day>
<Date-std_hour>20</Date-std_hour>
<Date-std_minute>30</Date-std_minute>
<Date-std_second>0</Date-std_second>
</Date-std>
</Date_std>
</Date>
</Gene-track_create-date>
<Gene-track_update-date>
<Date>
<Date_std>
<Date-std>
<Date-std_year>2005</Date-std_year>
<Date-std_month>4</Date-std_month>
<Date-std_day>27</Date-std_day>
<Date-std_hour>21</Date-std_hour>
<Date-std_minute>45</Date-std_minute>
<Date-std_second>0</Date-std_second>
</Date-std>
</Date_std>
</Date>
</Gene-track_update-date>
</Gene-track>
</Entrezgene_track-info>
<Entrezgene_type value="protein-coding">6</Entrezgene_type>
<Entrezgene_source>
<BioSource>
<BioSource_genome value="genomic">1</BioSource_genome>
<BioSource_origin value="natural">1</BioSource_origin>
<BioSource_org>
<Org-ref>
<Org-ref_taxname>Homo sapiens</Org-ref_taxname>
<Org-ref_common>human</Org-ref_common>
<Org-ref_db>
<Dbtag>
<Dbtag_db>taxon</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>9606</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
</Org-ref_db>
<Org-ref_syn>
<Org-ref_syn_E>man</Org-ref_syn_E>
</Org-ref_syn>
<Org-ref_orgname>
<OrgName>
<OrgName_name>
<OrgName_name_binomial>
<BinomialOrgName>
<BinomialOrgName_genus>Homo</BinomialOrgName_genus>
<BinomialOrgName_species>sapiens
</BinomialOrgName_species>
</BinomialOrgName>
</OrgName_name_binomial>
</OrgName_name>
<OrgName_lineage>Eukaryota; Metazoa; Chordata; Craniata;
Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates;
Catarrhini; Hominidae; Homo</OrgName_lineage>
<OrgName_gcode>1</OrgName_gcode>
<OrgName_mgcode>2</OrgName_mgcode>
<OrgName_div>PRI</OrgName_div>
</OrgName>
</Org-ref_orgname>
</Org-ref>
</BioSource_org>
<BioSource_subtype>
<SubSource>
<SubSource_subtype value="chromosome">1</SubSource_subtype>
<SubSource_name>X</SubSource_name>
</SubSource>
</BioSource_subtype>
</BioSource>
</Entrezgene_source>
<Entrezgene_gene>
<Gene-ref>
<Gene-ref_locus>OPN1MW</Gene-ref_locus>
<Gene-ref_desc>opsin 1 (cone pigments), medium-wave-sensitive (color
blindness, deutan)</Gene-ref_desc>
<Gene-ref_maploc>Xq28</Gene-ref_maploc>
<Gene-ref_db>
<Dbtag>
<Dbtag_db>MIM</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>303800</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
</Gene-ref_db>
<Gene-ref_syn>
<Gene-ref_syn_E>CBD</Gene-ref_syn_E>
<Gene-ref_syn_E>DCB</Gene-ref_syn_E>
<Gene-ref_syn_E>GCP</Gene-ref_syn_E>
<Gene-ref_syn_E>CBBM</Gene-ref_syn_E>
</Gene-ref_syn>
<Gene-ref_locus-tag>HGNC:4206</Gene-ref_locus-tag>
</Gene-ref>
</Entrezgene_gene>
<Entrezgene_prot>
<Prot-ref>
<Prot-ref_name>
<Prot-ref_name_E>opsin 1 (cone pigments), medium-wave-sensitive
(color blindness, deutan)</Prot-ref_name_E>
<Prot-ref_name_E>green cone pigment</Prot-ref_name_E>
</Prot-ref_name>
</Prot-ref>
</Entrezgene_prot>
<Entrezgene_location>
<Maps>
<Maps_display-str>Xq28</Maps_display-str>
<Maps_method>
<Maps_method_map-type value="cyto"/>
</Maps_method>
</Maps>
</Entrezgene_location>
<Entrezgene_gene-source>
<Gene-source>
<Gene-source_src>LocusLink</Gene-source_src>
<Gene-source_src-int>2652</Gene-source_src-int>
<Gene-source_src-str2>2652</Gene-source_src-str2>
</Gene-source>
</Entrezgene_gene-source>
<Entrezgene_locus>
<Gene-commentary>
<Gene-commentary_type value="genomic">1</Gene-commentary_type>
<Gene-commentary_heading>Reference</Gene-commentary_heading>
<Gene-commentary_accession>NC_000023</Gene-commentary_accession>
<Gene-commentary_version>8</Gene-commentary_version>
<Gene-commentary_seqs>
<Seq-loc>
<Seq-loc_int>
<Seq-interval>
<Seq-interval_from>152969013</Seq-interval_from>
<Seq-interval_to>152982377</Seq-interval_to>
<Seq-interval_strand>
<Na-strand value="plus"/>
</Seq-interval_strand>
<Seq-interval_id>
<Seq-id>
<Seq-id_gi>51511752</Seq-id_gi>
</Seq-id>
</Seq-interval_id>
</Seq-interval>
</Seq-loc_int>
</Seq-loc>
</Gene-commentary_seqs>
<Gene-commentary_products>
<Gene-commentary>
<Gene-commentary_type value="mRNA">3</Gene-commentary_type>
<Gene-commentary_heading>Reference</Gene-commentary_heading>
<Gene-commentary_accession>NM_000513</Gene-commentary_accession>
<Gene-commentary_version>1</Gene-commentary_version>
<Gene-commentary_genomic-coords>
<Seq-loc>
<Seq-loc_mix>
<Seq-loc-mix>
<Seq-loc>
<Seq-loc_int>
<Seq-interval>
<Seq-interval_from>152969013</Seq-interval_from>
<Seq-interval_to>152969124</Seq-interval_to>
<Seq-interval_strand>
<Na-strand value="plus"/>
</Seq-interval_strand>
<Seq-interval_id>
<Seq-id>
<Seq-id_gi>51511752</Seq-id_gi>
</Seq-id>
</Seq-interval_id>
</Seq-interval>
</Seq-loc_int>
</Seq-loc>
...
