                                   xmlget


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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Get XML data

Description

   xmlget fetches an XML entry from a file or a local or remote data
   resource.

Algorithm

   The XML data is parsed using a DOM parser, and can be rewritten in
   various formats.

Usage

   Here is a sample session with xmlget

% xmlget dbfetch:embl:x13776
Get XML data
Xml output file [x13776.xml]:

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

Get XML data
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-xml]               xml        Xml filename and optional format, or
                                  reference (input query)
  [-outfile]           outxml     (no help text) outxml value

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-xml" associated qualifiers
   -iformat1           string     Input xml format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -idbname1           string     User-provided database name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Xml output format

   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

   xmlget reads XML data.

  Input files for usage example

  Database entry: dbfetch:embl:x13776

ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT   Pseudomonas aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA sequence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   EuropePMC; PMC208179; 1907262.
DR   EuropePMC; PMC395554; 7813419.
DR   GOA; Q51417.

  [Part of this file has been deleted for brevity]

FT                   /db_xref="InterPro:IPR005561"
FT                   /db_xref="InterPro:IPR008327"
FT                   /db_xref="InterPro:IPR011006"
FT                   /db_xref="InterPro:IPR011991"
FT                   /db_xref="PDB:1QO0"
FT                   /db_xref="UniProtKB/Swiss-Prot:P10932"
FT                   /protein_id="CAA32023.1"
FT                   /translation="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPP
FT                   PEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHG
FT                   VITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWD
FT                   EREAHQHLSREAMKRREPILKIAQELLGNEPSA"
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//

Output file format

   xmlget writes XML data.

  Output files for usage example

  File: x13776.xml

<?xml version="1.0" standalone="yes"?>
<ROOT request="X13776'display=xml'limit=200">
<entry accession="X13776" version="1" entryVersion="24" dataClass="STD" taxonomi
cDivision="PRO" moleculeType="genomic DNA" sequenceLength="2167" topology="linea
r" firstPublic="1989-04-19" firstPublicRelease="19" lastUpdated="2006-11-14" las
tUpdatedRelease="89">
        <secondaryAccession>M43175</secondaryAccession>
        <description>Pseudomonas aeruginosa amiC and amiR gene for aliphatic ami
dase regulation</description>
        <comment>
Data kindly reviewed (04-SEP-1991) by Rice P. M.
        </comment>
        <keyword>aliphatic amidase regulator</keyword>
        <keyword>amiC gene</keyword>
        <keyword>amiR gene</keyword>
        <reference type="submission" number="1" location="1167-2167">
                <author>Rice P.M.</author>
                <submissionDate>1988-12-16</submissionDate>
                <referenceLocation>
Submitted (16-DEC-1988) to the INSDC.
Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
                </referenceLocation>
        </reference>
        <reference type="article" number="2" location="1167-2167">
                Nucleotide sequence of the aliphatic amidase regulator ge
ne (amiR) of Pseudomonas aeruginosa
                <author>Lowe N.</author>
                <author>Rice P.M.</author>
                <author>Drew R.E.</author>
                <journal>FEBS Lett.</journal>
                <year>1989</year>
                <volume>246</volume>
                <issue>1-2</issue>
                <firstPage>39</firstPage>
                <lastPage>43</lastPage>
                <referenceLocation>
FEBS Lett. 246(1-2):39-43(1989).
                </referenceLocation>
                <xref db="DOI" id="10.1016/0014-5793(89)80249-2"/>
                <xref db="PUBMED" id="2495988"/>
        </reference>
        <reference type="article" number="3" location="1-1292">
                Cloning and DNA sequence of amiC, a new gene regulating e
xpression of the Pseudomonas aeruginosa aliphatic amidase, and purification of t
he amiC product
                <author>Wilson S.</author>
                <author>Drew R.</author>
                <journal>J. Bacteriol.</journal>
                <year>1991</year>
                <volume>173</volume>
                <issue>16</issue>
                <firstPage>4914</firstPage>
                <lastPage>4921</lastPage>
                <referenceLocation>
J. Bacteriol. 173(16):4914-4921(1991).
                </referenceLocation>
                <xref db="PUBMED" id="1907262"/>

  [Part of this file has been deleted for brevity]

                        </value>
                </qualifier>
                <qualifier name="translation">
                        <value>
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRT
TLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRH
GWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA
                        </value>
                </qualifier>
        </feature>
        <sequence>
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg
aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg
agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc
ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg
tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg
agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga
acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga
ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa
gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct
acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg
cgcgcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcg
ccatcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcg
aggcggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt
acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttct
tcccggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgc
tcggccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgt
acgacatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccaca
gccgcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc
agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggt
ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg
cgagttgcaggtgctggtcctcaacccgccgggggaggtcagcgacgccctggtcttgca
gctgatccgcatcggttgttcggtgcgccagtgctggccgccgccggaagccttcgacgt
gccggtggacgtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgc
gctgctcgccgccgggactccgcgcactaccctggtggcgctggtggagtacgaaagccc
cgcggtgctctcgcagatcatcgagctggagtgccacggcgtgatcacccagccgctcga
tgcccaccgggtgctgcctgtgctggtatcggcgcggcgcatcagcgaggaaatggcgaa
gctgaagcagaagaccgagcagctccaggaccgcatcgccggccaggcccggatcaacca
ggccaaggtgttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacct
gtcgcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcaggagttgctggg
aaacgagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgt
catcatgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctg
gttgctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgct
gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa
ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt
cctcgag
        </sequence>
</entry>
</ROOT>

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
