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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: refseqget
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
refseqget
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Get reference sequence
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>
    Description
</H2>

<b>refseqget</b> reads a reference sequence and returns the data in
one of the EMBOSS reference sequence formats.



<H2>
    Usage
</H2>

<!--  
	Example usage, as run from the command-line.
        Many examples illustrating different behaviours is good.
 -->

Here is a sample session with <b>refseqget</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>refseqget -of embl </b>
Get reference sequence
-refsequence : enter refseq value: <b>tembl:em498477</b>
Reference sequence output file [em498477.embl]: <b>test.out</b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>



<H2>
    Command line arguments
</H2>

<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Get reference sequence
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-refsequence]       refseq     (no help text) refseq value
  [-outfile]           outrefseq  (no help text) outrefseq value

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

   "-refsequence" associated qualifiers
   -iformat1           string     Input reference sequence 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     Referece sequence 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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-refsequence]<br>(Parameter 1)</td>
<td>refseq</td>
<td>(no help text) refseq value</td>
<td>Reference sequence</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outrefseq</td>
<td>(no help text) outrefseq value</td>
<td>Reference sequence</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-refsequence" associated refseq qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iformat1<br>-iformat_refsequence</td>
<td>string</td>
<td>Input reference sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_refsequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_refsequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -idbname1<br>-idbname_refsequence</td>
<td>string</td>
<td>User-provided database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outrefseq qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -oformat2<br>-oformat_outfile</td>
<td>string</td>
<td>Referece sequence output format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->








<H2>
    Input file format
</H2>

<!-- 
        This includes example input file formats.
        This should be a detailed description and example - assume
        someone will want to parse this file and will want to know what
        happens in unusual cases - null input, etc. 
   -->

<b>refseqget</b> reads a reference sequence.
<p>

The input is a standard EMBOSS reference sequence query.

<p> The major reference sequence sources are files in one of the
common sequence formats, or remote files accessed by HTTP or FTP.


<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tembl:em498477' is a sequence entry in the example nucleic acid database 'tembl'
<p>
<p><h3>Database entry: tembl:em498477</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   EM498477; SV 1; linear; genomic DNA; CON; ENV; 1791 BP.
XX
AC   EM498477; AACY020000000;
XX
PR   Project:PRJNA13694;
XX
DT   14-APR-2007 (Rel. 91, Created)
DT   14-APR-2007 (Rel. 91, Last updated, Version 1)
XX
DE   marine metagenome JCVI_SCAF_1096627861213 genomic scaffold, whole genome
DE   shotgun sequence.
XX
KW   .
XX
OS   marine metagenome
OC   unclassified sequences; metagenomes; ecological metagenomes.
XX
RN   [1]
RP   1-1791
RX   DOI; 10.1371/journal.pbio.0050016.
RX   PUBMED; 17355171.
RA   Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J.,
RA   Remington K., Eisen J.A., Heidelberg K.B., Manning G., Li W.,
RA   Jaroszewski L., Cieplak P., Miller C.S., Li H., Mashiyama S.T.,
RA   Joachimiak M.P., van Belle C., Chandonia J.M., Soergel D.A., Zhai Y.,
RA   Natarajan K., Lee S., Raphael B.J., Bafna V., Friedman R., Brenner S.E.,
RA   Godzik A., Eisenberg D., Dixon J.E., Taylor S.S., Strausberg R.L.,
RA   Frazier M., Venter J.C.;
RT   "The Sorcerer II Global Ocean Sampling expedition: expanding the universe
RT   of protein families";
RL   PLoS Biol. 5(3):e16-e16(2007).
XX
RN   [2]
RP   1-1791
RX   DOI; 10.1371/journal.pbio.0050017.
RX   PUBMED; 17355172.
RA   Kannan N., Taylor S.S., Zhai Y., Venter J.C., Manning G.;
RT   "Structural and functional diversity of the microbial kinome";
RL   PLoS Biol. 5(3):e17-e17(2007).
XX
RN   [3]
RP   1-1791
RX   DOI; 10.1371/journal.pbio.0050077.
RX   PUBMED; 17355176.
RA   Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S.,
RA   Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., Beeson K.,
RA   Tran B., Smith H., Baden-Tillson H., Stewart C., Thorpe J., Freeman J.,
RA   Andrews-Pfannkoch C., Venter J.E., Li K., Kravitz S., Heidelberg J.F.,
RA   Utterback T., Rogers Y.H., Falcon L.I., Souza V., Bonilla-Rosso G.,
RA   Eguiarte L.E., Karl D.M., Sathyendranath S., Platt T., Bermingham E.,
RA   Gallardo V., Tamayo-Castillo G., Ferrari M.R., Strausberg R.L., Nealson K.,
RA   Friedman R., Frazier M., Venter J.C.;
RT   "The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic
RT   through eastern tropical Pacific";
RL   PLoS Biol. 5(3):e77-e77(2007).
XX
RN   [4]
RP   1-1791
RG   J. Craig Venter Institute
RA   ;
RT   ;
RL   Submitted (02-MAR-2007) to the INSDC.
RL   J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850,
RL   USA
XX
CC   For complete environmental metadata relating to this record,
CC   background on the Global Ocean Sampling expedition, as well as
CC   additional analysis results, please visit the CAMERA website
CC   (http://camera.calit2.net).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1791
FT                   /organism="marine metagenome"
FT                   /environmental_sample
FT                   /mol_type="genomic DNA"
FT                   /isolation_source="isolated as part of a large dataset
FT                   composed predominantly from surface water marine samples
FT                   collected along a voyage from Eastern North American coast
FT                   to the Eastern Pacific Ocean, including locations in the
FT                   Sargasso Sea, Panama Canal, and the Galapagos Islands"
FT                   /note="metagenomic"
FT                   /db_xref="taxon:408172"
XX
CO   join(AACY021843949.1:1..897,gap(51),complement(AACY020702065.1:1..843))
//
</pre>
</td></tr></table><p>





