diff --git a/docs/multitax.html b/docs/multitax.html index 505a642..e8bf787 100644 --- a/docs/multitax.html +++ b/docs/multitax.html @@ -131,7 +131,7 @@

View Source - 
__version__ = "1.3.0"
+            
__version__ = "1.3.1"
 
 __all__ = (
     'CustomTx',
diff --git a/docs/multitax/multitax.html b/docs/multitax/multitax.html
index 440005f..2889428 100644
--- a/docs/multitax/multitax.html
+++ b/docs/multitax/multitax.html
@@ -500,10 +500,6 @@ 

         if isinstance(nodes, str):
             nodes = [nodes]
 
-        # Cannot filter root node
-        if self.root_node in nodes:
-            raise ValueError("Root node [" + self.root_node + "] cannot be filtered.")
-
         # Keep track of nodes to be filtered out
         filtered_nodes = set(self._nodes)
         # Always keep root
@@ -512,7 +508,7 @@ 

         if desc:
             # Keep descendants of the given nodes
             for node in nodes:
-                # Check if node exists
+                # Check if node exists (skips root)
                 if node in filtered_nodes:
                     # For each leaf of the selected nodes
                     for leaf in self.leaves(node):
@@ -536,7 +532,6 @@ 

 
         # Delete aux. data structures
         self._reset_aux_data()
-
         self.check_consistency()
 
     def latest(self, node: str):
@@ -1212,10 +1207,6 @@ 

         if isinstance(nodes, str):
             nodes = [nodes]
 
-        # Cannot filter root node
-        if self.root_node in nodes:
-            raise ValueError("Root node [" + self.root_node + "] cannot be filtered.")
-
         # Keep track of nodes to be filtered out
         filtered_nodes = set(self._nodes)
         # Always keep root
@@ -1224,7 +1215,7 @@ 

         if desc:
             # Keep descendants of the given nodes
             for node in nodes:
-                # Check if node exists
+                # Check if node exists (skips root)
                 if node in filtered_nodes:
                     # For each leaf of the selected nodes
                     for leaf in self.leaves(node):
@@ -1248,7 +1239,6 @@ 

 
         # Delete aux. data structures
         self._reset_aux_data()
-
         self.check_consistency()
 
     def latest(self, node: str):
@@ -1715,7 +1705,7 @@ 

                             

                                             
#  
 
-        version = '1.3.0'
+        version = '1.3.1'
     

 
     
@@ -2041,10 +2031,6 @@ 

         if isinstance(nodes, str):
             nodes = [nodes]
 
-        # Cannot filter root node
-        if self.root_node in nodes:
-            raise ValueError("Root node [" + self.root_node + "] cannot be filtered.")
-
         # Keep track of nodes to be filtered out
         filtered_nodes = set(self._nodes)
         # Always keep root
@@ -2053,7 +2039,7 @@ 

         if desc:
             # Keep descendants of the given nodes
             for node in nodes:
-                # Check if node exists
+                # Check if node exists (skips root)
                 if node in filtered_nodes:
                     # For each leaf of the selected nodes
                     for leaf in self.leaves(node):
@@ -2077,7 +2063,6 @@ 

