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<title>The mcxdeblast manual</title>
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<p style="text-align:right">
16 May 2014
<a class="local" href="mcxdeblast.ps"><b>mcxdeblast</b></a>
14-137
</p>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#name">NAME</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#synopsis">SYNOPSIS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#description">DESCRIPTION</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#stream">STREAM MODE</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#assemble">ASSEMBLE MODE</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#options">OPTIONS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">7.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#author">AUTHOR</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">8.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#sealso">SEE ALSO</a>
</div>
</div>
<a name="name"></a>
<h2>NAME</h2>
<p style="margin-bottom:0" class="asd_par">
mcxdeblast — parse BLAST files and stream
output directly into mcl or write mcxassemble input.</p>
<a name="synopsis"></a>
<h2>SYNOPSIS</h2>
<b>mcxdeblast</b> file-name
<p style="margin-bottom:0" class="asd_par">
<b>mcxdeblast</b>
<a class="intern" href="#opt--score"><b>[--score=</b><b|e|r> (<i>bit scores|e-values|normalize bit score</i>)<b>]</b></a>
<a class="intern" href="#opt--m9"><b>[--m9</b> (<i>expect BLAST column format</i>)<b>]</b></a>
<a class="intern" href="#opt--out"><b>[--out</b> <fname> (<i>output file</i>)<b>]</b></a>
<a class="intern" href="#opt--line-mode"><b>[--line-mode</b> abc (<i>write ID1 ID2 score format</i>)<b>]</b></a>
<a class="intern" href="#opt--sort"><b>[--sort=</b><a|o> (<i>alphabetic|occurrence sorting</i>)<b>]</b></a>
<a class="intern" href="#opt--xi-dat"><b>[--xi-dat=</b><suf> (<i>strip <suf> from file-name</i>)<b>]</b></a>
<a class="intern" href="#opt--xo-dat"><b>[--xo-dat=</b><suf> (<i>add <suf> to base name</i>)<b>]</b></a>
<a class="intern" href="#opt--bcut"><b>[--bcut=</b><val> (<i>bit score cutoff</i>)<b>]</b></a>
<a class="intern" href="#opt--ecut"><b>[--ecut=</b><val> (<i>E-value cutoff</i>)<b>]</b></a>
<a class="intern" href="#opt--rcut"><b>[--rcut=</b><val> (<i>raw value cutoff</i>)<b>]</b></a>
<a class="intern" href="#opt--tab"><b>[--tab=</b><fname> (<i>tab file</i>)<b>]</b></a>
<file-name></p>
<a name="description"></a>
<h2>DESCRIPTION</h2>
<p style="margin-bottom:0" class="asd_par">
<b>mcxdeblast</b> parses BLAST files.</p>
<p style="margin-bottom:0" class="asd_par">
In <i>stream mode</i> mcxdeblast output can be directly streamed to mcl by
using the mcxdeblast <b>--line-mode</b>=<i>abc</i> option and equipping mcl with
either <b>--abc</b> or <b>--expect-abc</b>. This can be considered the
easy, lightweight and fast track. This functionality was recently acquired
by mcl.</p>
<p style="margin-bottom:0" class="asd_par">
In the classic and slightly more heavy-handed <i>assemble mode</i>, mcxdeblast
creates output files suitable for use by mcxassemble. The latter can in
turn create input suitable for mcl. This is the mode in which mcxdeblast is
employed by <b>mclblastline</b>.</p>
<a name="stream"></a>
<h2>STREAM MODE</h2>
<p style="margin-top:0em; margin-bottom:0em">Enter stream mode by specifiying <b>--line-mode</b>=<i>abc</i>.
Use <b>--m9</b> if the input is in columnar output. Pipe the result
to a file or directly to mcl. Example invocations can be found
in <a class="local sibling" href="mcl.html">the mcl manual</a>.</p>
<a name="assemble"></a>
<h2>ASSEMBLE MODE</h2>
<p style="margin-top:0em; margin-bottom:0em">
If the input file is named <tt>iput</tt>, mcxdeblast will by
default create files <tt>iput.hdr</tt>, <tt>iput.raw</tt>, <tt>iput.tab</tt>,
<tt>iput.map</tt>, and <tt>iput.err</tt>. The <tt>hdr</tt> file contains
information about the number of nodes found. It will be read
by <a class="local sibling" href="mcxassemble.html">mcxassemble</a>. The <tt>raw</tt> file contains the co-occurrence
scores between different nodes (peptides), also to be
read by mcxassemble. The co-occurrence scores are in
terms of mcl indentiers, which are subjected to rearranging
by mcxassemble in order to correctly align them with the tab file.
