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<div class="section" id="how-to-install-and-run-pbalign">
<h1>How to install and run pbalign<a class="headerlink" href="#how-to-install-and-run-pbalign" title="Permalink to this headline">¶</a></h1>
<p>pbalign is a tool for aligning PacBio reads to reference sequences.
It is part of the PacBio Bioinformatics tools, and will
be bundled in the 2.1 release of SMRTanalysis. You may also follow the
instructions below to install pbalign.</p>
<p><em>Note: the pseudo namespace pbtools has been removed in version 0.2.0.</em></p>
<p><em>Note: program name has been changed from `pbalign.py` in version 0.1.0
to `pbalign` in version 0.2.0.</em></p>
<p><em>Note: please install this software on an isolated machine that does
not have SMRTanalysis installed.</em></p>
<div class="section" id="background">
<h2>Background<a class="headerlink" href="#background" title="Permalink to this headline">¶</a></h2>
<p><strong>pbalign</strong> aligns PacBio reads to reference sequences, filters aligned
reads according to user-specific filtering criteria, and converts the
output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5)
format. The output Compare HDF5 file will be compatible with Quiver if
<code class="docutils literal"><span class="pre">--forQuiver</span></code> option is specified.</p>
</div>
<div class="section" id="required-software">
<h2>Required software<a class="headerlink" href="#required-software" title="Permalink to this headline">¶</a></h2>
<p>pbalign is available through the <code class="docutils literal"><span class="pre">pbalign</span></code> script from the
<code class="docutils literal"><span class="pre">pbalign</span></code> package. To use pbalign, the following PacBio software is
required,</p>
<ul class="simple">
<li><code class="docutils literal"><span class="pre">pbalign</span></code>, containing <code class="docutils literal"><span class="pre">pbalign</span></code></li>
<li><code class="docutils literal"><span class="pre">pbcore</span></code>, a package providing access to PacBio data files</li>
<li><code class="docutils literal"><span class="pre">blasr</span></code>, a package of PacBio aligner blasr, containing c++ executables
for processing PacBio data, such as <code class="docutils literal"><span class="pre">blasr</span></code>, <code class="docutils literal"><span class="pre">pls2fasta</span></code>,
<code class="docutils literal"><span class="pre">samFilter</span></code>, <code class="docutils literal"><span class="pre">samtoh5</span></code> and <code class="docutils literal"><span class="pre">loadPulses</span></code></li>
</ul>
<p>The following software is optionally required if <code class="docutils literal"><span class="pre">--forQuiver</span></code> option
will be used to convert the output Compare HDF5 file to be compatible
with Quiver.
- <code class="docutils literal"><span class="pre">pbh5tools.cmph5tools</span></code>, a PacBio Bioinformatics tools that manipulates Compare HDF5 files.
- <code class="docutils literal"><span class="pre">h5repack</span></code>, a HDF5 tool to compress and repack HDF5 files.</p>
<p>The default aligner that pbalign uses is <code class="docutils literal"><span class="pre">blasr</span></code>. If you want to use
bowtie2 as aligner, then the bowtie2 package also needs to be installed.</p>
</div>
<div class="section" id="required-libraries-and-tools">
<h2>Required libraries and tools<a class="headerlink" href="#required-libraries-and-tools" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Python 2.7.3</li>
<li>virtualenv (builds isolated Python environments)</li>
<li>numpy 1.6.1 (required by pbcore)</li>
<li>h5py 2.0.1 (required by pbcore)</li>
</ul>
<p>If you are within PacBio, these requirements are already installed
within the cluster environment.</p>
<p>Otherwise, you will need to install them yourself.</p>
</div>
<div class="section" id="data-file-requirements">
<h2>Data file requirements<a class="headerlink" href="#data-file-requirements" title="Permalink to this headline">¶</a></h2>
<p>pbalign distinguishes input and output file formats by file extensions.</p>
<p>The input PacBio reads can be in FASTA, Base HDF5, Pulse HDF5, Circular
Consensus Sequence (CCS) HDF5 or file or file names (FOFN). The supported
input file extensions are as follows.</p>
<ul class="simple">
<li>FASTA : .fa or .fasta</li>
<li>PacBio BASE HDF5 : .bas.h5 or .bax.h5</li>
<li>PacBio PULSE HDF5 : .pls.h5 or .plx.h5</li>