 
         # Delete aux. data structures
         self._reset_aux_data()
-
         self.check_consistency()
 

 
diff --git a/docs/search.js b/docs/search.js
index 79bba77..61b90dd 100644
--- a/docs/search.js
+++ b/docs/search.js
@@ -1,6 +1,6 @@
 window.pdocSearch = (function(){
 /** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n",e)},t.Pipeline.load=function(e){var n=new t.Pipeline;return e.forEach(function(e){var i=t.Pipeline.getRegisteredFunction(e);if(!i)throw new Error("Cannot load un-registered function: "+e);n.add(i)}),n},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(e){t.Pipeline.warnIfFunctionNotRegistered(e),this._queue.push(e)},this)},t.Pipeline.prototype.after=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i+1,0,n)},t.Pipeline.prototype.before=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i,0,n)},t.Pipeline.prototype.remove=function(e){var t=this._queue.indexOf(e);-1!==t&&this._queue.splice(t,1)},t.Pipeline.prototype.run=function(e){for(var 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this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return 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\n"}, {"fullname": "multitax.CustomTx", "modulename": "multitax", "qualname": "CustomTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.CustomTx.__init__", "modulename": "multitax", "qualname": "CustomTx.__init__", "type": "function", "doc": "
CustomTx()
\n\n
Parameters:
\n\n
    \n
  • cols [list, dict]: List of fields to be parsed or a dictionary with {field: column index}. Options: \"node\", \"parent\", \"rank\", \"name\"
    • \n
  • sep [str]: Separator of fields
    • \n
  • **kwargs defined at multitax.multitax.MultiTax
    • \n
\n\n
Example:
\n\n
tax_custom1 = CustomTx(files=\"my_custom_tax.tsv\", cols=[\"node\",\"parent\",\"rank\"])\ntax_custom2 = CustomTx(files=\"my_custom_tax.tsv\", cols={\"node\": 0, \"parent\": 1, \"name\": 5, \"rank\": 3})\n
\n", "signature": "(\n    self,\n    cols: list = ['node', 'parent', 'rank', 'name'],\n    sep: str = '\\t',\n    **kwargs\n)", "funcdef": "def"}, {"fullname": "multitax.DummyTx", "modulename": "multitax", "qualname": "DummyTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.DummyTx.__init__", "modulename": "multitax", "qualname": "DummyTx.__init__", "type": "function", "doc": "
DummyTx() - Dummy empty taxonomy
\n\n
Parameters:
\n\n
    \n
  • **kwargs defined at multitax.multitax.MultiTax
    • \n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.GreengenesTx", "modulename": "multitax", "qualname": "GreengenesTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.GreengenesTx.__init__", "modulename": "multitax", "qualname": "GreengenesTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.GtdbTx", "modulename": "multitax", "qualname": "GtdbTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.GtdbTx.__init__", "modulename": "multitax", "qualname": "GtdbTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx", "modulename": "multitax", "qualname": "NcbiTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.NcbiTx.__init__", "modulename": "multitax", "qualname": "NcbiTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.latest", "modulename": "multitax", "qualname": "NcbiTx.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.merged", "modulename": "multitax", "qualname": "NcbiTx.merged", "type": "function", "doc": "
Returns relative entry from the merged.dmp file of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.search_name", "modulename": "multitax", "qualname": "NcbiTx.search_name", "type": "function", "doc": "
Search node by exact or partial name.
\n\n
Default order (can be skipped with force_extended=True):
\n\n
1) Search names defined as \"scientific name\" on nodes.dmp
\n\n
2) If nothing was found, search text in all other categories (must be activated with NcbiTx(extended_names=True))
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
  • force_extended [bool]: Search for text in all categories at once.
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(\n    self,\n    text: str,\n    rank: str = None,\n    exact: bool = True,\n    force_extended: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.stats", "modulename": "multitax", "qualname": "NcbiTx.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.OttTx", "modulename": "multitax", "qualname": "OttTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.OttTx.__init__", "modulename": "multitax", "qualname": "OttTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.OttTx.forwards", "modulename": "multitax", "qualname": "OttTx.forwards", "type": "function", "doc": "
Returns relative entry from the forwards.tsv file of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.OttTx.latest", "modulename": "multitax", "qualname": "OttTx.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.OttTx.search_name", "modulename": "multitax", "qualname": "OttTx.search_name", "type": "function", "doc": "
Search node by exact or partial name.
\n\n
Default order (can be skipped with force_extended=True):
\n\n
1) Search default names defined on \"taxonomy.tsv\"
\n\n
2) If nothing was found, search in all other names defined on \"synonyms.tsv\" (must be activated with OttTx(extended_names=True))
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
  • force_extended [bool]: Search for text in all categories at once.
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(\n    self,\n    text: str,\n    rank: str = None,\n    exact: bool = True,\n    force_extended: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.OttTx.stats", "modulename": "multitax", "qualname": "OttTx.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.SilvaTx", "modulename": "multitax", "qualname": "SilvaTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.SilvaTx.__init__", "modulename": "multitax", "qualname": "SilvaTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.multitax", "modulename": "multitax.multitax", "type": "module", "doc": "
\n"}, {"fullname": "multitax.multitax.MultiTax", "modulename": "multitax.multitax", "qualname": "MultiTax", "type": "class", "doc": "
