pyham 2.0.0__py3-none-any.whl

pyham/TreeProfile.py

@@ -0,0 +1,408 @@
+from .abstractgene import HOG
+import logging
+import json
+from ete4 import Tree
+
+logger = logging.getLogger(__name__)
+
+
+class TreeProfile(object):
+    """
+    Object that map on each node of the Ham species tree the related evolutionary information such as the number of
+    genes the related genome contains or the number of evolutionary events (duplications, genes loss or gain of genes)
+    that occurs between the parent node and itself. This can be either applied to the full Ham comparative genomic setup
+    or for a specific HOG.
+
+    Attributes:
+        | pyham (:obj:`pyham.pyham.Ham`): :obj:`set` of HOG ids used by the FilterOrthoXMLParser.
+        | hog (:obj:`pyham.abstractgene.HOG`, optional): If specified, compute TreeProfile on a single HOGs. Defaults is None.
+        | treemap (:obj:`ete3.Etree`): Ete3 Etree object containing the taxonomy of interest with annotated node.
+    """
+
+    def __init__(self, ham, hog=None):
+
+        self.ham = ham
+        self.hog = hog
+
+        if hog is None:
+            self.treemap = self.compute_tree_profile_full()
+
+        elif isinstance(hog, HOG):
+            self.treemap = self.computeTP_hog(hog)
+        else:
+            raise TypeError("Invalid argument {} for HOG".format(hog))
+
+    def computeTP_hog(self, hog):
+        """
+        Create the treeMap object (ete3 Etree object with annotated nodes) that contained the following features for
+        each nodes (representing an AbstractGene):
+
+            - nbr_genes: numbers of HOG/Gene the genome contains. For leaves, it also counts the singletons.
+            - dupl: numbers of HOGs that have arose by duplication in between this node and its parent.
+            - retained: numbers of HOGs that have stay retained (in term of copy numbers) in between this node and
+              its parent.
+            - lost: numbers of HOGs that have been lost in between this node and its parent.
+
+        Returns:
+            TreeMap
+        """
+
+        # copy the required taxonomy using query hog as root level
+        treeMap = hog.genome.taxon.copy()
+
+
+        # create a dictionary that map node with related hogs/genes
+        levelGroups = {}
+        for lvl in treeMap.traverse():
+            levelGroups[lvl.name]=[]
+
+        # add all of subhog to the related level in levelGroups
+        for subhog in hog.get_all_descendant_hogs():
+            if subhog.genome.name in levelGroups:
+                levelGroups[subhog.genome.name].append(subhog)
+
+        # add empty extant genome to levelGroups
+        for extantGenome in treeMap.leaves():
+            levelGroups[extantGenome.name] = []
+
+        # add genes to related extant genome in levelGroups
+        for species, genes in hog.get_all_descendant_genes_clustered_by_species().items():
+            levelGroups[species.name] = genes
+
+        for lvl in treeMap.traverse():
+            lvl.add_prop("nbr_genes", len(levelGroups[lvl.name]))
+            lvl.add_prop("gain", None)
+
+            if not lvl.is_root:
+                cpt_dupl = 0
+                cpt_ident = 0
+                set_dup_parent = set()
+
+                for h in levelGroups[lvl.name]:
+                    if h.arose_by_duplication != False:
+                        cpt_dupl += 1
+                        set_dup_parent.add(h.parent)
+                    else:
+                        cpt_ident += 1
+
+                cpt_lost = 0
+                for h_up in levelGroups[lvl.up.name]:
+                    if len(h_up.children) != 0:
+                        found = False
+                        for child in h_up.children:
+                            if child.genome.taxon.name == lvl.name:
+                                found = True
+                        if found is False:
+                            cpt_lost += 1
+                    else:
+                        cpt_lost += 1
+
+                cpt_duplication = max(0, cpt_dupl - len(list(set_dup_parent)))
+                nbr_ev = cpt_lost + cpt_duplication
+
+
+            else:
+                cpt_dupl = None
+                cpt_ident = None
+                cpt_lost = None
+                cpt_duplication = None
+                nbr_ev = None
+
+            lvl.add_prop("dupl", cpt_dupl)
+            lvl.add_prop("lost", cpt_lost)
+            lvl.add_prop("retained", cpt_ident)
+            lvl.add_prop("nbr_events", nbr_ev)
+            lvl.add_prop("duplication", cpt_duplication)
+
+        return treeMap
+
+    def compute_tree_profile_full(self):
+        """
+        Create the treeMap object (ete3 Etree object with annotated nodes) that contained the following features for
+        each nodes (the root node contains only nbr_genes):
+
+            - nbr_genes: numbers of HOG/Gene the genome contains. For leaves, it also counts the singletons.
