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<a href="Bio-module.html">Package Bio</a> ::
Module pairwise2
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module pairwise2</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.pairwise2-pysrc.html">source code</a></span></p>
<p>This package implements pairwise sequence alignment using a dynamic
programming algorithm.</p>
<p>This provides functions to get global and local alignments between two
sequences. A global alignment finds the best concordance between all
characters in two sequences. A local alignment finds just the
subsequences that align the best.</p>
<p>When doing alignments, you can specify the match score and gap
penalties. The match score indicates the compatibility between an
alignment of two characters in the sequences. Highly compatible
characters should be given positive scores, and incompatible ones should
be given negative scores or 0. The gap penalties should be negative.</p>
<p>The names of the alignment functions in this module follow the
convention <alignment type>XX where <alignment type> is
either "global" or "local" and XX is a 2 character
code indicating the parameters it takes. The first character indicates
the parameters for matches (and mismatches), and the second indicates the
parameters for gap penalties.</p>
<p>The match parameters are CODE DESCRIPTION x No parameters.
Identical characters have score of 1, otherwise 0. m A match score is
the score of identical chars, otherwise mismatch score. d A
dictionary returns the score of any pair of characters. c A callback
function returns scores.</p>
<p>The gap penalty parameters are CODE DESCRIPTION x No gap
penalties. s Same open and extend gap penalties for both sequences. d
The sequences have different open and extend gap penalties. c A
callback function returns the gap penalties.</p>
<p>All the different alignment functions are contained in an object
"align". For example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio <span class="py-keyword">import</span> pairwise2
<span class="py-prompt">>>> </span>alignments = pairwise2.align.globalxx(<span class="py-string">"ACCGT"</span>, <span class="py-string">"ACG"</span>)</pre>
<p>will return a list of the alignments between the two strings. The
parameters of the alignment function depends on the function called. Some
examples:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>pairwise2.align.globalxx(<span class="py-string">"ACCGT"</span>, <span class="py-string">"ACG"</span>)
<span class="py-output"> # Find the best global alignment between the two sequences.</span>
<span class="py-output"> # Identical characters are given 1 point. No points are deducted</span>
<span class="py-output"> # for mismatches or gaps.</span></pre>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>pairwise2.align.localxx(<span class="py-string">"ACCGT"</span>, <span class="py-string">"ACG"</span>)
<span class="py-output"> # Same thing as before, but with a local alignment.</span></pre>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>pairwise2.align.globalmx(<span class="py-string">"ACCGT"</span>, <span class="py-string">"ACG"</span>, 2, -1)
<span class="py-output"> # Do a global alignment. Identical characters are given 2 points,</span>
<span class="py-output"> # 1 point is deducted for each non-identical character.</span></pre>
<pre class="py-doctest">
<span class="py-prompt">>>> </span>pairwise2.align.globalms(<span class="py-string">"ACCGT"</span>, <span class="py-string">"ACG"</span>, 2, -1, -.5, -.1)
<span class="py-output"> # Same as above, except now 0.5 points are deducted when opening a</span>
<span class="py-output"> # gap, and 0.1 points are deducted when extending it.</span></pre>
<p>To see a description of the parameters for a function, please look at
the docstring for the function.</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> newalign.align.localds.__doc__
<span class="py-output">localds(sequenceA, sequenceB, match_dict, open, extend) -> alignments</span></pre>
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<span class="summary-type"> </span>
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<a href="Bio.pairwise2.identity_match-class.html" class="summary-name">identity_match</a><br />
identity_match([match][, mismatch]) -> match_fn
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<span class="summary-type"> </span>
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<a href="Bio.pairwise2.dictionary_match-class.html" class="summary-name">dictionary_match</a><br />
dictionary_match(score_dict[, symmetric]) -> match_fn
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<a href="Bio.pairwise2.affine_penalty-class.html" class="summary-name">affine_penalty</a><br />
affine_penalty(open, extend[, penalize_extend_when_opening]) ->
gap_fn
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<td><span class="summary-sig"><a name="_align"></a><span class="summary-sig-name">_align</span>(<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">match_fn</span>,
<span class="summary-sig-arg">gap_A_fn</span>,
<span class="summary-sig-arg">gap_B_fn</span>,
<span class="summary-sig-arg">penalize_extend_when_opening</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>,
<span class="summary-sig-arg">align_globally</span>,
<span class="summary-sig-arg">gap_char</span>,
<span class="summary-sig-arg">force_generic</span>,
<span class="summary-sig-arg">score_only</span>,
<span class="summary-sig-arg">one_alignment_only</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_align">source code</a></span>
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<td><span class="summary-sig"><a name="_make_score_matrix_generic"></a><span class="summary-sig-name">_make_score_matrix_generic</span>(<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">match_fn</span>,
<span class="summary-sig-arg">gap_A_fn</span>,
<span class="summary-sig-arg">gap_B_fn</span>,
<span class="summary-sig-arg">penalize_extend_when_opening</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>,
<span class="summary-sig-arg">align_globally</span>,
<span class="summary-sig-arg">score_only</span>)</span></td>
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<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_make_score_matrix_generic">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_score_matrix_fast"></a><span class="summary-sig-name">_make_score_matrix_fast</span>(<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">match_fn</span>,
<span class="summary-sig-arg">open_A</span>,
<span class="summary-sig-arg">extend_A</span>,
<span class="summary-sig-arg">open_B</span>,
<span class="summary-sig-arg">extend_B</span>,
<span class="summary-sig-arg">penalize_extend_when_opening</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>,