\n"}, {"fullname": "multitax.multitax.MultiTax.__init__", "modulename": "multitax.multitax", "qualname": "MultiTax.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(\n    self,\n    files: list = None,\n    urls: list = None,\n    output_prefix: str = None,\n    root_node: str = None,\n    root_parent: str = '0',\n    root_name: str = None,\n    root_rank: str = None,\n    undefined_node: str = None,\n    undefined_name: str = None,\n    undefined_rank: str = None,\n    build_name_nodes: bool = False,\n    build_node_children: bool = False,\n    build_rank_nodes: bool = False,\n    extended_names: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.version", "modulename": "multitax.multitax", "qualname": "MultiTax.version", "type": "variable", "doc": "
\n", "default_value": " = '1.3.0'"}, {"fullname": "multitax.multitax.MultiTax.add", "modulename": "multitax.multitax", "qualname": "MultiTax.add", "type": "function", "doc": "
Add node to taxonomy.\nDeletes built lineages and translations.
\n", "signature": "(self, node: str, parent: str, name: str = None, rank: str = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.build_lineages", "modulename": "multitax.multitax", "qualname": "MultiTax.build_lineages", "type": "function", "doc": "
Stores lineages in memory for faster access.\nIt is valid for lineage(), rank_lineage() and name_lineage().\nIf keyword arguments (root_node, ranks) are used in those functions stored lineages are not used.
\n\n
Returns: None
\n", "signature": "(self, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.build_translation", "modulename": "multitax.multitax", "qualname": "MultiTax.build_translation", "type": "function", "doc": "
Create a translation of current taxonomy to another
\n\n
Parameters:
\n\n
    \n
  • tax [MultiTax]: A target taxonomy to be translated to.
    • \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
\n\n
Example:
\n\n
from multitax import GtdbTx, NcbiTx\ngtdb_tax = GtdbTx()\nncbi_tax = NcbiTx()\n\n# Automatically download translation files\ngtdb_tax.build_translation(ncbi_tax)\ngtdb_tax.translate(\"g__Escherichia\")\n    {'1301', '547', '561', '570', '590', '620'}\n\n# Using local files (NCBI <-> GTDB)\nncbi_tax.build_translation(gtdb_tax, files=[\"ar53_metadata.tar.gz\", \"bac120_metadata.tar.gz\"])\nncbi_tax.translate(\"620\")\n    {'g__Escherichia', 'g__Proteus', 'g__Serratia'}\n
\n", "signature": "(self, tax, files: list = None, urls: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.children", "modulename": "multitax.multitax", "qualname": "MultiTax.children", "type": "function", "doc": "
Returns list of direct children nodes of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.check_consistency", "modulename": "multitax.multitax", "qualname": "MultiTax.check_consistency", "type": "function", "doc": "
Checks consistency of the tree
\n\n
Returns: raise an Exception otherwise None
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.clear_lineages", "modulename": "multitax.multitax", "qualname": "MultiTax.clear_lineages", "type": "function", "doc": "
Clear built lineages.
\n\n
Returns: None
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.closest_parent", "modulename": "multitax.multitax", "qualname": "MultiTax.closest_parent", "type": "function", "doc": "
Returns the closest parent node based on a defined list of ranks
\n", "signature": "(self, node: str, ranks: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.filter", "modulename": "multitax.multitax", "qualname": "MultiTax.filter", "type": "function", "doc": "
Filters taxonomy given a list of nodes.\nBy default keep all the ancestors of the given nodes.\nIf desc=True, keep all descendants instead.\nDeletes built lineages and translations.
\n\n
Example:
\n\n
from multitax import GtdbTx\ntax = GtdbTx()\n\ntax.lineage('s__Enterovibrio marina')\n# ['1', 'd__Bacteria', 'p__Proteobacteria', 'c__Gammaproteobacteria', 'o__Enterobacterales', 'f__Vibrionaceae', 'g__Enterovibrio', 's__Enterovibrio marina']\n# Keep only ancestors of 'g__Enterovibrio'\ntax.filter('g__Enterovibrio')\n\n# Reload taxonomy\ntax = GtdbTx()\n# Keep only descendants of 'g__Enterovibrio'\ntax.filter('g__Enterovibrio', desc=True)\n
\n", "signature": "(self, nodes: list, desc: bool = False)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.latest", "modulename": "multitax.multitax", "qualname": "MultiTax.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.leaves", "modulename": "multitax.multitax", "qualname": "MultiTax.leaves", "type": "function", "doc": "
Returns a list of leaf nodes of a given node.
\n", "signature": "(self, node: str = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.lineage", "type": "function", "doc": "
Returns a list with the lineage of a given node.\nIf ranks is provided, returns only nodes annotated with such ranks.\nIf root_node is provided, use it instead of default root of tree.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.name", "modulename": "multitax.multitax", "qualname": "MultiTax.name", "type": "function", "doc": "
Returns name of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.name_lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.name_lineage", "type": "function", "doc": "
Returns a list with the name lineage of a given node.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.nodes_rank", "modulename": "multitax.multitax", "qualname": "MultiTax.nodes_rank", "type": "function", "doc": "
Returns list of nodes of a given rank.
\n", "signature": "(self, rank: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.parent", "modulename": "multitax.multitax", "qualname": "MultiTax.parent", "type": "function", "doc": "
Returns the direct parent node of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.parent_rank", "modulename": "multitax.multitax", "qualname": "MultiTax.parent_rank", "type": "function", "doc": "
Returns the parent node of a given rank in the specified rank.
\n", "signature": "(self, node: str, rank: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.prune", "modulename": "multitax.multitax", "qualname": "MultiTax.prune", "type": "function", "doc": "
Prunes branches of the tree under the given nodes.\nDeletes built lineages and translations.
\n", "signature": "(self, nodes: list)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.rank", "modulename": "multitax.multitax", "qualname": "MultiTax.rank", "type": "function", "doc": "
Returns the rank of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.rank_lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.rank_lineage", "type": "function", "doc": "