<li>PacBio CCS HDF5 : .ccs.h5</li>
<li>File of file names : .fofn</li>
</ul>
<p>The input reference sequences can be in a FASTA file or a reference deposit
directory created by referenceUploader (a PacBio tool for uploading
references to the server and data preprocessing).</p>
<p>The output file can either be a SAM file or a Compare HDF5 file. The output
Compare HDF5 file cannot be consumed by Quiver directly unleis <code class="docutils literal"><span class="pre">--forQuiver</span></code>
option is specified. The supported output file extensions are as follows.</p>
<ul class="simple">
<li>SAM : .sam</li>
<li>PacBio Compare HDF5: .cmp.h5</li>
</ul>
</div>
<div class="section" id="manual-installation-instructions">
<h2>Manual installation instructions<a class="headerlink" href="#manual-installation-instructions" title="Permalink to this headline">¶</a></h2>
<div class="section" id="step-1-set-up-your-python-virtual-environment">
<h3>Step 1: Set up your Python virtual environment<a class="headerlink" href="#step-1-set-up-your-python-virtual-environment" title="Permalink to this headline">¶</a></h3>
<p>To install <code class="docutils literal"><span class="pre">Python</span> <span class="pre">2.7</span></code>, please visit</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">python</span><span class="o">.</span><span class="n">org</span><span class="o">/</span>
</pre></div>
</div>
<p>, or if you have root permission on Ubuntu, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">python</span>
</pre></div>
</div>
<p>To install <code class="docutils literal"><span class="pre">pip</span></code>, please visit</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">pypi</span><span class="o">.</span><span class="n">python</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">pypi</span><span class="o">/</span><span class="n">pip</span>
</pre></div>
</div>
<p>, or if you have root permission using Ubuntu, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">sudo</span> <span class="n">apt</span><span class="o">-</span><span class="n">get</span> <span class="n">install</span> <span class="n">python</span><span class="o">-</span><span class="n">pip</span>
</pre></div>
</div>
<p>To install <code class="docutils literal"><span class="pre">virtualenv</span></code>, please visit</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">pypi</span><span class="o">.</span><span class="n">python</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">pypi</span><span class="o">/</span><span class="n">virtualenv</span>
</pre></div>
</div>
<p>, or execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">virtualenv</span>
</pre></div>
</div>
<p>To set up a new virtualenv, do</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ cd; virtualenv -p python2.7 --no-site-packages my_env
</pre></div>
</div>
<p>, and activate the virtualenv using</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ source ~/my_env/bin/activate
</pre></div>
</div>
<p>To install <code class="docutils literal"><span class="pre">git</span></code>, please visit</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">git</span><span class="o">-</span><span class="n">scm</span><span class="o">.</span><span class="n">com</span><span class="o">/.</span>
</pre></div>
</div>
</div>
<div class="section" id="step-2-install-required-software-and-library">
<h3>Step 2: Install required software and library<a class="headerlink" href="#step-2-install-required-software-and-library" title="Permalink to this headline">¶</a></h3>
<p>To install blasr, please execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ git clone https://github.com/PacificBiosciences/blasr
</pre></div>
</div>
<p>, and follow instructions at</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">PacificBiosciences</span><span class="o">/</span><span class="n">blasr</span><span class="o">/</span><span class="n">blob</span><span class="o">/</span><span class="n">master</span><span class="o">/</span><span class="n">README</span><span class="o">.</span><span class="n">md</span>
</pre></div>
</div>
<p>Before installing pbcore, you may need to install numpy and h5py from</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">numpy</span><span class="o">.</span><span class="n">org</span><span class="o">/</span>
<span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">code</span><span class="o">.</span><span class="n">google</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">p</span><span class="o">/</span><span class="n">h5py</span><span class="o">/</span>