<H2>
    Output file format
</H2>


<b>refseqget</b> writes data in one of the reference sequence output formats.

<p>

The output is a standard EMBOSS reference sequence.

<p> The major reference sequence formats are the most common sequence
formats.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: test.out</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
ID   EM498477; SV 1; linear; unassigned DNA; STD; UNC; 1791 BP.
XX
DE   marine metagenome JCVI_SCAF_1096627861213 genomic scaffold, whole genome
DE   shotgun sequence.
XX
SQ   Sequence 1791 BP; 583 A; 286 C; 326 G; 545 T; 51 other;
     agtacacaat atcctacaaa ttttaatcca ggaacaagtt tctttttggc aaatagtttt        60
     gcaagatcac aggcacaatt tttgggagat agcacaggta taacaattaa tgaagttaat       120
     agaatatcta aagctactgg accacttact gctgccactg gtgaaacttc atcatcagat       180
     ccacatgctg gatttcagct tggtgtatta aatccttatg cttatgaacc tgctgatatt       240
     gatgaatgta gtttgttaag cacatgttat tttaaattag gagatgccac ggtagatacg       300
     gttaataata caattgatgt tggatttcct catggcctta gtgatttagt tttaggtaga       360
     gtttttccgg gggcaggtaa taccttacct actggattaa ctgaaagaaa ttattatata       420
     caagttatca attcaacaac acttgcattt tctaccagaa aatcaggaac taccacattt       480
     agagcaaatt tatctacttc tggtagtgat gcaggaatag caaaggtttg tattgcaaca       540
     gggataacat gttattattt ccaaaccagt ggatatgtat attttaccag ggacactcgc       600
     gctcatttta gttataataa taatattgca cgagcacatt tatcgccagt aacaagatgg       660
     ggtttacata ctgcaaatac aactgcaagg tctagagttg ataatggatt taattcctta       720
     ggaggtgctg atatacgtgc taatcctaat ggattaatgg atataccaga gggtggaaac       780
     ggtggcaata atgcacattt atattatcct tatggtagta caagtagaac taataataca       840
     aattatttat attatggtat gagattagct cgtactcaag atggtggcac aaattatNNN       900
     NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNta tgctagatta       960
     ttctgaagat ggtaacgaag atgccgatca gtacgcatta tggcttgcat ataaagaagt      1020
     ttccgaaccg aattcgttct acattgcaaa tcatggtttt acaacgggcg acattgtaac      1080
     atatagttca actggaactc ttcctgctgg tctcaatggt tttacaacgg caactgctca      1140
     aataacaagt gctaacagat ttaaatttaa tagaaatagt gcagcagtaa atattgaaag      1200
     tgtaggagtt gctggccaag atattacatt tactgcagtt tcattaaatc cacttggaaa      1260
     ttcaattaac ttagtaggaa attcattaac caatggtgaa caagtttcat atacaaataa      1320
     tggcgcatca aatattggtg gtcttacaag tggcactagt tattttgttt ttgatagaac      1380
     atctgataca attaaacttg ccacaacgtt aactggttat accggagatg aagttttagt      1440
     tgatacagat gccacatcag caacaggtgc tgcagcattt attaactcaa caaatggtag      1500
     aattcaaggt atttctagta cagcaggaat tgatacgttc caagatggaa gcattgtgca      1560
     aatagaacaa gtatccggtt ccactgatca tggattaaaa aatggagcat ttttatttgt      1620
     taataaaatt aattccaaaa ccttcgagct ttacccaacc gattctgata gagtggctac      1680
     taccaatcaa tatgttccat cacgtacatc agttgatgga caagtaaaat taaaagaaac      1740
     cacacttgtt gatttaacag catttgattc tggtacacat agtattacag c               1791
//
</pre>
</td></tr></table><p>