Returns a list with the rank lineage of a given node.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.remove", "modulename": "multitax.multitax", "qualname": "MultiTax.remove", "type": "function", "doc": "
Removes node from taxonomy. Can break the tree if a parent node is removed. To remove a certain branch, use prune.\nRunning check consistency after removing a node is recommended.\nDeletes built lineages and translations.
\n", "signature": "(self, node: str, check_consistency: bool = False)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.search_name", "modulename": "multitax.multitax", "qualname": "MultiTax.search_name", "type": "function", "doc": "
Search node by exact or partial name
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(self, text: str, rank: str = None, exact: bool = True)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.stats", "modulename": "multitax.multitax", "qualname": "MultiTax.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.translate", "modulename": "multitax.multitax", "qualname": "MultiTax.translate", "type": "function", "doc": "
Returns the translated node from another taxonomy. Translated nodes are generated with the build_translation function.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.write", "modulename": "multitax.multitax", "qualname": "MultiTax.write", "type": "function", "doc": "
Writes loaded taxonomy to a file.
\n\n
Parameters:
\n\n
    \n
  • cols [list]: Options: \"node\", \"latest\", \"parent\", \"rank\", \"name\", \"leaves\", \"children\", \"lineage\", \"rank_lineage\", \"name_lineage\"
    • \n
  • sep [str]: Separator of fields
    • \n
  • sep_multi [str]: Separator of multi-valued fields
    • \n
  • ranks [list]: Ranks to report
    • \n
  • gz [bool]: Gzip output
    • \n
\n\n
Returns: None
\n", "signature": "(\n    self,\n    output_file: str,\n    cols: list = ['node', 'parent', 'rank', 'name'],\n    sep: str = '\\t',\n    sep_multi: str = '|',\n    ranks: list = None,\n    gz: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.utils", "modulename": "multitax.utils", "type": "module", "doc": "
\n"}, {"fullname": "multitax.utils.check_dir", "modulename": "multitax.utils", "qualname": "check_dir", "type": "function", "doc": "
\n", "signature": "(prefix: str)", "funcdef": "def"}, {"fullname": "multitax.utils.check_file", "modulename": "multitax.utils", "qualname": "check_file", "type": "function", "doc": "
\n", "signature": "(file: str)", "funcdef": "def"}, {"fullname": "multitax.utils.check_no_file", "modulename": "multitax.utils", "qualname": "check_no_file", "type": "function", "doc": "
\n", "signature": "(file: str)", "funcdef": "def"}, {"fullname": "multitax.utils.close_files", "modulename": "multitax.utils", "qualname": "close_files", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • fhs [dict]: {file: file handler}
    • \n
\n\n
Returns: Nothing
\n", "signature": "(fhs: dict)", "funcdef": "def"}, {"fullname": "multitax.utils.download_files", "modulename": "multitax.utils", "qualname": "download_files", "type": "function", "doc": "
Download and open files (memory/stream) or write to disk (multitax.utils.save_urls)
\n\n
Parameters:
\n\n
    \n
  • urls [list]: List of files to download (text, \".gz\", \".tar.gz\", \".tgz\")
    • \n
  • output_prefix [str]: Output directory to save files
    • \n
\n\n
Returns:
\n\n
    \n
  • OrderedDict {file: file handler} (same order as input)
    • \n
\n", "signature": "(urls: list, output_prefix: str = None, retry_attempts: int = 1)", "funcdef": "def"}, {"fullname": "multitax.utils.filter_function", "modulename": "multitax.utils", "qualname": "filter_function", "type": "function", "doc": "
\n", "signature": "(elements, function, value)", "funcdef": "def"}, {"fullname": "multitax.utils.join_check", "modulename": "multitax.utils", "qualname": "join_check", "type": "function", "doc": "
\n", "signature": "(elements, sep: str)", "funcdef": "def"}, {"fullname": "multitax.utils.load_url_mem", "modulename": "multitax.utils", "qualname": "load_url_mem", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • url [str]: URL to load into memory
    • \n
\n\n
Returns:
\n\n
    \n
  • io.BytesIO of the requested url
    • \n
\n", "signature": "(url: str)", "funcdef": "def"}, {"fullname": "multitax.utils.open_files", "modulename": "multitax.utils", "qualname": "open_files", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • files [list]: List of files to open (text, \".gz\", \".tar.gz\", \".tgz\")
    • \n
\n\n
Returns:
\n\n
    \n
  • OrderedDict {file: file handler} (same order as input)
    • \n
\n", "signature": "(files: list)", "funcdef": "def"}, {"fullname": "multitax.utils.reverse_dict", "modulename": "multitax.utils", "qualname": "reverse_dict", "type": "function", "doc": "
\n", "signature": "(d: dict)", "funcdef": "def"}, {"fullname": "multitax.utils.save_urls", "modulename": "multitax.utils", "qualname": "save_urls", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • urls [list]: List of urls to download
    • \n
  • output_prefix [str]: Output directory to save files
    • \n
\n\n
Returns:
\n\n
    \n
  • list of files saved
    • \n
\n", "signature": "(urls: list, output_prefix: str)", "funcdef": "def"}, {"fullname": "multitax.utils.warning_on_one_line", "modulename": "multitax.utils", "qualname": "warning_on_one_line", "type": "function", "doc": "
\n", "signature": "(message, category, filename, lineno, file=None, line=None)", "funcdef": "def"}];
+    /** pdoc search index */const docs = [{"fullname": "multitax", "modulename": "multitax", "type": "module", "doc": "
\n"}, {"fullname": "multitax.CustomTx", "modulename": "multitax", "qualname": "CustomTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.CustomTx.__init__", "modulename": "multitax", "qualname": "CustomTx.__init__", "type": "function", "doc": "
CustomTx()
\n\n
Parameters:
\n\n
    \n
  • cols [list, dict]: List of fields to be parsed or a dictionary with {field: column index}. Options: \"node\", \"parent\", \"rank\", \"name\"
    • \n
  • sep [str]: Separator of fields
    • \n
  • **kwargs defined at multitax.multitax.MultiTax
    • \n
\n\n
Example:
\n\n
tax_custom1 = CustomTx(files=\"my_custom_tax.tsv\", cols=[\"node\",\"parent\",\"rank\"])\ntax_custom2 = CustomTx(files=\"my_custom_tax.tsv\", cols={\"node\": 0, \"parent\": 1, \"name\": 5, \"rank\": 3})\n