</pre></div>
</div>
<p>, or if you have root permission on Ubuntu, do</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install numpy
$ sudo apt-get install libhdf5-serial-dev
$ pip install h5py
</pre></div>
</div>
<p>To install pbcore, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install git+https://github.com/PacificBiosciences/pbcore
</pre></div>
</div>
</div>
<div class="section" id="step-3-install-optionally-required-software-and-library">
<h3>Step 3: Install optionally required software and library<a class="headerlink" href="#step-3-install-optionally-required-software-and-library" title="Permalink to this headline">¶</a></h3>
<p>To install pbh5tools, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install git+https://github.com/PacificBiosciences/pbh5tools
</pre></div>
</div>
<p>To install <code class="docutils literal"><span class="pre">HDF5</span> <span class="pre">tools</span></code>, visit</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">http</span><span class="p">:</span><span class="o">//</span><span class="n">www</span><span class="o">.</span><span class="n">hdfgroup</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">products</span><span class="o">/</span><span class="n">hdf5_tools</span><span class="o">/</span>
</pre></div>
</div>
<p>, or if you have root permission on Ubuntu, do</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ sudo apt-get install hdf5-tools
</pre></div>
</div>
</div>
<div class="section" id="step-4-install-pbalign">
<h3>Step 4: Install pbalign<a class="headerlink" href="#step-4-install-pbalign" title="Permalink to this headline">¶</a></h3>
<p>To <em>uninstall</em> pbalign, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip uninstall pbalign
</pre></div>
</div>
<p>To install pbalign, execute</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pip install git+https://github.com/PacificBiosciences/pbalign
</pre></div>
</div>
<p>, or to download the whole pbalign package with examples</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ git clone https://github.com/PacificBiosciences/pbalign.git
$ cd pbalign
$ pip install .
</pre></div>
</div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li>Basic usage of pbalign.</li>
</ol>
<ul>
<li><p class="first">Example (1.1)</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pbalign tests/data/example_read.fasta \
tests/data/example_ref.fasta \
example.sam
</pre></div>
</div>
</li>
<li><p class="first">Example (1.2)</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pbalign tests/data/example_read.fasta \
tests/data/example_ref.fasta \
example.cmp.h5
</pre></div>
</div>
</li>
<li><p class="first">Example (1.3) - with optional arguments</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pbalign --maxHits 10 --hitPolicy all \
tests/data/example_read.fasta \
tests/data/example_ref.fasta \
example.sam
</pre></div>
</div>
</li>
</ul>
<ol class="arabic simple" start="2">
<li>Advanced usage of pbalign.</li>
</ol>
<ul>
<li><p class="first">Example (2.1) - Import pre-defined options from a config File</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pbalign --configFile=tests/data/1.config \
tests/data/example_read.fasta \
tests/data/example_ref.fasta \
example.sam
</pre></div>
</div>
</li>
<li><p class="first">Example (2.2) - Pass options through to aligner</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ pbalign --algorithmOptions='-nCandidates 10 -sdpTupleSize 12' \
tests/data/example_read.fasta \
tests/data/example_ref.fasta \
example.sam
</pre></div>
</div>
</li>
<li><p class="first">Example (2.3) - Create a cmp.h5 file with –forQuiver option</p>
<div class="highlight-default"><div class="highlight"><pre><span></span># The output cmp.h5 file will loaded with quality values (pulses)
# from the input bas/bax.h5 file, sorted and repacked, and therefore
# can be consumed by Quiver directly, (Note that in order to use
# --forQuiver option, cmph5tools and h5repack are required.)
$ pbalign --forQuiver your_movie.bas.h5 your_reference.fasta out.cmp.h5
</pre></div>
</div>
</li>
</ul>
<ol class="arabic simple" start="3">
<li>Use pbalign as a library through Python API.</li>
</ol>
<ul>
<li><p class="first">Example (3.1)</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>$ python
>>> from pbalign.pbalignrunner import PBAlignRunner
>>> # Specify arguments in a list.