<H2>
    Data files
</H2>

<!-- 
        Any data files used (e.g. translation table file)
        This includes example data file formats if they are
        not obvious.

	If you wish to include the standard description of what data
	files are and how to use embossdata to inspect and retrieve
	them, use:

        #include file="inc/localfiles.ihtml"
   -->

None.

<H2>
    Notes
</H2>

<!-- 
        Restrictions.
        Interesting behaviour.
        Useful things you can do with this program.
   -->

None.







<H2>
    References
</H2>

<!-- 
        Bibliography for methods used.
<ol>

<li>

</ol>

   -->

None.








<H2>
    Warnings
</H2>

<!-- 
        Potentially stupid things the program will let you do.
   -->

None.







<H2>
    Diagnostic Error Messages
</H2>

<!-- 
        Error messages specific to this program, eg:
        "FATAL xxx" - means you have not set up the xxx data using program <b>prog</b>.<p>
   -->

None.







<H2>
    Exit status
</H2>

<!-- 
        Description of the exit status for various error conditions
   -->

It always exits with status 0.








<H2>
    Known bugs
</H2>


<!-- 
        Bugs noted but not yet fixed.
   -->

None.








<!--
<H2>
    See also
</H2>
-->
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="abiview.html">abiview</a></td>
<td>Display the trace in an ABI sequencer file</td>
</tr>

<tr>
<td><a href="coderet.html">coderet</a></td>
<td>Extract CDS, mRNA and translations from feature tables</td>
</tr>

<tr>
<td><a href="entret.html">entret</a></td>
<td>Retrieve sequence entries from flatfile databases and files</td>
</tr>

<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>Extract regions from a sequence alignment</td>
</tr>

<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>Display basic information about a multiple sequence alignment</td>
</tr>

<tr>
<td><a href="infoseq.html">infoseq</a></td>
<td>Display basic information about sequences</td>
</tr>

<tr>
<td><a href="seqxref.html">seqxref</a></td>
<td>Retrieve all database cross-references for a sequence entry</td>
</tr>

<tr>
<td><a href="seqxrefget.html">seqxrefget</a></td>
<td>Retrieve all cross-referenced data for a sequence entry</td>
</tr>

<tr>
<td><a href="showalign.html">showalign</a></td>
<td>Display a multiple sequence alignment in pretty format</td>
</tr>

<tr>
<td><a href="variationget.html">variationget</a></td>
<td>Get sequence variations</td>
</tr>

<tr>
<td><a href="whichdb.html">whichdb</a></td>
<td>Search all sequence databases for an entry and retrieve it</td>
</tr>

</table>
<!-- 
        Add any comments about other associated programs (to prepare
        data files?) that seealso doesn't find. 
   -->










<H2>
    Author(s)
</H2>

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

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>
<!--
        Date written and what changes have been made go in this file.
   -->




<H2>
    Target users
</H2>
<!--
        For general users, use this text
   -->
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
<!--
        User/developer/other comments go in this file.
   -->
None


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