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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PopGen-module.html">Package PopGen</a> ::
<a href="Bio.PopGen.SimCoal-module.html">Package SimCoal</a> ::
Module Template
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module Template</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html">source code</a></span></p>
<!-- ==================== FUNCTIONS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="exec_template"></a><span class="summary-sig-name">exec_template</span>(<span class="summary-sig-arg">template</span>)</span></td>
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<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#exec_template">source code</a></span>
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<td><span class="summary-sig"><a name="process_para"></a><span class="summary-sig-name">process_para</span>(<span class="summary-sig-arg">in_string</span>,
<span class="summary-sig-arg">out_file_prefix</span>,
<span class="summary-sig-arg">para_list</span>,
<span class="summary-sig-arg">curr_values</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#process_para">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="dupe"></a><span class="summary-sig-name">dupe</span>(<span class="summary-sig-arg">motif</span>,
<span class="summary-sig-arg">times</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#dupe">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_xy_from_matrix"></a><span class="summary-sig-name">get_xy_from_matrix</span>(<span class="summary-sig-arg">x_max</span>,
<span class="summary-sig-arg">y_max</span>,
<span class="summary-sig-arg">pos</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_xy_from_matrix">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_step_2d"></a><span class="summary-sig-name">get_step_2d</span>(<span class="summary-sig-arg">x_max</span>,
<span class="summary-sig-arg">y_max</span>,
<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">y</span>,
<span class="summary-sig-arg">mig</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_step_2d">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="generate_ssm2d_mat"></a><span class="summary-sig-name">generate_ssm2d_mat</span>(<span class="summary-sig-arg">x_max</span>,
<span class="summary-sig-arg">y_max</span>,
<span class="summary-sig-arg">mig</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_ssm2d_mat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="generate_island_mat"></a><span class="summary-sig-name">generate_island_mat</span>(<span class="summary-sig-arg">total_size</span>,
<span class="summary-sig-arg">mig</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_island_mat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="generate_null_mat"></a><span class="summary-sig-name">generate_null_mat</span>(<span class="summary-sig-arg">total_size</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_null_mat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="generate_join_events"></a><span class="summary-sig-name">generate_join_events</span>(<span class="summary-sig-arg">t</span>,
<span class="summary-sig-arg">total_size</span>,
<span class="summary-sig-arg">join_size</span>,
<span class="summary-sig-arg">orig_size</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_join_events">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="no_processor"></a><span class="summary-sig-name">no_processor</span>(<span class="summary-sig-arg">in_string</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#no_processor">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="process_text"></a><span class="summary-sig-name">process_text</span>(<span class="summary-sig-arg">in_string</span>,
<span class="summary-sig-arg">out_file_prefix</span>,
<span class="summary-sig-arg">para_list</span>,
<span class="summary-sig-arg">curr_values</span>,
<span class="summary-sig-arg">specific_processor</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#process_text">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="generate_model"></a><span class="summary-sig-name">generate_model</span>(<span class="summary-sig-arg">par_stream</span>,
<span class="summary-sig-arg">out_prefix</span>,
<span class="summary-sig-arg">params</span>,
<span class="summary-sig-arg">specific_processor</span>=<span class="summary-sig-default"><function no_processor at 0x4da77d0></span>,
<span class="summary-sig-arg">out_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_model">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PopGen.SimCoal.Template-module.html#get_demography_template" class="summary-sig-name">get_demography_template</a>(<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">model</span>,
<span class="summary-sig-arg">tp_dir</span>=<span class="summary-sig-default">None</span>)</span><br />
Gets a demograpy template.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_demography_template">source code</a></span>
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<td><span class="summary-sig"><a name="_gen_loci"></a><span class="summary-sig-name">_gen_loci</span>(<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">loci</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#_gen_loci">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PopGen.SimCoal.Template-module.html#get_chr_template" class="summary-sig-name">get_chr_template</a>(<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">chrs</span>)</span><br />
Writes a Simcoal2 loci template part.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_chr_template">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.PopGen.SimCoal.Template-module.html#generate_simcoal_from_template" class="summary-sig-name">generate_simcoal_from_template</a>(<span class="summary-sig-arg">model</span>,
<span class="summary-sig-arg">chrs</span>,
<span class="summary-sig-arg">params</span>,
<span class="summary-sig-arg">out_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">tp_dir</span>=<span class="summary-sig-default">None</span>)</span><br />
Writes a complete SimCoal2 template file.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_simcoal_from_template">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_demography_template</span>(<span class="sig-arg">stream</span>,
<span class="sig-arg">model</span>,
<span class="sig-arg">tp_dir</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_demography_template">source code</a></span>
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<pre class="literalblock">
Gets a demograpy template.
Most probably this model needs to be sent to GenCases.
stream - Writable stream.
param - Template file.
tp_dir - Directory where to find the template, if None
use an internal template
</pre>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_chr_template</span>(<span class="sig-arg">stream</span>,
<span class="sig-arg">chrs</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#get_chr_template">source code</a></span>
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<pre class="literalblock">
Writes a Simcoal2 loci template part.
stream - Writable stream.
chr - Chromosome list.
Current loci list:
[(chr_repeats,[(marker, (params))])]
chr_repeats --> Number of chromosome repeats
marker --> 'SNP', 'DNA', 'RFLP', 'MICROSAT'
params --> Simcoal2 parameters for markers (list of floats
or ints - if to be processed by generate_model)
</pre>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">generate_simcoal_from_template</span>(<span class="sig-arg">model</span>,
<span class="sig-arg">chrs</span>,
<span class="sig-arg">params</span>,
<span class="sig-arg">out_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">tp_dir</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PopGen.SimCoal.Template-pysrc.html#generate_simcoal_from_template">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Writes a complete SimCoal2 template file.
This joins together get_demography_template and get_chr_template,
which are feed into generate_model
Please check the three functions for parameters (model from
get_demography_template, chrs from get_chr_template and
params from generate_model).
</pre>
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