>>> args = ['--maxHits', '20', 'tests/data/example_read.fasta',\
... 'tests/data/example_ref.fasta', 'example.sam']
>>> # Create a PBAlignRunner object.
>>> a = PBAlignRunner(args)
>>> # Execute.
>>> exitCode = a.start()
>>> # Show all files used.
>>> print a.fileNames
</pre></div>
</div>
</li>
</ul>
</div>
<div class="section" id="usage">
<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">usage</span><span class="p">:</span> <span class="n">pbalign</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">verbose</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">version</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">profile</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">debug</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">regionTable</span> <span class="n">REGIONTABLE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">configFile</span> <span class="n">CONFIGFILE</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">algorithm</span> <span class="p">{</span><span class="n">blasr</span><span class="p">,</span><span class="n">bowtie</span><span class="p">}]</span> <span class="p">[</span><span class="o">--</span><span class="n">maxHits</span> <span class="n">MAXHITS</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">minAnchorSize</span> <span class="n">MINANCHORSIZE</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">useccs</span> <span class="p">{</span><span class="n">useccs</span><span class="p">,</span><span class="n">useccsall</span><span class="p">,</span><span class="n">useccsdenovo</span><span class="p">}]</span>
<span class="p">[</span><span class="o">--</span><span class="n">noSplitSubreads</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">nproc</span> <span class="n">NPROC</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">algorithmOptions</span> <span class="n">ALGORITHMOPTIONS</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">maxDivergence</span> <span class="n">MAXDIVERGENCE</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">minAccuracy</span> <span class="n">MINACCURACY</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">minLength</span> <span class="n">MINLENGTH</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">scoreFunction</span> <span class="p">{</span><span class="n">alignerscore</span><span class="p">,</span><span class="n">editdist</span><span class="p">,</span><span class="n">blasrscore</span><span class="p">}]</span>
<span class="p">[</span><span class="o">--</span><span class="n">scoreCutoff</span> <span class="n">SCORECUTOFF</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">hitPolicy</span> <span class="p">{</span><span class="n">randombest</span><span class="p">,</span><span class="n">allbest</span><span class="p">,</span><span class="n">random</span><span class="p">,</span><span class="nb">all</span><span class="p">}]</span> <span class="p">[</span><span class="o">--</span><span class="n">forQuiver</span><span class="p">]</span>
<span class="p">[</span><span class="o">--</span><span class="n">seed</span> <span class="n">SEED</span><span class="p">]</span> <span class="p">[</span><span class="o">--</span><span class="n">tmpDir</span> <span class="n">TMPDIR</span><span class="p">]</span>
<span class="n">inputFileName</span> <span class="n">referencePath</span> <span class="n">outputFileName</span>
<span class="n">Mapping</span> <span class="n">PacBio</span> <span class="n">sequences</span> <span class="n">to</span> <span class="n">references</span> <span class="n">using</span> <span class="n">an</span> <span class="n">algorithm</span>
<span class="n">selected</span> <span class="kn">from</span> <span class="nn">a</span> <span class="n">selection</span> <span class="n">of</span> <span class="n">supported</span> <span class="n">command</span><span class="o">-</span><span class="n">line</span> <span class="n">alignment</span>
<span class="n">algorithms</span><span class="o">.</span> <span class="n">Input</span> <span class="n">can</span> <span class="n">be</span> <span class="n">a</span> <span class="n">fasta</span><span class="p">,</span> <span class="n">pls</span><span class="o">.</span><span class="n">h5</span><span class="p">,</span> <span class="n">bas</span><span class="o">.</span><span class="n">h5</span> <span class="ow">or</span> <span class="n">ccs</span><span class="o">.</span><span class="n">h5</span>