\n", "signature": "(\n    self,\n    cols: list = ['node', 'parent', 'rank', 'name'],\n    sep: str = '\\t',\n    **kwargs\n)", "funcdef": "def"}, {"fullname": "multitax.DummyTx", "modulename": "multitax", "qualname": "DummyTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.DummyTx.__init__", "modulename": "multitax", "qualname": "DummyTx.__init__", "type": "function", "doc": "
DummyTx() - Dummy empty taxonomy
\n\n
Parameters:
\n\n
    \n
  • **kwargs defined at multitax.multitax.MultiTax
    • \n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.GreengenesTx", "modulename": "multitax", "qualname": "GreengenesTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.GreengenesTx.__init__", "modulename": "multitax", "qualname": "GreengenesTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.GtdbTx", "modulename": "multitax", "qualname": "GtdbTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.GtdbTx.__init__", "modulename": "multitax", "qualname": "GtdbTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx", "modulename": "multitax", "qualname": "NcbiTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.NcbiTx.__init__", "modulename": "multitax", "qualname": "NcbiTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.latest", "modulename": "multitax", "qualname": "NcbiTx.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.merged", "modulename": "multitax", "qualname": "NcbiTx.merged", "type": "function", "doc": "
Returns relative entry from the merged.dmp file of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.search_name", "modulename": "multitax", "qualname": "NcbiTx.search_name", "type": "function", "doc": "
Search node by exact or partial name.
\n\n
Default order (can be skipped with force_extended=True):
\n\n
1) Search names defined as \"scientific name\" on nodes.dmp
\n\n
2) If nothing was found, search text in all other categories (must be activated with NcbiTx(extended_names=True))
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
  • force_extended [bool]: Search for text in all categories at once.
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(\n    self,\n    text: str,\n    rank: str = None,\n    exact: bool = True,\n    force_extended: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.NcbiTx.stats", "modulename": "multitax", "qualname": "NcbiTx.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.OttTx", "modulename": "multitax", "qualname": "OttTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.OttTx.__init__", "modulename": "multitax", "qualname": "OttTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.OttTx.forwards", "modulename": "multitax", "qualname": "OttTx.forwards", "type": "function", "doc": "
Returns relative entry from the forwards.tsv file of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.OttTx.latest", "modulename": "multitax", "qualname": "OttTx.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.OttTx.search_name", "modulename": "multitax", "qualname": "OttTx.search_name", "type": "function", "doc": "
Search node by exact or partial name.
\n\n
Default order (can be skipped with force_extended=True):
\n\n
1) Search default names defined on \"taxonomy.tsv\"
\n\n
2) If nothing was found, search in all other names defined on \"synonyms.tsv\" (must be activated with OttTx(extended_names=True))
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
  • force_extended [bool]: Search for text in all categories at once.
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(\n    self,\n    text: str,\n    rank: str = None,\n    exact: bool = True,\n    force_extended: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.OttTx.stats", "modulename": "multitax", "qualname": "OttTx.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.SilvaTx", "modulename": "multitax", "qualname": "SilvaTx", "type": "class", "doc": "
\n", "bases": "multitax.multitax.MultiTax"}, {"fullname": "multitax.SilvaTx.__init__", "modulename": "multitax", "qualname": "SilvaTx.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(self, **kwargs)", "funcdef": "def"}, {"fullname": "multitax.multitax", "modulename": "multitax.multitax", "type": "module", "doc": "
\n"}, {"fullname": "multitax.multitax.MultiTax", "modulename": "multitax.multitax", "qualname": "MultiTax", "type": "class", "doc": "
\n"}, {"fullname": "multitax.multitax.MultiTax.__init__", "modulename": "multitax.multitax", "qualname": "MultiTax.__init__", "type": "function", "doc": "
Main constructor of MultiTax and sub-classes
\n\n
Parameters:
\n\n
    \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
  • output_prefix [str]: Directory to write downloaded files.
    • \n
  • root_node [str]: Define an alternative root node.
    • \n
  • root_parent [str]: Define the root parent node identifier.
    • \n
  • root_name [str]: Define an alternative root name. Set to None to use original name.
    • \n
  • root_rank [str]: Define an alternative root rank. Set to None to use original name.
    • \n
  • undefined_node [str]: Define a default return value for undefined nodes.
    • \n
  • undefined_name [str]: Define a default return value for undefined names.
    • \n
  • undefined_rank [str]: Define a default return value for undefined ranks.
    • \n
  • build_node_children [bool]: Build node,children dict (otherwise it will be created on first use).
    • \n
  • build_name_nodes [bool]: Build name,nodes dict (otherwise it will be created on first use).
    • \n
  • build_rank_nodes [bool]: Build rank,nodes dict (otherwise it will be created on first use).
    • \n
  • extended_names [bool]: Parse extended names if available.
    • \n
\n\n
Example:
\n\n
tax_ncbi = NcbiTx()\ntax_gtdb = GtdbTx(files=[\"file1.gz\", \"file2.txt\"])\ntax_silva = SilvaTx(urls=[\"https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/taxonomy/tax_slv_lsu_138.1.txt.gz\"])\ntax_ott = OttTx(root_node=\"844192\")\ntax_gg = GreengenesTx(output_prefix=\"save/to/prefix_\")\n
\n", "signature": "(\n    self,\n    files: list = None,\n    urls: list = None,\n    output_prefix: str = None,\n    root_node: str = None,\n    root_parent: str = '0',\n    root_name: str = None,\n    root_rank: str = None,\n    undefined_node: str = None,\n    undefined_name: str = None,\n    undefined_rank: str = None,\n    build_name_nodes: bool = False,\n    build_node_children: bool = False,\n    build_rank_nodes: bool = False,\n    extended_names: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.version", "modulename": "multitax.multitax", "qualname": "MultiTax.version", "type": "variable", "doc": "
