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|
<HTML>
<HEAD>
<TITLE>
EMBOSS: jaspextract
</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">
jaspextract
</font></b>
</td></tr>
</table>
<br>
<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>
Extract data from JASPAR
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>
Description
</H2>
JASPAR is a collection of transcription factor DNA-binding preferences,
modelled as matrices. These can be converted into Position Weight
Matrices (PWMs or PSSMs), used for scanning genomic sequences.
<p>
JASPAR is the only database with this scope where the data can be used
with no restrictions (open-source).
<p>
This program copies the JASPAR distribution into its component
matrix sets (e.g. JASPAR_CORE, JASPAR_PHYLOFACTS etc) and copies
them into the EMBOSS data directories, performing any necessary
conversions
<p>
The home page of JASPAR
is: <a href="http://jaspar.genereg.net/">http://jaspar.genereg.net/</a>
<p>
The EMBOSS program jaspscan will not work unless this program is run.
<p>
Running this program may be the job of your system manager.
<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>jaspextract</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>jaspextract </b>
Extract data from JASPAR
JASPAR database directory [.]: <b>jaspar</b>
</pre></td></tr></table><p>
<p>
<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>
Extract data from JASPAR
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-directory] directory The FlatFileDir directory containing the
.pfm files and the matrix_list.txt file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-directory" associated qualifiers
-extension1 string Default file extension
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>[-directory]<br>(Parameter 1)</td>
<td>directory</td>
<td>The FlatFileDir directory containing the .pfm files and the matrix_list.txt file</td>
<td>Directory</td>
<td> </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>"-directory" associated directory qualifiers
</td>
</tr>
<tr bgcolor="#FFFFCC">
<td> -extension1<br>-extension_directory</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td> </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>
<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.
-->
The input files are part of the uncompressed and extracted Archive.zip
file provided in the JASPAR html/DOWNLOAD directory of the JASPAR
homepage <a href="http://jaspar.genereg.net">(http://jaspar.genereg.net).</a>
After extracting the file you should specify the all_data/FlatFileDir
directory when running jasparextract. It is advisable to first delete
any old data files from your EMBOSS data file area e.g. from the
/usr/local/emboss/share/EMBOSS/data/JASPAR_* directories
<H2>
Output file format
</H2>
<!--
This includes example output 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 output, errors etc.
If you wish to include the standard description of the avalable
report formats, use:
#include file="inc/reportformats.ihtml"
-->
The output file format is currently the same as the JASPAR
distribution format, but with the matrix files separated into
directories according to their type.
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: JASPAR_CNE</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_CORE</h3>
<p>This directory contains output files, for example MA0070.1.pfm MA0071.1.pfm MA0072.1.pfm MA0073.1.pfm MA0074.1.pfm MA0075.1.pfm MA0076.1.pfm MA0077.1.pfm MA0078.1.pfm MA0079.1.pfm and matrix_list.txt.
<p><h3>File: JASPAR_CORE/MA0070.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
5 3 16 1 0 17 17 0 0 16 12 8
6 9 1 1 18 1 0 0 18 1 0 2
2 3 1 0 0 0 0 1 0 0 1 2
5 3 0 16 0 0 1 17 0 1 5 6
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0071.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
15 9 6 11 21 0 0 0 0 25
1 1 12 2 0 0 0 0 25 0
2 0 4 5 4 25 25 0 0 0
7 15 3 7 0 0 0 25 0 0
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0072.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
9 17 15 35 23 2 0 28 0 0 0 0 36 15
8 2 0 1 0 12 0 0 0 0 0 36 0 6
8 7 3 0 0 13 0 8 36 36 0 0 0 10
11 10 18 0 13 9 36 0 0 0 36 0 0 5
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0073.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
3 1 3 0 7 9 8 4 0 11 4 1 3 4 2 4 4 4 1 4
8 10 8 11 4 2 3 6 11 0 7 10 8 6 9 5 5 6 7 4
0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 3 2
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 2 1 1 0 1
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0074.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
3 0 0 0 0 9 4 2 2 5 0 0 1 0 7
0 0 0 0 9 0 2 4 0 0 0 0 0 9 1
7 10 9 0 0 1 0 2 8 5 10 0 0 0 2
0 0 1 10 1 0 4 2 0 0 0 10 9 1 0
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0075.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
52 59 0 0 58
2 0 0 0 0
4 0 1 0 1
1 0 58 59 0
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0076.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
16 0 0 0 0 20 16 4 1
1 20 20 0 0 0 0 1 6
2 0 0 20 20 0 0 15 0
1 0 0 0 0 0 4 0 13
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0077.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
24 54 59 0 65 71 4 24 9
7 6 4 72 4 2 0 6 9
31 7 0 2 0 1 1 38 55
14 9 13 2 7 2 71 8 3
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0078.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
7 8 3 30 0 0 0 0 0
9 8 18 0 1 0 0 0 17
6 4 1 0 0 0 31 2 10
9 11 9 1 30 31 0 29 4