<span class="n">file</span> <span class="ow">or</span> <span class="n">a</span> <span class="n">fofn</span> <span class="p">(</span><span class="n">file</span> <span class="n">of</span> <span class="n">file</span> <span class="n">names</span><span class="p">)</span><span class="o">.</span> <span class="n">Output</span> <span class="ow">is</span> <span class="ow">in</span> <span class="n">either</span>
<span class="nb">cmp</span><span class="o">.</span><span class="n">h5</span> <span class="ow">or</span> <span class="n">sam</span> <span class="nb">format</span><span class="o">.</span>
<span class="n">positional</span> <span class="n">arguments</span><span class="p">:</span>
<span class="n">inputFileName</span> <span class="n">The</span> <span class="nb">input</span> <span class="n">file</span> <span class="n">can</span> <span class="n">be</span> <span class="n">a</span> <span class="n">fasta</span><span class="p">,</span> <span class="n">pls</span><span class="o">.</span><span class="n">h5</span><span class="p">,</span> <span class="n">bas</span><span class="o">.</span><span class="n">h5</span><span class="p">,</span> <span class="n">ccs</span><span class="o">.</span><span class="n">h5</span>
<span class="n">file</span> <span class="ow">or</span> <span class="n">a</span> <span class="n">fofn</span><span class="o">.</span>
<span class="n">referencePath</span> <span class="n">Either</span> <span class="n">a</span> <span class="n">reference</span> <span class="n">fasta</span> <span class="n">file</span> <span class="ow">or</span> <span class="n">a</span> <span class="n">reference</span> <span class="n">repository</span><span class="o">.</span>
<span class="n">outputFileName</span> <span class="n">The</span> <span class="n">output</span> <span class="nb">cmp</span><span class="o">.</span><span class="n">h5</span> <span class="ow">or</span> <span class="n">sam</span> <span class="n">file</span><span class="o">.</span>
<span class="n">optional</span> <span class="n">arguments</span><span class="p">:</span>
<span class="o">-</span><span class="n">h</span><span class="p">,</span> <span class="o">--</span><span class="n">help</span> <span class="n">show</span> <span class="n">this</span> <span class="n">help</span> <span class="n">message</span> <span class="ow">and</span> <span class="n">exit</span>
<span class="o">--</span><span class="n">verbose</span><span class="p">,</span> <span class="o">-</span><span class="n">v</span> <span class="n">Set</span> <span class="n">the</span> <span class="n">verbosity</span> <span class="n">level</span>
<span class="o">--</span><span class="n">version</span> <span class="n">show</span> <span class="n">program</span><span class="s1">'s version number and exit</span>
<span class="o">--</span><span class="n">profile</span> <span class="n">Print</span> <span class="n">runtime</span> <span class="n">profile</span> <span class="n">at</span> <span class="n">exit</span>
<span class="o">--</span><span class="n">debug</span> <span class="n">Run</span> <span class="n">within</span> <span class="n">a</span> <span class="n">debugger</span> <span class="n">session</span>
<span class="o">--</span><span class="n">regionTable</span> <span class="n">REGIONTABLE</span>
<span class="n">Specify</span> <span class="n">a</span> <span class="n">region</span> <span class="n">table</span> <span class="k">for</span> <span class="n">filtering</span> <span class="n">reads</span><span class="o">.</span>
<span class="o">--</span><span class="n">configFile</span> <span class="n">CONFIGFILE</span>
<span class="n">Specify</span> <span class="n">a</span> <span class="nb">set</span> <span class="n">of</span> <span class="n">user</span><span class="o">-</span><span class="n">defined</span> <span class="n">argument</span> <span class="n">values</span><span class="o">.</span>
<span class="o">--</span><span class="n">algorithm</span> <span class="p">{</span><span class="n">blasr</span><span class="p">,</span><span class="n">bowtie</span><span class="p">}</span>
<span class="n">Select</span> <span class="n">an</span> <span class="n">aligorithm</span> <span class="kn">from</span> <span class="p">(</span><span class="s1">'blasr'</span><span class="p">,</span> <span class="s1">'bowtie'</span><span class="p">)</span><span class="o">.</span>
