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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Emboss-module.html">Package Emboss</a> ::
Module primer3_format
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module primer3_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Emboss.primer3_format-pysrc.html">source code</a></span></p>
<p>Martel definitions for the output files produced by primer3.</p>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
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<td align="left"><span class="table-header">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></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="any_space"></a><span class="summary-name">any_space</span> = <code title="Martel.Re("[ ]+")">Martel.Re("[ ]+")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blank_line"></a><span class="summary-name">blank_line</span> = <code title="Martel.AnyEol()">Martel.AnyEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="comment_line"></a><span class="summary-name">comment_line</span> = <code title="Martel.Str("#")+ Martel.ToEol()">Martel.Str("#")+ Martel.ToEol()</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#comments" class="summary-name">comments</a> = <code title="Martel.Group("comments", blank_line+ comment_line+ blank_line+ comment\
_line)">Martel.Group("comments", blank_line+ comment_line+ <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="product_size"></a><span class="summary-name">product_size</span> = <code title="Martel.Group("product_size", Martel.Re("[\d]+"))">Martel.Group("product_size", Martel.Re("[\d]+"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#start_primer" class="summary-name">start_primer</a> = <code title="Martel.Group("start_primer", any_space+ Martel.Re("[\d]+")+ Martel.Str\
(" PRODUCT SIZE: "))">Martel.Group("start_primer", any_space+ Martel.<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#primer_start_line" class="summary-name">primer_start_line</a> = <code title="Martel.Group("primer_start_line", start_primer+ product_size+ Martel.A\
nyEol())">Martel.Group("primer_start_line", start_pr<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#single_primer_line" class="summary-name">single_primer_line</a> = <code title="Martel.Group("single_primer_line", blank_line)">Martel.Group("single_primer_line", blank_<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="primer_space"></a><span class="summary-name">primer_space</span> = <code title="Martel.Str(" "* 5)">Martel.Str(" "* 5)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="any_integer"></a><span class="summary-name">any_integer</span> = <code title="Martel.Re("[\d]+")">Martel.Re("[\d]+")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="any_float"></a><span class="summary-name">any_float</span> = <code title="Martel.Re("[\d\.]+")">Martel.Re("[\d\.]+")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sequence"></a><span class="summary-name">sequence</span> = <code title="Martel.Re("[GATCN]+")">Martel.Re("[GATCN]+")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="forward_primer_start"></a><span class="summary-name">forward_primer_start</span> = <code title="Martel.Group("forward_start", any_integer)">Martel.Group("forward_start", any_integer)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#forward_primer_length" class="summary-name">forward_primer_length</a> = <code title="Martel.Group("forward_length", any_integer)">Martel.Group("forward_length", any_int<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="forward_primer_tm"></a><span class="summary-name">forward_primer_tm</span> = <code title="Martel.Group("forward_tm", any_float)">Martel.Group("forward_tm", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="forward_primer_gc"></a><span class="summary-name">forward_primer_gc</span> = <code title="Martel.Group("forward_gc", any_float)">Martel.Group("forward_gc", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="forward_primer_seq"></a><span class="summary-name">forward_primer_seq</span> = <code title="Martel.Group("forward_seq", sequence)">Martel.Group("forward_seq", sequence)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#forward_line" class="summary-name">forward_line</a> = <code title="Martel.Group("forward_line", primer_space+ Martel.Str("FORWARD PRIMER"\
)+ any_space+ forward_primer_start+ any_space+ forward_primer_length+ \
any_space+ forward_primer_tm+ any_space+ forward_primer_gc+ any_space+\
forward_primer_seq+ Martel.AnyEol())">Martel.Group("forward_line", primer_space+ Mart<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reverse_primer_start"></a><span class="summary-name">reverse_primer_start</span> = <code title="Martel.Group("reverse_start", any_integer)">Martel.Group("reverse_start", any_integer)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#reverse_primer_length" class="summary-name">reverse_primer_length</a> = <code title="Martel.Group("reverse_length", any_integer)">Martel.Group("reverse_length", any_int<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reverse_primer_tm"></a><span class="summary-name">reverse_primer_tm</span> = <code title="Martel.Group("reverse_tm", any_float)">Martel.Group("reverse_tm", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reverse_primer_gc"></a><span class="summary-name">reverse_primer_gc</span> = <code title="Martel.Group("reverse_gc", any_float)">Martel.Group("reverse_gc", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reverse_primer_seq"></a><span class="summary-name">reverse_primer_seq</span> = <code title="Martel.Group("reverse_seq", sequence)">Martel.Group("reverse_seq", sequence)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#reverse_line" class="summary-name">reverse_line</a> = <code title="Martel.Group("reverse_line", primer_space+ Martel.Str("REVERSE PRIMER"\
)+ any_space+ reverse_primer_start+ any_space+ reverse_primer_length+ \
any_space+ reverse_primer_tm+ any_space+ reverse_primer_gc+ any_space+\