\n", "default_value": " = '1.3.1'"}, {"fullname": "multitax.multitax.MultiTax.add", "modulename": "multitax.multitax", "qualname": "MultiTax.add", "type": "function", "doc": "
Add node to taxonomy.\nDeletes built lineages and translations.
\n", "signature": "(self, node: str, parent: str, name: str = None, rank: str = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.build_lineages", "modulename": "multitax.multitax", "qualname": "MultiTax.build_lineages", "type": "function", "doc": "
Stores lineages in memory for faster access.\nIt is valid for lineage(), rank_lineage() and name_lineage().\nIf keyword arguments (root_node, ranks) are used in those functions stored lineages are not used.
\n\n
Returns: None
\n", "signature": "(self, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.build_translation", "modulename": "multitax.multitax", "qualname": "MultiTax.build_translation", "type": "function", "doc": "
Create a translation of current taxonomy to another
\n\n
Parameters:
\n\n
    \n
  • tax [MultiTax]: A target taxonomy to be translated to.
    • \n
  • files [str, list]: One or more local files to parse.
    • \n
  • urls [str, list]: One or more urls to download and parse.
    • \n
\n\n
Example:
\n\n
from multitax import GtdbTx, NcbiTx\ngtdb_tax = GtdbTx()\nncbi_tax = NcbiTx()\n\n# Automatically download translation files\ngtdb_tax.build_translation(ncbi_tax)\ngtdb_tax.translate(\"g__Escherichia\")\n    {'1301', '547', '561', '570', '590', '620'}\n\n# Using local files (NCBI <-> GTDB)\nncbi_tax.build_translation(gtdb_tax, files=[\"ar53_metadata.tar.gz\", \"bac120_metadata.tar.gz\"])\nncbi_tax.translate(\"620\")\n    {'g__Escherichia', 'g__Proteus', 'g__Serratia'}\n
\n", "signature": "(self, tax, files: list = None, urls: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.children", "modulename": "multitax.multitax", "qualname": "MultiTax.children", "type": "function", "doc": "
Returns list of direct children nodes of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.check_consistency", "modulename": "multitax.multitax", "qualname": "MultiTax.check_consistency", "type": "function", "doc": "
Checks consistency of the tree
\n\n
Returns: raise an Exception otherwise None
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.clear_lineages", "modulename": "multitax.multitax", "qualname": "MultiTax.clear_lineages", "type": "function", "doc": "
Clear built lineages.
\n\n
Returns: None
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.closest_parent", "modulename": "multitax.multitax", "qualname": "MultiTax.closest_parent", "type": "function", "doc": "
Returns the closest parent node based on a defined list of ranks
\n", "signature": "(self, node: str, ranks: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.filter", "modulename": "multitax.multitax", "qualname": "MultiTax.filter", "type": "function", "doc": "
Filters taxonomy given a list of nodes.\nBy default keep all the ancestors of the given nodes.\nIf desc=True, keep all descendants instead.\nDeletes built lineages and translations.
\n\n
Example:
\n\n
from multitax import GtdbTx\ntax = GtdbTx()\n\ntax.lineage('s__Enterovibrio marina')\n# ['1', 'd__Bacteria', 'p__Proteobacteria', 'c__Gammaproteobacteria', 'o__Enterobacterales', 'f__Vibrionaceae', 'g__Enterovibrio', 's__Enterovibrio marina']\n# Keep only ancestors of 'g__Enterovibrio'\ntax.filter('g__Enterovibrio')\n\n# Reload taxonomy\ntax = GtdbTx()\n# Keep only descendants of 'g__Enterovibrio'\ntax.filter('g__Enterovibrio', desc=True)\n
\n", "signature": "(self, nodes: list, desc: bool = False)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.latest", "modulename": "multitax.multitax", "qualname": "MultiTax.latest", "type": "function", "doc": "
Returns latest/updated version of a given node.\nIf node is already the latests, returns itself.\nMainly used for NCBI (merged.dmp) and OTT (forwards.tsv)
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.leaves", "modulename": "multitax.multitax", "qualname": "MultiTax.leaves", "type": "function", "doc": "
Returns a list of leaf nodes of a given node.
\n", "signature": "(self, node: str = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.lineage", "type": "function", "doc": "
Returns a list with the lineage of a given node.\nIf ranks is provided, returns only nodes annotated with such ranks.\nIf root_node is provided, use it instead of default root of tree.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.name", "modulename": "multitax.multitax", "qualname": "MultiTax.name", "type": "function", "doc": "
Returns name of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.name_lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.name_lineage", "type": "function", "doc": "
Returns a list with the name lineage of a given node.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.nodes_rank", "modulename": "multitax.multitax", "qualname": "MultiTax.nodes_rank", "type": "function", "doc": "
Returns list of nodes of a given rank.
\n", "signature": "(self, rank: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.parent", "modulename": "multitax.multitax", "qualname": "MultiTax.parent", "type": "function", "doc": "
Returns the direct parent node of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.parent_rank", "modulename": "multitax.multitax", "qualname": "MultiTax.parent_rank", "type": "function", "doc": "
Returns the parent node of a given rank in the specified rank.
\n", "signature": "(self, node: str, rank: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.prune", "modulename": "multitax.multitax", "qualname": "MultiTax.prune", "type": "function", "doc": "
Prunes branches of the tree under the given nodes.\nDeletes built lineages and translations.
\n", "signature": "(self, nodes: list)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.rank", "modulename": "multitax.multitax", "qualname": "MultiTax.rank", "type": "function", "doc": "
Returns the rank of a given node.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.rank_lineage", "modulename": "multitax.multitax", "qualname": "MultiTax.rank_lineage", "type": "function", "doc": "
Returns a list with the rank lineage of a given node.