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/MA0079.1.pfm</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
1 2 0 0 0 2 0 0 1 2
1 1 0 0 5 0 1 0 1 0
4 4 8 8 2 4 5 6 6 0
2 1 0 0 1 2 2 2 0 6
</pre>
</td></tr></table><p>
<p><h3>File: JASPAR_CORE/matrix_list.txt</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
MA0079.2 11.1288626921664 SP1 Zinc-coordinating ; acc "P08047" ; collection "CORE" ; comment "Annotations from PAZAR SP1 + SP1_MOUSE + SP1_HUMAN + SP1_RAT in the pleiades genes project (TF0000105, TF0000121, TF0000137, TF0000146)." ; family "BetaBetaAlpha-zinc finger" ; medline "17916232" ; pazar_tf_id "TF0000055" ; species "9606,10090,10116" ; tax_group "vertebrates" ; type "COMPILED"
MA0074.1 20.4511671987138 RXRA::VDR Zinc-coordinating ; acc "P19793,P11473" ; collection "CORE" ; comment "heterodimer between RXRA and VDR" ; family "Hormone-nuclear Receptor" ; medline "8674817" ; pazar_tf_id "TF0000050" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0076.1 14.123230134165 ELK4 Winged Helix-Turn-Helix ; acc "P28324" ; collection "CORE" ; comment "-" ; family "Ets" ; medline "8524663" ; pazar_tf_id "TF0000052" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0077.1 9.07881462267178 SOX9 Other Alpha-Helix ; acc "P48436" ; collection "CORE" ; comment "-" ; family "High Mobility Group" ; medline "9973626" ; pazar_tf_id "TF0000053" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0079.1 9.7185757452318 SP1 Zinc-coordinating ; acc "P08047" ; collection "CORE" ; comment "-" ; family "BetaBetaAlpha-zinc finger" ; medline "2192357" ; pazar_tf_id "TF0000055" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0072.1 17.4248426117905 RORA_2 Zinc-coordinating ; acc "NP_599022" ; collection "CORE" ; comment "isoform type" ; family "Hormone-nuclear Receptor" ; medline "7926749" ; pazar_tf_id "TF0000048" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0071.1 13.1897301896459 RORA_1 Zinc-coordinating ; acc "NP_599023" ; collection "CORE" ; comment "isoform type" ; family "Hormone-nuclear Receptor" ; medline "7926749" ; pazar_tf_id "TF0000047" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0078.1 10.5018372361999 Sox17 Other Alpha-Helix ; acc "Q61473" ; collection "CORE" ; comment "-" ; family "High Mobility Group" ; medline "8636240" ; pazar_tf_id "TF0000054" ; species "10090" ; tax_group "vertebrates" ; type "SELEX"
MA0073.1 22.2782723704014 RREB1 Zinc-coordinating ; acc "Q92766" ; collection "CORE" ; comment "-" ; family "BetaBetaAlpha-zinc finger" ; medline "8816445" ; pazar_tf_id "TF0000049" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
MA0075.1 9.06306510239134 Prrx2 Helix-Turn-Helix ; acc "Q06348" ; collection "CORE" ; comment "-" ; family "Homeo" ; medline "7901837" ; pazar_tf_id "TF0000051" ; species "10090" ; tax_group "vertebrates" ; type "SELEX"
MA0070.1 14.6408952002356 PBX1 Helix-Turn-Helix ; acc "Q5T486" ; collection "CORE" ; comment "-" ; family "Homeo" ; medline "7910944" ; pazar_tf_id "TF0000046" ; species "9606" ; tax_group "vertebrates" ; type "SELEX"
</pre>
</td></tr></table><p>
<p><h3>Directory: JASPAR_FAM</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_PBM</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_PBM_HLH</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_PBM_HOMEO</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_PHYLOFACTS</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_POLII</h3>
<p>This directory contains output files.
<p>
<p><h3>Directory: JASPAR_SPLICE</h3>
<p>This directory contains output files.
<p>
<H2>
Data files
</H2>
None
<H2>
Notes
</H2>
<!--
Restrictions.
Interesting behaviour.
Useful things you can do with this program.
-->
The home page of JASPAR
is: <a href="http://jaspar.genereg.net/">http://jaspar.genereg.net</a>
Running this program may be the job of your system manager.
<H2>
References
</H2>
<!--
Bibliography for methods used.
<ol>
<li>
</ol>
-->
<OL>
<LI>DNA binding sites: representation and discovery Bioinformatics. 2000
Jan;16(1):16-23
<LI>Applied bioinformatics for the identification of regulatory elements
Nat Rev Genet. 2004 Apr;5(4):276-87
</OL>
<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 unless an error is reported
<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="aaindexextract.html">aaindexextract</a></td>
<td>Extract amino acid property data from AAINDEX</td>
</tr>
<tr>
<td><a href="cutgextract.html">cutgextract</a></td>
<td>Extract codon usage tables from CUTG database</td>
</tr>
<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS database for use by pscan</td>
</tr>
<tr>
<td><a href="prosextract.html">prosextract</a></td>
<td>Process the PROSITE motif database for use by patmatmotifs</td>
</tr>
<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Process the REBASE database for use by restriction enzyme applications</td>
</tr>
<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Process TRANSFAC transcription factor database for use by tfscan</td>
</tr>
</table>
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<H2>
Author(s)
</H2>
Alan Bleasby
<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 © emboss.open-bio.org) not to the original author.
<H2>
History
</H2>
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Completed 23rd July 2007
<H2>
Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance.
<H2>
Comments
</H2>
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None
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