fix names

README.md

@@ -17,7 +17,7 @@ Python library that provides a common interface to obtain, parse and interact wi
 
 ### conda
 
-	conda install multitax
+	conda install -c bioconda multitax
 
 ### local
 
@@ -91,7 +91,7 @@ tax.rank_lineage("g__Escherichia")
 tax.lineage("g__Escherichia", root_node="p__Proteobacteria", ranks=["phylum", "class", "family", "genus"])
 # ['p__Proteobacteria', 'c__Gammaproteobacteria', 'f__Enterobacteriaceae', 'g__Escherichia']
 
-# Pre-build lineages in memory for faster access
+# Build lineages in memory for faster access
 tax.build_lineages()
 
 # Get leaf nodes

docs/multitax.html

@@ -498,9 +498,9 @@ <h5>Inherited Members</h5>
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>
@@ -639,9 +639,9 @@ <h5>Inherited Members</h5>
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>
@@ -826,9 +826,9 @@ <h5>Inherited Members</h5>
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>
@@ -1102,9 +1102,9 @@ <h5>Inherited Members</h5>
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>
@@ -1335,9 +1335,9 @@ <h5>Inherited Members</h5>
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>

docs/multitax/multitax.html

@@ -153,9 +153,9 @@ <h1 class="modulename">
 <span class="sd">        * **undefined_node** *[str]*: Define a default return value for undefined nodes</span>
 <span class="sd">        * **undefined_name** *[str]*: Define a default return value for undefined names</span>
 <span class="sd">        * **undefined_rank** *[str]*: Define a default return value for undefined ranks</span>
-<span class="sd">        * **build_node_children** *[bool]*: Pre-build node,children dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_name_nodes** *[bool]*: Pre-build name,nodes dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_rank_nodes** *[bool]*: Pre-build rank,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_node_children** *[bool]*: Build node,children dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_name_nodes** *[bool]*: Build name,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_rank_nodes** *[bool]*: Build rank,nodes dict (otherwise it will be created on first use)</span>
 <span class="sd">        </span>
 <span class="sd">        Example:</span>
 
@@ -393,7 +393,7 @@ <h1 class="modulename">
 <span class="sd">        If ranks is provide, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># If lineages were pre-built and no special subset is required</span>
+        <span class="c1"># If lineages were built and no special subset is required</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">[</span><span class="n">node</span><span class="p">]</span>
         <span class="k">else</span><span class="p">:</span>
@@ -505,7 +505,7 @@ <h1 class="modulename">
 
     <span class="k">def</span> <span class="nf">clear_lineages</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Clear pre-built lineages.</span>
+<span class="sd">        Clear built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -531,7 +531,7 @@ <h1 class="modulename">
 <span class="sd">        Filters taxonomy given a list of nodes.</span>
 <span class="sd">        By default keep all the ancestors of the given nodes.</span>
 <span class="sd">        If desc=True, keep all descendants instead.</span>
-<span class="sd">        Deletes pre-built lineages.</span>
+<span class="sd">        Deletes built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 
@@ -697,9 +697,9 @@ <h1 class="modulename">
 <span class="sd">        * **undefined_node** *[str]*: Define a default return value for undefined nodes</span>
 <span class="sd">        * **undefined_name** *[str]*: Define a default return value for undefined names</span>
 <span class="sd">        * **undefined_rank** *[str]*: Define a default return value for undefined ranks</span>
-<span class="sd">        * **build_node_children** *[bool]*: Pre-build node,children dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_name_nodes** *[bool]*: Pre-build name,nodes dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_rank_nodes** *[bool]*: Pre-build rank,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_node_children** *[bool]*: Build node,children dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_name_nodes** *[bool]*: Build name,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_rank_nodes** *[bool]*: Build rank,nodes dict (otherwise it will be created on first use)</span>
 <span class="sd">        </span>
 <span class="sd">        Example:</span>
 
@@ -937,7 +937,7 @@ <h1 class="modulename">
 <span class="sd">        If ranks is provide, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># If lineages were pre-built and no special subset is required</span>
+        <span class="c1"># If lineages were built and no special subset is required</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">[</span><span class="n">node</span><span class="p">]</span>
         <span class="k">else</span><span class="p">:</span>
@@ -1049,7 +1049,7 @@ <h1 class="modulename">
 
     <span class="k">def</span> <span class="nf">clear_lineages</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Clear pre-built lineages.</span>
+<span class="sd">        Clear built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -1075,7 +1075,7 @@ <h1 class="modulename">
 <span class="sd">        Filters taxonomy given a list of nodes.</span>
 <span class="sd">        By default keep all the ancestors of the given nodes.</span>
 <span class="sd">        If desc=True, keep all descendants instead.</span>
-<span class="sd">        Deletes pre-built lineages.</span>
+<span class="sd">        Deletes built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 
@@ -1247,9 +1247,9 @@ <h1 class="modulename">
 <span class="sd">        * **undefined_node** *[str]*: Define a default return value for undefined nodes</span>
 <span class="sd">        * **undefined_name** *[str]*: Define a default return value for undefined names</span>
 <span class="sd">        * **undefined_rank** *[str]*: Define a default return value for undefined ranks</span>
-<span class="sd">        * **build_node_children** *[bool]*: Pre-build node,children dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_name_nodes** *[bool]*: Pre-build name,nodes dict (otherwise it will be created on first use)</span>
-<span class="sd">        * **build_rank_nodes** *[bool]*: Pre-build rank,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_node_children** *[bool]*: Build node,children dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_name_nodes** *[bool]*: Build name,nodes dict (otherwise it will be created on first use)</span>
+<span class="sd">        * **build_rank_nodes** *[bool]*: Build rank,nodes dict (otherwise it will be created on first use)</span>
 <span class="sd">        </span>
 <span class="sd">        Example:</span>
 