\n", "signature": "(self, node: str, root_node: str = None, ranks: list = None)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.remove", "modulename": "multitax.multitax", "qualname": "MultiTax.remove", "type": "function", "doc": "
Removes node from taxonomy. Can break the tree if a parent node is removed. To remove a certain branch, use prune.\nRunning check consistency after removing a node is recommended.\nDeletes built lineages and translations.
\n", "signature": "(self, node: str, check_consistency: bool = False)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.search_name", "modulename": "multitax.multitax", "qualname": "MultiTax.search_name", "type": "function", "doc": "
Search node by exact or partial name
\n\n
Parameters:
\n\n
    \n
  • text [str]: Text to search.
    • \n
  • rank [str]: Filter results by rank.
    • \n
  • exact [bool]: Exact or partial name search (both case sensitive).
    • \n
\n\n
Returns: list of matching nodes
\n", "signature": "(self, text: str, rank: str = None, exact: bool = True)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.stats", "modulename": "multitax.multitax", "qualname": "MultiTax.stats", "type": "function", "doc": "
Returns a dict with general numbers of the taxonomic tree
\n\n
Example:
\n\n
from pprint import pprint\nfrom multitax import GtdbTx\ntax = GtdbTx()\n\npprint(tax.stats())\n{'leaves': 30238,\n 'names': 42739,\n 'nodes': 42739,\n 'ranked_leaves': Counter({'species': 30238}),\n 'ranked_nodes': Counter({'species': 30238,\n                          'genus': 8778,\n                          'family': 2323,\n                          'order': 930,\n                          'class': 337,\n                          'phylum': 131,\n                          'domain': 1,\n                          'root': 1}),\n 'ranks': 42739}\n
\n", "signature": "(self)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.translate", "modulename": "multitax.multitax", "qualname": "MultiTax.translate", "type": "function", "doc": "
Returns the translated node from another taxonomy. Translated nodes are generated with the build_translation function.
\n", "signature": "(self, node: str)", "funcdef": "def"}, {"fullname": "multitax.multitax.MultiTax.write", "modulename": "multitax.multitax", "qualname": "MultiTax.write", "type": "function", "doc": "
Writes loaded taxonomy to a file.
\n\n
Parameters:
\n\n
    \n
  • cols [list]: Options: \"node\", \"latest\", \"parent\", \"rank\", \"name\", \"leaves\", \"children\", \"lineage\", \"rank_lineage\", \"name_lineage\"
    • \n
  • sep [str]: Separator of fields
    • \n
  • sep_multi [str]: Separator of multi-valued fields
    • \n
  • ranks [list]: Ranks to report
    • \n
  • gz [bool]: Gzip output
    • \n
\n\n
Returns: None
\n", "signature": "(\n    self,\n    output_file: str,\n    cols: list = ['node', 'parent', 'rank', 'name'],\n    sep: str = '\\t',\n    sep_multi: str = '|',\n    ranks: list = None,\n    gz: bool = False\n)", "funcdef": "def"}, {"fullname": "multitax.utils", "modulename": "multitax.utils", "type": "module", "doc": "
\n"}, {"fullname": "multitax.utils.check_dir", "modulename": "multitax.utils", "qualname": "check_dir", "type": "function", "doc": "
\n", "signature": "(prefix: str)", "funcdef": "def"}, {"fullname": "multitax.utils.check_file", "modulename": "multitax.utils", "qualname": "check_file", "type": "function", "doc": "
\n", "signature": "(file: str)", "funcdef": "def"}, {"fullname": "multitax.utils.check_no_file", "modulename": "multitax.utils", "qualname": "check_no_file", "type": "function", "doc": "
\n", "signature": "(file: str)", "funcdef": "def"}, {"fullname": "multitax.utils.close_files", "modulename": "multitax.utils", "qualname": "close_files", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • fhs [dict]: {file: file handler}
    • \n
\n\n
Returns: Nothing
\n", "signature": "(fhs: dict)", "funcdef": "def"}, {"fullname": "multitax.utils.download_files", "modulename": "multitax.utils", "qualname": "download_files", "type": "function", "doc": "
Download and open files (memory/stream) or write to disk (multitax.utils.save_urls)
\n\n
Parameters:
\n\n
    \n
  • urls [list]: List of files to download (text, \".gz\", \".tar.gz\", \".tgz\")
    • \n
  • output_prefix [str]: Output directory to save files
    • \n
\n\n
Returns:
\n\n
    \n
  • OrderedDict {file: file handler} (same order as input)
    • \n
\n", "signature": "(urls: list, output_prefix: str = None, retry_attempts: int = 1)", "funcdef": "def"}, {"fullname": "multitax.utils.filter_function", "modulename": "multitax.utils", "qualname": "filter_function", "type": "function", "doc": "
\n", "signature": "(elements, function, value)", "funcdef": "def"}, {"fullname": "multitax.utils.join_check", "modulename": "multitax.utils", "qualname": "join_check", "type": "function", "doc": "
\n", "signature": "(elements, sep: str)", "funcdef": "def"}, {"fullname": "multitax.utils.load_url_mem", "modulename": "multitax.utils", "qualname": "load_url_mem", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • url [str]: URL to load into memory
    • \n
\n\n
Returns:
\n\n
    \n
  • io.BytesIO of the requested url
    • \n
\n", "signature": "(url: str)", "funcdef": "def"}, {"fullname": "multitax.utils.open_files", "modulename": "multitax.utils", "qualname": "open_files", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • files [list]: List of files to open (text, \".gz\", \".tar.gz\", \".tgz\")
    • \n
\n\n
Returns:
\n\n
    \n
  • OrderedDict {file: file handler} (same order as input)
    • \n
\n", "signature": "(files: list)", "funcdef": "def"}, {"fullname": "multitax.utils.reverse_dict", "modulename": "multitax.utils", "qualname": "reverse_dict", "type": "function", "doc": "
\n", "signature": "(d: dict)", "funcdef": "def"}, {"fullname": "multitax.utils.save_urls", "modulename": "multitax.utils", "qualname": "save_urls", "type": "function", "doc": "
Parameters:
\n\n
    \n
  • urls [list]: List of urls to download
    • \n
  • output_prefix [str]: Output directory to save files
    • \n
\n\n
Returns:
\n\n
    \n
  • list of files saved
    • \n
\n", "signature": "(urls: list, output_prefix: str)", "funcdef": "def"}, {"fullname": "multitax.utils.warning_on_one_line", "modulename": "multitax.utils", "qualname": "warning_on_one_line", "type": "function", "doc": "
\n", "signature": "(message, category, filename, lineno, file=None, line=None)", "funcdef": "def"}];
 
