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<a href="Bio-module.html">Package Bio</a> ::
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Module _parse_yn00
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module _parse_yn00</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo.PAML._parse_yn00-pysrc.html">source code</a></span></p>
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<td><span class="summary-sig"><a href="Bio.Phylo.PAML._parse_yn00-module.html#parse_ng86" class="summary-sig-name">parse_ng86</a>(<span class="summary-sig-arg">lines</span>,
<span class="summary-sig-arg">results</span>)</span><br />
Parse the Nei & Gojobori (1986) section of the resuls.</td>
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<td><span class="summary-sig"><a href="Bio.Phylo.PAML._parse_yn00-module.html#parse_yn00" class="summary-sig-name">parse_yn00</a>(<span class="summary-sig-arg">lines</span>,
<span class="summary-sig-arg">results</span>,
<span class="summary-sig-arg">sequences</span>)</span><br />
Parse the Yang & Nielsen (2000) part of the results.</td>
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<span class="codelink"><a href="Bio.Phylo.PAML._parse_yn00-pysrc.html#parse_yn00">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Phylo.PAML._parse_yn00-module.html#parse_others" class="summary-sig-name">parse_others</a>(<span class="summary-sig-arg">lines</span>,
<span class="summary-sig-arg">results</span>,
<span class="summary-sig-arg">sequences</span>)</span><br />
Parse the results from the other methods.</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.Phylo.PAML'"><code class="variable-quote">'</code><code class="variable-string">Bio.Phylo.PAML</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse_ng86</span>(<span class="sig-arg">lines</span>,
<span class="sig-arg">results</span>)</span>
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><span class="codelink"><a href="Bio.Phylo.PAML._parse_yn00-pysrc.html#parse_ng86">source code</a></span>
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<p>Parse the Nei & Gojobori (1986) section of the resuls.
Nei_Gojobori results are organized in a lower triangular mattrix, with
the sequence names labeling the rows and statistics in the format: w (dN
dS) per column Example row (2 columns): 0.0000 (0.0000 0.0207) 0.0000
(0.0000 0.0421)</p>
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<a name="parse_yn00"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse_yn00</span>(<span class="sig-arg">lines</span>,
<span class="sig-arg">results</span>,
<span class="sig-arg">sequences</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML._parse_yn00-pysrc.html#parse_yn00">source code</a></span>
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<p>Parse the Yang & Nielsen (2000) part of the results. Yang &
Nielsen results are organized in a table with each row comprising one
pairwise species comparison. Rows are labeled by spequence number rather
than by sequence name.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">parse_others</span>(<span class="sig-arg">lines</span>,
<span class="sig-arg">results</span>,
<span class="sig-arg">sequences</span>)</span>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML._parse_yn00-pysrc.html#parse_others">source code</a></span>
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<p>Parse the results from the other methods.</p>
<p>The remaining methods are grouped together. Statistics for all three
are listed for each of the pairwise species comparisons, with each
method's results on its own line. The stats in this section must be
handled differently due to the possible presence of NaN values, which
won't get caught by my typical "line_floats" method used
above.</p>
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