@@ -1329,9 +1329,9 @@ <h1 class="modulename">
 <li><strong>undefined_node</strong> <em>[str]</em>: Define a default return value for undefined nodes</li>
 <li><strong>undefined_name</strong> <em>[str]</em>: Define a default return value for undefined names</li>
 <li><strong>undefined_rank</strong> <em>[str]</em>: Define a default return value for undefined ranks</li>
-<li><strong>build_node_children</strong> <em>[bool]</em>: Pre-build node,children dict (otherwise it will be created on first use)</li>
-<li><strong>build_name_nodes</strong> <em>[bool]</em>: Pre-build name,nodes dict (otherwise it will be created on first use)</li>
-<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Pre-build rank,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_node_children</strong> <em>[bool]</em>: Build node,children dict (otherwise it will be created on first use)</li>
+<li><strong>build_name_nodes</strong> <em>[bool]</em>: Build name,nodes dict (otherwise it will be created on first use)</li>
+<li><strong>build_rank_nodes</strong> <em>[bool]</em>: Build rank,nodes dict (otherwise it will be created on first use)</li>
 </ul>
 
 <p>Example:</p>
@@ -1635,7 +1635,7 @@ <h1 class="modulename">
 <span class="sd">        If ranks is provide, returns only nodes annotated with such ranks.</span>
 <span class="sd">        If root_node is provided, use it instead of default root of tree.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># If lineages were pre-built and no special subset is required</span>
+        <span class="c1"># If lineages were built and no special subset is required</span>
         <span class="k">if</span> <span class="n">node</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">:</span>
             <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lineages</span><span class="p">[</span><span class="n">node</span><span class="p">]</span>
         <span class="k">else</span><span class="p">:</span>
@@ -1881,7 +1881,7 @@ <h1 class="modulename">
             <summary>View Source</summary>
             <div class="codehilite"><pre><span></span>    <span class="k">def</span> <span class="nf">clear_lineages</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">        Clear pre-built lineages.</span>
+<span class="sd">        Clear built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 <span class="sd">        &quot;&quot;&quot;</span>
@@ -1890,7 +1890,7 @@ <h1 class="modulename">
 
         </details>
 
-            <div class="docstring"><p>Clear pre-built lineages.</p>
+            <div class="docstring"><p>Clear built lineages.</p>
 
 <p>Returns: None</p>
 </div>
@@ -1947,7 +1947,7 @@ <h1 class="modulename">
 <span class="sd">        Filters taxonomy given a list of nodes.</span>
 <span class="sd">        By default keep all the ancestors of the given nodes.</span>
 <span class="sd">        If desc=True, keep all descendants instead.</span>
-<span class="sd">        Deletes pre-built lineages.</span>
+<span class="sd">        Deletes built lineages.</span>
 
 <span class="sd">        Returns: None</span>
 
@@ -2016,7 +2016,7 @@ <h1 class="modulename">
             <div class="docstring"><p>Filters taxonomy given a list of nodes.
 By default keep all the ancestors of the given nodes.
 If desc=True, keep all descendants instead.
-Deletes pre-built lineages.</p>
+Deletes built lineages.</p>
 
 <p>Returns: None</p>
 

multitax/multitax.py

@@ -37,9 +37,9 @@ def __init__(self,
         * **undefined_node** *[str]*: Define a default return value for undefined nodes
         * **undefined_name** *[str]*: Define a default return value for undefined names
         * **undefined_rank** *[str]*: Define a default return value for undefined ranks
-        * **build_node_children** *[bool]*: Pre-build node,children dict (otherwise it will be created on first use)
-        * **build_name_nodes** *[bool]*: Pre-build name,nodes dict (otherwise it will be created on first use)
-        * **build_rank_nodes** *[bool]*: Pre-build rank,nodes dict (otherwise it will be created on first use)
+        * **build_node_children** *[bool]*: Build node,children dict (otherwise it will be created on first use)
+        * **build_name_nodes** *[bool]*: Build name,nodes dict (otherwise it will be created on first use)
+        * **build_rank_nodes** *[bool]*: Build rank,nodes dict (otherwise it will be created on first use)
         
         Example:
 
@@ -277,7 +277,7 @@ def lineage(self, node: str, root_node: str=None, ranks: list=None):
         If ranks is provide, returns only nodes annotated with such ranks.
         If root_node is provided, use it instead of default root of tree.
         """
-        # If lineages were pre-built and no special subset is required
+        # If lineages were built and no special subset is required
         if node in self._lineages:
             return self._lineages[node]
         else:
@@ -389,7 +389,7 @@ def build_lineages(self, root_node: str=None, ranks: list=None):
 
     def clear_lineages(self):
         """
-        Clear pre-built lineages.
+        Clear built lineages.
 
         Returns: None
         """
@@ -415,7 +415,7 @@ def filter(self, nodes: list, desc: bool=False):
         Filters taxonomy given a list of nodes.
         By default keep all the ancestors of the given nodes.
         If desc=True, keep all descendants instead.
-        Deletes pre-built lineages.
+        Deletes built lineages.
 
         Returns: None