<span class="n">Default</span> <span class="n">algorithm</span> <span class="ow">is</span> <span class="n">blasr</span><span class="o">.</span>
<span class="o">--</span><span class="n">maxHits</span> <span class="n">MAXHITS</span> <span class="n">The</span> <span class="n">maximum</span> <span class="n">number</span> <span class="n">of</span> <span class="n">matches</span> <span class="n">of</span> <span class="n">each</span> <span class="n">read</span> <span class="n">to</span> <span class="n">the</span>
<span class="n">reference</span> <span class="n">sequence</span> <span class="n">that</span> <span class="n">will</span> <span class="n">be</span> <span class="n">evaluated</span><span class="o">.</span> <span class="n">Default</span>
<span class="n">value</span> <span class="ow">is</span> <span class="mf">10.</span>
<span class="o">--</span><span class="n">minAnchorSize</span> <span class="n">MINANCHORSIZE</span>
<span class="n">The</span> <span class="n">minimum</span> <span class="n">anchor</span> <span class="n">size</span> <span class="n">defines</span> <span class="n">the</span> <span class="n">length</span> <span class="n">of</span> <span class="n">the</span> <span class="n">read</span>
<span class="n">that</span> <span class="n">must</span> <span class="n">match</span> <span class="n">against</span> <span class="n">the</span> <span class="n">reference</span> <span class="n">sequence</span><span class="o">.</span> <span class="n">Default</span>
<span class="n">value</span> <span class="ow">is</span> <span class="mf">12.</span>
<span class="o">--</span><span class="n">useccs</span> <span class="p">{</span><span class="n">useccs</span><span class="p">,</span><span class="n">useccsall</span><span class="p">,</span><span class="n">useccsdenovo</span><span class="p">}</span>
<span class="n">Map</span> <span class="n">the</span> <span class="n">ccsSequence</span> <span class="n">to</span> <span class="n">the</span> <span class="n">genome</span> <span class="n">first</span><span class="p">,</span> <span class="n">then</span> <span class="n">align</span>
<span class="n">subreads</span> <span class="n">to</span> <span class="n">the</span> <span class="n">interval</span> <span class="n">that</span> <span class="n">the</span> <span class="n">CCS</span> <span class="n">reads</span> <span class="n">mapped</span> <span class="n">to</span><span class="o">.</span>
<span class="n">useccs</span><span class="p">:</span> <span class="n">only</span> <span class="n">maps</span> <span class="n">subreads</span> <span class="n">that</span> <span class="n">span</span> <span class="n">the</span> <span class="n">length</span> <span class="n">of</span>
<span class="n">the</span> <span class="n">template</span><span class="o">.</span>
<span class="n">useccsall</span><span class="p">:</span> <span class="n">maps</span> <span class="nb">all</span> <span class="n">subreads</span><span class="o">.</span>
<span class="n">useccsdenovo</span><span class="p">:</span> <span class="n">maps</span> <span class="n">ccs</span> <span class="n">only</span><span class="o">.</span>
<span class="o">--</span><span class="n">noSplitSubreads</span> <span class="n">Do</span> <span class="ow">not</span> <span class="n">split</span> <span class="n">reads</span> <span class="n">into</span> <span class="n">subreads</span> <span class="n">even</span> <span class="k">if</span> <span class="n">subread</span>
<span class="n">regions</span> <span class="n">are</span> <span class="n">available</span><span class="o">.</span>
<span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="kc">False</span><span class="o">.</span>
<span class="o">--</span><span class="n">nproc</span> <span class="n">NPROC</span> <span class="n">Number</span> <span class="n">of</span> <span class="n">threads</span><span class="o">.</span> <span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="mf">8.</span>
<span class="o">--</span><span class="n">algorithmOptions</span> <span class="n">ALGORITHMOPTIONS</span>
<span class="n">Pass</span> <span class="n">alignment</span> <span class="n">options</span> <span class="n">through</span><span class="o">.</span>
<span class="o">--</span><span class="n">maxDivergence</span> <span class="n">MAXDIVERGENCE</span>