The <tt>tab</tt> file contains bindings between mcl identifiers
(after rearranging as specified in the map file) and the BLAST labels
(peptide identifiers). Refer to the manual of <a class="local sibling" href="mcxassemble.html">mcxassemble</a>
for the syntax of a tab file.
The <tt>err</tt> file contains a list of any errors encountered.</p>
<p style="margin-bottom:0" class="asd_par">
If the <b>--tab</b>=<b>fname</b> option is used mcxdeblast changes
its behaviour. It will read the file <b>fname</b>, and use
the bindings found therein. It will no longer output any
of the <tt>hdr</tt>, <tt>map</tt>, or <tt>tab</tt> files. The <tt>hdr</tt>
file should be provided by the same application that generated
the specified tab file, and the <tt>map</tt> file should no longer be
necessary (it might be convenient though and perhaps the
future will bring a new <b>--map</b> option).</p>
<p style="margin-bottom:0" class="asd_par">
The <b>--tab</b>=<b>fname</b> option can be convenient e.g. if
you split a BLAST job over multiple machines and want
to apply mcxdeblast to each of the subresults. You do
this by generating a single central tab file in advance.
Then provide each instance of mcxdeblast with this tab file.
Each instance will generate a <tt>raw</tt> file. The respective
<tt>raw</tt> files can simply be concatenated and fed to mcxassemble
using its <b>-raw</b> option. Additionally, a <tt>hdr</tt> file
has to be specified for mcxassemble using its <b>-hdr</b>
option. The syntax of <tt>hdr</tt> files is described in
the <a class="local sibling" href="mcxassemble.html">mcxassemble</a> manual.
Currently there is usually only one variable
in the <tt>hdr</tt> file, which is the number of bindings
listed in the tab file. This number, in turn, should equal
the total number of different peptides encountered in the BLAST input.</p>
<a name="options"></a>
<h2>OPTIONS</h2>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--tab"></a><b>--tab</b>=<fname> (<i>tab file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Specify a tab file to use, rather than automatically generating one.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--out"></a><b>--out</b> <fname> (<i>output file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Specify the name for the output file.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--score"></a><b>--score</b>=<b|e|r> (<i>bit scores|e-values|norm bit score</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Specify whether to use bit scores, E-values, or bit scores
normalized by length of the HSP.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--sort"></a><b>--sort</b>=<a|o> (<i>alphabetic|occurrence sorting</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Specify how to sort labels.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--m9"></a><b>--m9</b> (<i>expect BLAST column format</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Use this option to parse BLAST output formatted with the -m 9 option.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--line-mode"></a><b>--line-mode</b>=abc (<i>write ID1 ID2 SCORE format</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Use this to stream output directly into mcl. Here <tt>abc</tt>
is a literal; <b>--line-mode</b> may acquire other line output
modes.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xi-dat"></a><b>--xi-dat</b>=<suf> (<i>strip <suf> from <file-name></i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
If set, the suffix <suf> is stripped from file-name in order
to obtain the base name for output. If <file-name> does not
end with suffix, it is assumed to be the base name, and <suf> is
added in order to obtain the (real) file-name.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--xo-dat"></a><b>--xo-dat</b>=<suf> (<i>add <suf> to base name</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Attaches the suffix to the base name. Use this to distinguish
between different parses. One might for example
use <b>--score</b>=<i>b</i> <b>--bcut</b>=<i>5</i> <b>--xo-dat</b>=<i>b</i>.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--bcut"></a><b>--bcut</b>=<val> (<i>bit score cutoff</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Bit scores below the cutoff value are ignored. This
triggers the output of bit scores and ignores all other values.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--ecut"></a><b>--ecut</b>=<val> (<i>E-value cutoff</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
E-values below the cutoff value are ignored. This triggers
the output of E-values and ignores all other values.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--rcut"></a><b>--rcut</b>=<val> (<i>raw value cutoff</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Raw values below the cutoff value are ignored. This
triggers the output of raw values and ignores all other values.
</p>
</div>
</div>
<a name="author"></a>
<h2>AUTHOR</h2>
Stijn van Dongen.
Jason Stajich implemented the <b>--m9</b> option.
Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments
and fixes.
<a name="sealso"></a>
<h2>SEE ALSO</h2>
<a class="local sibling" href="mclblastline.html">mclblastline</a>, <a class="local sibling" href="mcxassemble.html">mcxassemble</a>, <a class="local sibling" href="mcl.html">mcl</a>,
<a class="local sibling" href="clmformat.html">clmformat</a>.
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