<span class="summary-sig-arg">align_globally</span>,
<span class="summary-sig-arg">score_only</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_make_score_matrix_fast">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_recover_alignments"></a><span class="summary-sig-name">_recover_alignments</span>(<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">starts</span>,
<span class="summary-sig-arg">score_matrix</span>,
<span class="summary-sig-arg">trace_matrix</span>,
<span class="summary-sig-arg">align_globally</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>,
<span class="summary-sig-arg">gap_char</span>,
<span class="summary-sig-arg">one_alignment_only</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_recover_alignments">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_find_start"></a><span class="summary-sig-name">_find_start</span>(<span class="summary-sig-arg">score_matrix</span>,
<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">gap_A_fn</span>,
<span class="summary-sig-arg">gap_B_fn</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>,
<span class="summary-sig-arg">align_globally</span>)</span></td>
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<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_find_start">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_find_global_start"></a><span class="summary-sig-name">_find_global_start</span>(<span class="summary-sig-arg">sequenceA</span>,
<span class="summary-sig-arg">sequenceB</span>,
<span class="summary-sig-arg">score_matrix</span>,
<span class="summary-sig-arg">gap_A_fn</span>,
<span class="summary-sig-arg">gap_B_fn</span>,
<span class="summary-sig-arg">penalize_end_gaps</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_find_global_start">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_find_local_start"></a><span class="summary-sig-name">_find_local_start</span>(<span class="summary-sig-arg">score_matrix</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_find_local_start">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_clean_alignments"></a><span class="summary-sig-name">_clean_alignments</span>(<span class="summary-sig-arg">alignments</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_clean_alignments">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_pad_until_equal"></a><span class="summary-sig-name">_pad_until_equal</span>(<span class="summary-sig-arg">s1</span>,
<span class="summary-sig-arg">s2</span>,
<span class="summary-sig-arg">char</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_pad_until_equal">source code</a></span>
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<td><span class="summary-sig"><a name="_lpad_until_equal"></a><span class="summary-sig-name">_lpad_until_equal</span>(<span class="summary-sig-arg">s1</span>,
<span class="summary-sig-arg">s2</span>,
<span class="summary-sig-arg">char</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_lpad_until_equal">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_pad"></a><span class="summary-sig-name">_pad</span>(<span class="summary-sig-arg">s</span>,
<span class="summary-sig-arg">char</span>,
<span class="summary-sig-arg">n</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_pad">source code</a></span>
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<span class="summary-type"> </span>
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a name="_lpad"></a><span class="summary-sig-name">_lpad</span>(<span class="summary-sig-arg">s</span>,
<span class="summary-sig-arg">char</span>,
<span class="summary-sig-arg">n</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#_lpad">source code</a></span>
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<td><span class="summary-sig"><a name="rint"></a><span class="summary-sig-name">rint</span>(<span class="summary-sig-arg">x</span>,
<span class="summary-sig-arg">precision</span>=<span class="summary-sig-default">1000</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#rint">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="calc_affine_penalty"></a><span class="summary-sig-name">calc_affine_penalty</span>(<span class="summary-sig-arg">length</span>,
<span class="summary-sig-arg">open</span>,
<span class="summary-sig-arg">extend</span>,
<span class="summary-sig-arg">penalize_extend_when_opening</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#calc_affine_penalty">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.pairwise2-module.html#print_matrix" class="summary-sig-name">print_matrix</a>(<span class="summary-sig-arg">matrix</span>)</span><br />
Print out a matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#print_matrix">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">string</span>
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<td><span class="summary-sig"><a name="format_alignment"></a><span class="summary-sig-name">format_alignment</span>(<span class="summary-sig-arg">align1</span>,
<span class="summary-sig-arg">align2</span>,
<span class="summary-sig-arg">score</span>,
<span class="summary-sig-arg">begin</span>,
<span class="summary-sig-arg">end</span>)</span><br />
Format the alignment prettily into a string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.pairwise2-pysrc.html#format_alignment">source code</a></span>
</td>
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</td>
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<!-- ==================== VARIABLES ==================== -->
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<td align="left"><span class="table-header">Variables</span></td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="MAX_ALIGNMENTS"></a><span class="summary-name">MAX_ALIGNMENTS</span> = <code title="1000">1000</code>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="align"></a><span class="summary-name">align</span> = <code title="align()">align()</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="_PRECISION"></a><span class="summary-name">_PRECISION</span> = <code title="1000">1000</code>
</td>
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<span class="summary-type"> </span>
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<a name="this_module"></a><span class="summary-name">this_module</span> = <code title="sys.modules [__name__]">sys.modules [__name__]</code>
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<!-- ==================== FUNCTION DETAILS ==================== -->
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<h3 class="epydoc"><span class="sig"><span class="sig-name">print_matrix</span>(<span class="sig-arg">matrix</span>)</span>
</h3>
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<p>Print out a matrix. For debugging purposes.</p>
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