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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.MetaTool-module.html">Package MetaTool</a> ::
Module Input
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<h1 class="epydoc">Module Input</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.MetaTool.Input-pysrc.html">source code</a></span></p>
<p>This module provides code to convert Bio.Pathway.System objects into a
text file that can be used as input for the MetaTool program.</p>
<p>For more information on MetaTool, please refer to:</p>
<p>http://www2.bioinf.mdc-berlin.de/metabolic/metatool/</p>
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<td><span class="summary-sig"><a href="Bio.MetaTool.Input-module.html#system_to_metatool" class="summary-sig-name">system_to_metatool</a>(<span class="summary-sig-arg">system</span>,
<span class="summary-sig-arg">metext</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">metint</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">generate_names</span>=<span class="summary-sig-default">1</span>)</span><br />
Converts a Bio.Pathway.System object to a MetaTool input string.</td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">system_to_metatool</span>(<span class="sig-arg">system</span>,
<span class="sig-arg">metext</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">metint</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">generate_names</span>=<span class="sig-default">1</span>)</span>
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<pre class="literalblock">
Converts a Bio.Pathway.System object to a MetaTool input string.
Note that to be a valid input string, the enzyme names of the reactions
in the system must conform to the MetaTool requirements.
Enzyme names are automatically genrated from the catalys attribute of
each reaction using the following scheme:
enzyme_name = "_".join([str(x[0]) for x in r.catalysts])
If an enzyme name has already been used, a positive integer will be
appended to this name to meet the MetaTool input requirements. If this
behaviour is undesired, set the optional parameter 'generate_names' to
false. All enzyme names will the be 'E_x', where x is an unique integer.
The optional parameters metext and metint can be used to specify the
external and internal metabolites according to the following rules:
1. If metext is set, the species in it will be considered external.
All other species will be considered internal.
2. Otherwise, if metint is set, the species in it will be considered
internal. All other species will be considered external.
3. Otherwise, all species will be considered external.
If specified, metext and metint must not contains species that are not
contained in the input system.
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