reverse_primer_seq+ Martel.AnyEol())">Martel.Group("reverse_line", primer_space+ Mart<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#internal_oligo_start" class="summary-name">internal_oligo_start</a> = <code title="Martel.Group("internal_start", any_integer)">Martel.Group("internal_start", any_inte<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#internal_oligo_length" class="summary-name">internal_oligo_length</a> = <code title="Martel.Group("internal_length", any_integer)">Martel.Group("internal_length", any_in<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="internal_oligo_tm"></a><span class="summary-name">internal_oligo_tm</span> = <code title="Martel.Group("internal_tm", any_float)">Martel.Group("internal_tm", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="internal_oligo_gc"></a><span class="summary-name">internal_oligo_gc</span> = <code title="Martel.Group("internal_gc", any_float)">Martel.Group("internal_gc", any_float)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="internal_oligo_seq"></a><span class="summary-name">internal_oligo_seq</span> = <code title="Martel.Group("internal_seq", sequence)">Martel.Group("internal_seq", sequence)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#internal_line" class="summary-name">internal_line</a> = <code title="Martel.Group("internal_line", primer_space+ Martel.Str("INTERNAL OLIGO\
")+ any_space+ internal_oligo_start+ any_space+ internal_oligo_length+\
any_space+ internal_oligo_tm+ any_space+ internal_oligo_gc+ any_space\
+ internal_oligo_seq+ Martel.AnyEol())">Martel.Group("internal_line", primer_space+ Ma<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Emboss.primer3_format-module.html#record" class="summary-name">record</a> = <code title="Martel.Group("primer3_record", comments+ Martel.Alt(Martel.Str("\n"* 3\
)+ Martel.Opt(Martel.Str("\n"* 4)), Martel.Rep(Martel.Alt(blank_line+ \
primer_start_line, single_primer_line)+ Martel.Alt(forward_line+ blank\
_line+ reverse_line+ blank_line, reverse_line+ blank_line, forward_lin\
e+ blank_line, internal_line+ blank_line))+ blank_line+ blank_line+ Ma\
rtel.Rep(blank_line)))">Martel.Group("primer3_record", comments+ Martel.Alt(M<code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="comments"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">comments</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("comments", blank_line+ comment_line+ blank_line+ comment<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_line)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="start_primer"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">start_primer</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("start_primer", any_space+ Martel.Re("[\d]+")+ Martel.Str<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(" PRODUCT SIZE: "))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="primer_start_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">primer_start_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("primer_start_line", start_primer+ product_size+ Martel.A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="single_primer_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">single_primer_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("single_primer_line", blank_line)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="forward_primer_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">forward_primer_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("forward_length", any_integer)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="forward_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">forward_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("forward_line", primer_space+ Martel.Str("FORWARD PRIMER"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ any_space+ forward_primer_start+ any_space+ forward_primer_length+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
any_space+ forward_primer_tm+ any_space+ forward_primer_gc+ any_space+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
forward_primer_seq+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reverse_primer_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reverse_primer_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reverse_length", any_integer)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reverse_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reverse_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reverse_line", primer_space+ Martel.Str("REVERSE PRIMER"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ any_space+ reverse_primer_start+ any_space+ reverse_primer_length+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
any_space+ reverse_primer_tm+ any_space+ reverse_primer_gc+ any_space+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
reverse_primer_seq+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="internal_oligo_start"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">internal_oligo_start</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("internal_start", any_integer)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="internal_oligo_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">internal_oligo_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("internal_length", any_integer)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="internal_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">internal_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("internal_line", primer_space+ Martel.Str("INTERNAL OLIGO<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ any_space+ internal_oligo_start+ any_space+ internal_oligo_length+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
any_space+ internal_oligo_tm+ any_space+ internal_oligo_gc+ any_space<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ internal_oligo_seq+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("primer3_record", comments+ Martel.Alt(Martel.Str("\n"* 3<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Opt(Martel.Str("\n"* 4)), Martel.Rep(Martel.Alt(blank_line+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
primer_start_line, single_primer_line)+ Martel.Alt(forward_line+ blank<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_line+ reverse_line+ blank_line, reverse_line+ blank_line, forward_lin<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
e+ blank_line, internal_line+ blank_line))+ blank_line+ blank_line+ Ma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
rtel.Rep(blank_line)))
</pre></td></tr></table>
</dd>
</dl>
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