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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Mindy-module.html">Package Mindy</a> ::
Module compression
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<h1 class="epydoc">Source Code for <a href="Bio.Mindy.compression-module.html">Module Bio.Mindy.compression</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">commands</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.Mindy.compression._uncompress_table=Bio.Mindy.compression-module.html#_uncompress_table"><a title="Bio.Mindy.compression._uncompress_table" class="py-name" href="#" onclick="return doclink('link-0', '_uncompress_table', 'link-0');">_uncompress_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> <tt class="py-string">".bz"</tt><tt class="py-op">:</tt> <tt class="py-string">"bzip2"</tt><tt class="py-op">,</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-string">".BZ"</tt><tt class="py-op">:</tt> <tt class="py-string">"bzip2"</tt><tt class="py-op">,</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-string">".gz"</tt><tt class="py-op">:</tt> <tt class="py-string">"gzip"</tt><tt class="py-op">,</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-string">".GZ"</tt><tt class="py-op">:</tt> <tt class="py-string">"gzip"</tt><tt class="py-op">,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-string">".Z"</tt><tt class="py-op">:</tt> <tt class="py-string">"compress"</tt><tt class="py-op">,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="open_file"></a><div id="open_file-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="open_file-toggle" onclick="return toggle('open_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Mindy.compression-module.html#open_file">open_file</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">mode</tt> <tt class="py-op">=</tt> <tt class="py-string">"rb"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="open_file-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="open_file-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">ext</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">splitext</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt id="link-1" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-1', 'type', 'link-1');">type</a></tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name"><a title="Bio.Mindy.compression._uncompress_table" class="py-name" href="#" onclick="return doclink('link-2', '_uncompress_table', 'link-0');">_uncompress_table</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-3', 'get', 'link-3');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">ext</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-4" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-4', 'type', 'link-1');">type</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-5" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-5', 'open', 'link-5');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-6" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-6', 'type', 'link-1');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"gzip"</tt><tt class="py-op">:</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">gzip</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-name">gzip</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-7', 'open', 'link-5');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-8" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-8', 'type', 'link-1');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"bzip2"</tt><tt class="py-op">:</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"bzcat --decompress"</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">+=</tt> <tt class="py-name">commands</tt><tt class="py-op">.</tt><tt class="py-name">mkarg</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-name">cmd</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-9" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-9', 'type', 'link-1');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"compress"</tt><tt class="py-op">:</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"zcat -d"</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">+=</tt> <tt class="py-name">commands</tt><tt class="py-op">.</tt><tt class="py-name">mkarg</tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">popen</tt><tt class="py-op">(</tt><tt class="py-name">cmd</tt><tt class="py-op">,</tt> <tt class="py-name">mode</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"What's a %r?"</tt> <tt class="py-op">%</tt> <tt id="link-10" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-10', 'type', 'link-1');">type</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt><script type="text/javascript">
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