<span class="n">The</span> <span class="n">maximum</span> <span class="n">allowed</span> <span class="n">percentage</span> <span class="n">divergence</span> <span class="n">of</span> <span class="n">a</span> <span class="n">read</span>
<span class="kn">from</span> <span class="nn">the</span> <span class="n">reference</span> <span class="n">sequence</span><span class="o">.</span> <span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="mf">30.</span>
<span class="o">--</span><span class="n">minAccuracy</span> <span class="n">MINACCURACY</span>
<span class="n">The</span> <span class="n">minimum</span> <span class="n">percentage</span> <span class="n">accuracy</span> <span class="n">of</span> <span class="n">alignments</span> <span class="n">that</span>
<span class="n">will</span> <span class="n">be</span> <span class="n">evaluated</span><span class="o">.</span> <span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="mf">70.</span>
<span class="o">--</span><span class="n">minLength</span> <span class="n">MINLENGTH</span>
<span class="n">The</span> <span class="n">minimum</span> <span class="n">aligned</span> <span class="n">read</span> <span class="n">length</span> <span class="n">of</span> <span class="n">alignments</span> <span class="n">that</span>
<span class="n">will</span> <span class="n">be</span> <span class="n">evaluated</span><span class="o">.</span> <span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="mf">50.</span>
<span class="o">--</span><span class="n">scoreFunction</span> <span class="p">{</span><span class="n">alignerscore</span><span class="p">,</span><span class="n">editdist</span><span class="p">,</span><span class="n">blasrscore</span><span class="p">}</span>
<span class="n">Specify</span> <span class="n">a</span> <span class="n">score</span> <span class="n">function</span> <span class="k">for</span> <span class="n">evaluating</span> <span class="n">alignments</span><span class="o">.</span>
<span class="n">alignerscore</span> <span class="p">:</span> <span class="n">aligner</span><span class="s1">'s score in the SAM tag '</span><span class="k">as</span><span class="s1">'.</span>
<span class="n">editdist</span> <span class="p">:</span> <span class="n">edit</span> <span class="n">distance</span> <span class="n">between</span> <span class="n">read</span> <span class="ow">and</span> <span class="n">reference</span><span class="o">.</span>
<span class="n">blasrscore</span> <span class="p">:</span> <span class="n">blasr</span><span class="s1">'s default score function.</span>
<span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="n">alignerscore</span><span class="o">.</span>
<span class="o">--</span><span class="n">scoreCutoff</span> <span class="n">SCORECUTOFF</span>
<span class="n">The</span> <span class="n">worst</span> <span class="n">score</span> <span class="n">to</span> <span class="n">output</span> <span class="n">an</span> <span class="n">alignment</span><span class="o">.</span>
<span class="o">--</span><span class="n">hitPolicy</span> <span class="p">{</span><span class="n">randombest</span><span class="p">,</span><span class="n">allbest</span><span class="p">,</span><span class="n">random</span><span class="p">,</span><span class="nb">all</span><span class="p">}</span>
<span class="n">Specify</span> <span class="n">a</span> <span class="n">policy</span> <span class="k">for</span> <span class="n">how</span> <span class="n">to</span> <span class="n">treat</span> <span class="n">multiple</span> <span class="n">hit</span>
<span class="n">random</span> <span class="p">:</span> <span class="n">selects</span> <span class="n">a</span> <span class="n">random</span> <span class="n">hit</span><span class="o">.</span>
<span class="nb">all</span> <span class="p">:</span> <span class="n">selects</span> <span class="nb">all</span> <span class="n">hits</span><span class="o">.</span>
<span class="n">allbest</span> <span class="p">:</span> <span class="n">selects</span> <span class="nb">all</span> <span class="n">the</span> <span class="n">best</span> <span class="n">score</span> <span class="n">hits</span><span class="o">.</span>
<span class="n">randombest</span><span class="p">:</span> <span class="n">selects</span> <span class="n">a</span> <span class="n">random</span> <span class="n">hit</span> <span class="kn">from</span> <span class="nn">all</span> <span class="n">best</span>
