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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Clustalw-module.html">Package Clustalw</a> ::
Class MultipleAlignCL
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class MultipleAlignCL</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL">source code</a></span></p>
<p>Represent a clustalw multiple alignment command line.</p>
<p>This is meant to make it easy to code the command line options you
want to submit to clustalw.</p>
<p>Clustalw has a ton of options and things to do but this is set up to
represent a clustalw mutliple alignment.</p>
<p>Warning: I don't use all of these options personally, so if you find
one to be broken for any reason, please let us know!</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Clustalw.MultipleAlignCL-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence_file</span>,
<span class="summary-sig-arg">command</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">clustalw</code><code class="variable-quote">'</code></span>)</span><br />
Initialize some general parameters that can be set as attributes.</td>
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<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br />
Write out the command line as a string.</td>
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<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.__str__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="set_output"></a><span class="summary-sig-name">set_output</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">output_file</span>,
<span class="summary-sig-arg">output_type</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">output_order</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">change_case</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">add_seqnos</span>=<span class="summary-sig-default">None</span>)</span><br />
Set the output parameters for the command line.</td>
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<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_output">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Clustalw.MultipleAlignCL-class.html#set_guide_tree" class="summary-sig-name">set_guide_tree</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree_file</span>)</span><br />
Provide a file to use as the guide tree for alignment.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_guide_tree">source code</a></span>
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<td><span class="summary-sig"><a name="set_new_guide_tree"></a><span class="summary-sig-name">set_new_guide_tree</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">tree_file</span>)</span><br />
Set the name of the guide tree file generated in the alignment.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_new_guide_tree">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Clustalw.MultipleAlignCL-class.html#set_protein_matrix" class="summary-sig-name">set_protein_matrix</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">protein_matrix</span>)</span><br />
Set the type of protein matrix to use.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_protein_matrix">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Clustalw.MultipleAlignCL-class.html#set_dna_matrix" class="summary-sig-name">set_dna_matrix</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dna_matrix</span>)</span><br />
Set the type of DNA matrix to use.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_dna_matrix">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Clustalw.MultipleAlignCL-class.html#set_type" class="summary-sig-name">set_type</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">residue_type</span>)</span><br />
Set the type of residues within the file.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_type">source code</a></span>
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<!-- ==================== CLASS VARIABLES ==================== -->
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<a name="OUTPUT_TYPES"></a><span class="summary-name">OUTPUT_TYPES</span> = <code title="['GCG', 'GDE', 'PHYLIP', 'PIR', 'NEXUS', 'FASTA']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">GCG</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GDE</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PHYLIP</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PIR</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">NEXUS</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">FASTA</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
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<a name="OUTPUT_ORDER"></a><span class="summary-name">OUTPUT_ORDER</span> = <code title="['INPUT', 'ALIGNED']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">INPUT</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ALIGNED</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="OUTPUT_CASE"></a><span class="summary-name">OUTPUT_CASE</span> = <code title="['LOWER', 'UPPER']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">LOWER</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">UPPER</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="OUTPUT_SEQNOS"></a><span class="summary-name">OUTPUT_SEQNOS</span> = <code title="['OFF', 'ON']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">OFF</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ON</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="RESIDUE_TYPES"></a><span class="summary-name">RESIDUE_TYPES</span> = <code title="['PROTEIN', 'DNA']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">PROTEIN</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">DNA</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="PROTEIN_MATRIX"></a><span class="summary-name">PROTEIN_MATRIX</span> = <code title="['BLOSUM', 'PAM', 'GONNET', 'ID']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">BLOSUM</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">PAM</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">GONNET</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">ID</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="DNA_MATRIX"></a><span class="summary-name">DNA_MATRIX</span> = <code title="['IUB', 'CLUSTALW']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">IUB</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">CLUSTALW</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sequence_file</span>,
<span class="sig-arg">command</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">clustalw</code><code class="variable-quote">'</code></span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.__init__">source code</a></span>
</td>
</tr></table>
<p>Initialize some general parameters that can be set as attributes.</p>
<p>Arguments: o sequence_file - The file to read the sequences for
alignment from. o command - The command used to run clustalw. This
defaults to just 'clustalw' (ie. assumes you have it on your path
somewhere).</p>
<p>General attributes that can be set: o is_quick - if set as 1, will use
a fast algorithm to create the alignment guide tree. o allow_negative -
allow negative values in the alignment matrix.</p>
<p>Multiple alignment attributes that can be set as attributes: o
gap_open_pen - Gap opening penalty o gap_ext_pen - Gap extension penalty
o is_no_end_pen - A flag as to whether or not there should be a gap
separation penalty for the ends. o gap_sep_range - The gap separation
penalty range. o is_no_pgap - A flag to turn off residue specific gaps o
is_no_hgap - A flag to turn off hydrophilic gaps o h_gap_residues - A
list of residues to count a hydrophilic o max_div - A percent identity to
use for delay (? - I don't undertand this!) o trans_weight - The weight
to use for transitions</p>
<dl class="fields">
</dl>
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<a name="set_guide_tree"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_guide_tree</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">tree_file</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_guide_tree">source code</a></span>
</td>
</tr></table>
<p>Provide a file to use as the guide tree for alignment.</p>
<p>Raises: o IOError - If the tree_file doesn't exist.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_protein_matrix"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_protein_matrix</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">protein_matrix</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_protein_matrix">source code</a></span>
</td>
</tr></table>
<p>Set the type of protein matrix to use.</p>
<p>Protein matrix can be either one of the defined types (blosum, pam,
gonnet or id) or a file with your own defined matrix.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_dna_matrix"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_dna_matrix</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">dna_matrix</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_dna_matrix">source code</a></span>
</td>
</tr></table>
<p>Set the type of DNA matrix to use.</p>
<p>The dna_matrix can either be one of the defined types (iub or
clustalw) or a file with the matrix to use.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_type"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_type</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">residue_type</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Clustalw-pysrc.html#MultipleAlignCL.set_type">source code</a></span>
</td>
</tr></table>
<p>Set the type of residues within the file.</p>
<p>Clustal tries to guess whether the info is protein or DNA based on the
number of GATCs, but this can be wrong if you have a messed up protein or
DNA you are working with, so this allows you to set it explicitly.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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