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<a href="Bio-module.html">Package Bio</a> ::
Package SubsMat
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<!-- ==================== PACKAGE DESCRIPTION ==================== -->
<h1 class="epydoc">Package SubsMat</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SubsMat-pysrc.html">source code</a></span></p>
<p>Substitution matrices, log odds matrices, and operations on them.</p>
<!-- ==================== SUBMODULES ==================== -->
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<li> <strong class="uidlink"><a href="Bio.SubsMat.FreqTable-module.html">Bio.SubsMat.FreqTable</a></strong> </li>
<li> <strong class="uidlink"><a href="Bio.SubsMat.MatrixInfo-module.html">Bio.SubsMat.MatrixInfo</a></strong>: <em class="summary">A whole bunch of substitution matrices for use in alignments, etc.</em> </li>
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<a href="Bio.SubsMat.BadMatrix-class.html" class="summary-name">BadMatrix</a><br />
Exception raised when verifying a matrix
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<a href="Bio.SubsMat.SeqMat-class.html" class="summary-name">SeqMat</a><br />
A Generic sequence matrix class The key is a 2-tuple containing the
letter indices of the matrix.
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<td><span class="summary-sig"><a name="_build_obs_freq_mat"></a><span class="summary-sig-name">_build_obs_freq_mat</span>(<span class="summary-sig-arg">acc_rep_mat</span>)</span><br />
build_obs_freq_mat(acc_rep_mat): Build the observed frequency matrix,
from an accepted replacements matrix The accRep matrix should be
generated by the user.</td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#_build_obs_freq_mat">source code</a></span>
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<td><span class="summary-sig"><a name="_exp_freq_table_from_obs_freq"></a><span class="summary-sig-name">_exp_freq_table_from_obs_freq</span>(<span class="summary-sig-arg">obs_freq_mat</span>)</span></td>
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<td><span class="summary-sig"><a name="_build_exp_freq_mat"></a><span class="summary-sig-name">_build_exp_freq_mat</span>(<span class="summary-sig-arg">exp_freq_table</span>)</span><br />
Build an expected frequency matrix exp_freq_table: should be a
FreqTable instance</td>
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<td><span class="summary-sig"><a name="_build_subs_mat"></a><span class="summary-sig-name">_build_subs_mat</span>(<span class="summary-sig-arg">obs_freq_mat</span>,
<span class="summary-sig-arg">exp_freq_mat</span>)</span><br />
Build the substitution matrix</td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#_build_subs_mat">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SubsMat-module.html#_build_log_odds_mat" class="summary-sig-name" onclick="show_private();">_build_log_odds_mat</a>(<span class="summary-sig-arg">subs_mat</span>,
<span class="summary-sig-arg">logbase</span>=<span class="summary-sig-default">2</span>,
<span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">10.0</span>,
<span class="summary-sig-arg">round_digit</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">keep_nd</span>=<span class="summary-sig-default">0</span>)</span><br />
_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1):
Build a log-odds matrix logbase=2: base of logarithm used to build
(default 2) factor=10.: a factor by which each matrix entry is
multiplied round_digit: roundoff place after decimal point keep_nd:
if true, keeps the -999 value for non-determined values (for which
there are no substitutions in the frequency substitutions matrix).</td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#_build_log_odds_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="make_log_odds_matrix"></a><span class="summary-sig-name">make_log_odds_matrix</span>(<span class="summary-sig-arg">acc_rep_mat</span>,
<span class="summary-sig-arg">exp_freq_table</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">logbase</span>=<span class="summary-sig-default">2</span>,
<span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">1.0</span>,
<span class="summary-sig-arg">round_digit</span>=<span class="summary-sig-default">9</span>,
<span class="summary-sig-arg">keep_nd</span>=<span class="summary-sig-default">0</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#make_log_odds_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="observed_frequency_to_substitution_matrix"></a><span class="summary-sig-name">observed_frequency_to_substitution_matrix</span>(<span class="summary-sig-arg">obs_freq_mat</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#observed_frequency_to_substitution_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="read_text_matrix"></a><span class="summary-sig-name">read_text_matrix</span>(<span class="summary-sig-arg">data_file</span>,
<span class="summary-sig-arg">mat_type</span>=<span class="summary-sig-default">0</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#read_text_matrix">source code</a></span>
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<td><span class="summary-sig"><a name="two_mat_relative_entropy"></a><span class="summary-sig-name">two_mat_relative_entropy</span>(<span class="summary-sig-arg">mat_1</span>,
<span class="summary-sig-arg">mat_2</span>,
<span class="summary-sig-arg">logbase</span>=<span class="summary-sig-default">2</span>,
<span class="summary-sig-arg">diag</span>=<span class="summary-sig-default">3</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#two_mat_relative_entropy">source code</a></span>
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<td><span class="summary-sig"><a name="two_mat_DJS"></a><span class="summary-sig-name">two_mat_DJS</span>(<span class="summary-sig-arg">mat_1</span>,
<span class="summary-sig-arg">mat_2</span>,
<span class="summary-sig-arg">pi_1</span>=<span class="summary-sig-default">0.5</span>,
<span class="summary-sig-arg">pi_2</span>=<span class="summary-sig-default">0.5</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#two_mat_DJS">source code</a></span>
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<a name="NOTYPE"></a><span class="summary-name">NOTYPE</span> = <code title="0">0</code>
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<a name="ACCREP"></a><span class="summary-name">ACCREP</span> = <code title="1">1</code>
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<a name="OBSFREQ"></a><span class="summary-name">OBSFREQ</span> = <code title="2">2</code>
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<a name="SUBS"></a><span class="summary-name">SUBS</span> = <code title="3">3</code>
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<a name="EXPFREQ"></a><span class="summary-name">EXPFREQ</span> = <code title="4">4</code>
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<a name="LO"></a><span class="summary-name">LO</span> = <code title="5">5</code>
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<a name="EPSILON"></a><span class="summary-name">EPSILON</span> = <code title="1e-14">1e-14</code>
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<a name="BadMatrixError"></a><span class="summary-name">BadMatrixError</span> = <code title="BadMatrix()">BadMatrix()</code>
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<a name="diagNO"></a><span class="summary-name">diagNO</span> = <code title="1">1</code>
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<a name="diagONLY"></a><span class="summary-name">diagONLY</span> = <code title="2">2</code>
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<a name="diagALL"></a><span class="summary-name">diagALL</span> = <code title="3">3</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_build_log_odds_mat</span>(<span class="sig-arg">subs_mat</span>,
<span class="sig-arg">logbase</span>=<span class="sig-default">2</span>,
<span class="sig-arg">factor</span>=<span class="sig-default">10.0</span>,
<span class="sig-arg">round_digit</span>=<span class="sig-default">0</span>,
<span class="sig-arg">keep_nd</span>=<span class="sig-default">0</span>)</span>
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<p>_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1):
Build a log-odds matrix logbase=2: base of logarithm used to build
(default 2) factor=10.: a factor by which each matrix entry is multiplied
round_digit: roundoff place after decimal point keep_nd: if true, keeps
the -999 value for non-determined values (for which there are no
substitutions in the frequency substitutions matrix). If false, plants
the minimum log-odds value of the matrix in entries containing -999</p>
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