</Seq-loc-mix>
</Seq-loc_mix>
</Seq-loc>
</Gene-commentary_genomic-coords>
<Gene-commentary_seqs>
<Seq-loc>
<Seq-loc_whole>
<Seq-id>
<Seq-id_gi>4503964</Seq-id_gi>
</Seq-id>
</Seq-loc_whole>
</Seq-loc>
</Gene-commentary_seqs>
<Gene-commentary_products>
<Gene-commentary>
<Gene-commentary_type value="peptide">8</Gene-commentary_type>
<Gene-commentary_heading>Reference</Gene-commentary_heading>
<Gene-commentary_accession>NP_000504
</Gene-commentary_accession>
<Gene-commentary_version>1</Gene-commentary_version>
<Gene-commentary_genomic-coords>
<Seq-loc>
<Seq-loc_packed-int>
<Packed-seqint>
<Seq-interval>
<Seq-interval_from>152969013</Seq-interval_from>
<Seq-interval_to>152969124</Seq-interval_to>
<Seq-interval_strand>
<Na-strand value="plus"/>
</Seq-interval_strand>
<Seq-interval_id>
<Seq-id>
<Seq-id_gi>51511752</Seq-id_gi>
</Seq-id>
</Seq-interval_id>
</Seq-interval>
...
</Packed-seqint>
</Seq-loc_packed-int>
</Seq-loc>
</Gene-commentary_genomic-coords>
<Gene-commentary_seqs>
<Seq-loc>
<Seq-loc_whole>
<Seq-id>
<Seq-id_gi>4503965</Seq-id_gi>
</Seq-id>
</Seq-loc_whole>
</Seq-loc>
</Gene-commentary_seqs>
</Gene-commentary>
</Gene-commentary_products>
</Gene-commentary>
</Gene-commentary_products>
</Gene-commentary>
...
</Entrezgene_locus>
<Entrezgene_properties>
<Gene-commentary>
<Gene-commentary_type value="comment">254</Gene-commentary_type>
<Gene-commentary_label>Nomenclature</Gene-commentary_label>
<Gene-commentary_source>
<Other-source>
<Other-source_anchor>HUGO Gene Nomenclature Committee
</Other-source_anchor>
</Other-source>
</Gene-commentary_source>
<Gene-commentary_properties>
<Gene-commentary>
<Gene-commentary_type value="property">16</Gene-commentary_type>
<Gene-commentary_label>Official Symbol</Gene-commentary_label>
<Gene-commentary_text>OPN1MW</Gene-commentary_text>
</Gene-commentary>
<Gene-commentary>
<Gene-commentary_type value="property">16</Gene-commentary_type>
<Gene-commentary_label>Official Full Name</Gene-commentary_label>
<Gene-commentary_text>opsin 1 (cone pigments),
medium-wave-sensitive (color blindness, deutan)</Gene-commentary_text>
</Gene-commentary>
</Gene-commentary_properties>
</Gene-commentary>
...
</Entrezgene_properties>
<Entrezgene_comments>
<Gene-commentary>
<Gene-commentary_type value="comment">254</Gene-commentary_type>
<Gene-commentary_heading>LocusTagLink</Gene-commentary_heading>
<Gene-commentary_source>
<Other-source>
<Other-source_src>
<Dbtag>
<Dbtag_db>HGNC</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>4206</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
</Other-source_src>
</Other-source>
</Gene-commentary_source>
</Gene-commentary>
...
</Entrezgene_comments>
<Entrezgene_unique-keys>
<Dbtag>
<Dbtag_db>LocusID</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>2652</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
<Dbtag>
<Dbtag_db>MIM</Dbtag_db>
<Dbtag_tag>
<Object-id>
<Object-id_id>303800</Object-id_id>
</Object-id>
</Dbtag_tag>
</Dbtag>
</Entrezgene_unique-keys>
<Entrezgene_xtra-index-terms>
<Entrezgene_xtra-index-terms_E>LOC2652</Entrezgene_xtra-index-terms_E>
</Entrezgene_xtra-index-terms>
<Entrezgene_xtra-properties>
<Xtra-Terms>
<Xtra-Terms_tag>PROP</Xtra-Terms_tag>
<Xtra-Terms_value>phenotype</Xtra-Terms_value>
</Xtra-Terms>
</Entrezgene_xtra-properties>
</Entrezgene>
</Entrezgene-Set>
|