     // mirrored in build-search-index.js (part 1)
     // Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/multitax/__init__.py b/multitax/__init__.py
index b7f5275..dfbe3ef 100644
--- a/multitax/__init__.py
+++ b/multitax/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "1.3.0"
+__version__ = "1.3.1"
 
 __all__ = (
     'CustomTx',
diff --git a/multitax/multitax.py b/multitax/multitax.py
index 1b6d50e..fc7605a 100644
--- a/multitax/multitax.py
+++ b/multitax/multitax.py
@@ -365,10 +365,6 @@ def filter(self, nodes: list, desc: bool = False):
         if isinstance(nodes, str):
             nodes = [nodes]
 
-        # Cannot filter root node
-        if self.root_node in nodes:
-            raise ValueError("Root node [" + self.root_node + "] cannot be filtered.")
-
         # Keep track of nodes to be filtered out
         filtered_nodes = set(self._nodes)
         # Always keep root
@@ -377,7 +373,7 @@ def filter(self, nodes: list, desc: bool = False):
         if desc:
             # Keep descendants of the given nodes
             for node in nodes:
-                # Check if node exists
+                # Check if node exists (skips root)
                 if node in filtered_nodes:
                     # For each leaf of the selected nodes
                     for leaf in self.leaves(node):
@@ -401,7 +397,6 @@ def filter(self, nodes: list, desc: bool = False):
 
         # Delete aux. data structures
         self._reset_aux_data()
-
         self.check_consistency()
 
     def latest(self, node: str):
diff --git a/setup.py b/setup.py
index 3d710f4..025f351 100755
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@
 
 setup(
     name="multitax",
-    version="1.3.0",
+    version="1.3.1",
     url="https://www.github.com/pirovc/multitax",
     license="MIT",
     author="Vitor C. Piro",
diff --git a/tests/multitax/unit/test_functions.py b/tests/multitax/unit/test_functions.py
index c2c1a9e..e6ccbbb 100644
--- a/tests/multitax/unit/test_functions.py
+++ b/tests/multitax/unit/test_functions.py
@@ -500,16 +500,6 @@ def test_filter(self):
         self.assertCountEqual(tax.lineage("4.5"), [])
         self.assertCountEqual(tax.leaves("1"), ["4.2", "4.3", "5.1", "5.2"])
 
-        # No filter for root
-        tax = CustomTx(files=self.test_file)
-        self.assertEqual(tax.stats()["nodes"], 14)
-        with self.assertRaises(ValueError):
-            tax.filter(tax.root_node)
-            tax.filter(["2.2", tax.root_node])
-            tax.filter(tax.root_node, desc=True)
-            tax.filter(["2.2", tax.root_node], desc=True)
-        self.assertEqual(tax.stats()["nodes"], 14)
-
         tax = CustomTx(files=self.test_file)
         self.assertEqual(tax.stats()["nodes"], 14)
         tax.filter("XXXXX", desc=True)