<span class="n">alignment</span> <span class="n">score</span> <span class="n">hits</span><span class="o">.</span>
<span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="n">randombest</span><span class="o">.</span>
<span class="o">--</span><span class="n">forQuiver</span> <span class="n">The</span> <span class="n">output</span> <span class="nb">cmp</span><span class="o">.</span><span class="n">h5</span> <span class="n">file</span> <span class="n">which</span> <span class="n">will</span> <span class="n">be</span> <span class="nb">sorted</span><span class="p">,</span> <span class="n">loaded</span>
<span class="k">with</span> <span class="n">pulse</span> <span class="n">information</span><span class="p">,</span> <span class="ow">and</span> <span class="n">repacked</span><span class="p">,</span> <span class="n">so</span> <span class="n">that</span> <span class="n">it</span>
<span class="n">can</span> <span class="n">be</span> <span class="n">consumed</span> <span class="n">by</span> <span class="n">quiver</span> <span class="n">directly</span><span class="o">.</span> <span class="n">This</span> <span class="n">requires</span>
<span class="n">the</span> <span class="nb">input</span> <span class="n">file</span> <span class="n">to</span> <span class="n">be</span> <span class="ow">in</span> <span class="n">PacBio</span> <span class="n">bas</span><span class="o">/</span><span class="n">pls</span><span class="o">.</span><span class="n">h5</span> <span class="nb">format</span><span class="o">.</span>
<span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="kc">False</span><span class="o">.</span>
<span class="o">--</span><span class="n">seed</span> <span class="n">SEED</span> <span class="n">Initialize</span> <span class="n">the</span> <span class="n">random</span> <span class="n">number</span> <span class="n">generator</span> <span class="k">with</span> <span class="n">a</span> <span class="n">none</span><span class="o">-</span><span class="n">zero</span>
<span class="n">integer</span><span class="o">.</span> <span class="n">Zero</span> <span class="n">means</span> <span class="n">that</span> <span class="n">current</span> <span class="n">system</span> <span class="n">time</span> <span class="ow">is</span> <span class="n">used</span><span class="o">.</span>
<span class="n">Default</span> <span class="n">value</span> <span class="ow">is</span> <span class="mf">1.</span>
<span class="o">--</span><span class="n">tmpDir</span> <span class="n">TMPDIR</span> <span class="n">Specify</span> <span class="n">a</span> <span class="n">directory</span> <span class="k">for</span> <span class="n">saving</span> <span class="n">temporary</span> <span class="n">files</span><span class="o">.</span>
<span class="n">Default</span> <span class="ow">is</span> <span class="o">/</span><span class="n">scratch</span><span class="o">.</span>
</pre></div>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">How to install and run pbalign</a><ul>
<li><a class="reference internal" href="#background">Background</a></li>
<li><a class="reference internal" href="#required-software">Required software</a></li>
<li><a class="reference internal" href="#required-libraries-and-tools">Required libraries and tools</a></li>
<li><a class="reference internal" href="#data-file-requirements">Data file requirements</a></li>
<li><a class="reference internal" href="#manual-installation-instructions">Manual installation instructions</a><ul>
<li><a class="reference internal" href="#step-1-set-up-your-python-virtual-environment">Step 1: Set up your Python virtual environment</a></li>
<li><a class="reference internal" href="#step-2-install-required-software-and-library">Step 2: Install required software and library</a></li>
<li><a class="reference internal" href="#step-3-install-optionally-required-software-and-library">Step 3: Install optionally required software and library</a></li>
<li><a class="reference internal" href="#step-4-install-pbalign">Step 4: Install pbalign</a></li>
</ul>
</li>
<li><a class="reference internal" href="#examples">Examples</a></li>
<li><a class="reference internal" href="#usage">Usage</a></li>
</ul>
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