+            - dupl: numbers of HOGs that have arose by duplication in between this node and its parent.
+            - lost: numbers of HOGs that have been lost in between this node and its parent.
+            - gain: numbers of HOGs that have "emerged" at this node.
+            - retained: numbers of HOGs that have stay retained (in term of copy numbers) in between this node and
+              its parent.
+
+        In order to get all those node informations, the HOGMap between each node and its parent is computed.
+
+        Returns:
+            TreeMap
+        """
+
+        def _add_annot(node: Tree, nbr, dupl, lost, gain, retained, duplication, nbr_ev):
+            node.add_prop("nbr_genes", nbr)
+            node.add_prop("nbr_events", nbr_ev)
+            node.add_prop("dupl", dupl)
+            node.add_prop("lost", lost)
+            node.add_prop("gain", gain)
+            node.add_prop("retained", retained)
+            node.add_prop("duplication", duplication)
+
+
+        treeMap = self.ham.taxonomy.tree.copy()
+        for node in treeMap.traverse():
+            if node.is_root:
+                node_genome = self.ham.get_ancestral_genome_by_name(node.name)
+                _add_annot(node, len(node_genome.genes), None, None, None, None, None, None)
+
+            else:
+                node_genome_up = self.ham._get_ancestral_genome_by_name(node.up.name)
+
+                if node.is_leaf:
+                    node_genome = self.ham._get_extant_genome_by_name(name=node.name)
+                    nbr = node_genome.get_number_genes(singleton=True)
+
+                else:
+                    node_genome = self.ham._get_ancestral_genome_by_name(node.name)
+                    nbr = node_genome.get_number_genes()
+
+                hogmap = self.ham._get_HOGMap({node_genome, node_genome_up})
+
+                nbr_duplicate = 0
+                for gs in hogmap.DUPLICATE.values():
+                    nbr_duplicate += len(gs)
+
+                nbr_ev = hogmap.number_duplication + len(hogmap.LOSS) + len(hogmap.GAIN)
+
+                _add_annot(node, nbr, nbr_duplicate, len(hogmap.LOSS), len(hogmap.GAIN), len(hogmap.RETAINED.keys()), hogmap.number_duplication, nbr_ev)
+
+        return treeMap
+
+    def export(self, output, layout_function=None, display_internal_histogram=True):
+
+        """
+        Method to export the tree profile object as figure (available format .SVG, .PDF, .PNG).
+
+        -- Some magic going there --
+
+        Args:
+            | output (:obj:`str`): output file name. The extension of output will set the format of the figure (SVG, .PDF, .PNG)
+            | layout_function (:obj:`function`, optional): custom layout_fn for ete3 TreeStyle.
+            | display_internal_histogram (:obj:`Boolean`, optional): Display internal node as histogram or raw text with numbers. Defaults to True.
+        """
+
+        from ete4 import TreeStyle, TextFace, NodeStyle, BarChartFace
+
+        # maximum number of genes per node in this treeMap
+        max_genes = max([d for d in self.treemap.traverse()], key=lambda x:x.nbr_genes).nbr_genes
+
+        if self.hog is None:
+            _color_scheme = ["#41c1c2","#bdc3c7","#f39c12","#27ae60","#e74c3c"]
+            _label_legend = ["Genes","Retained","Duplicated","Novel","Lost"]
+            _values_legend = [max_genes,max_genes,max_genes,max_genes,max_genes]
+            w_legend = 50 # todo calculate base on len(_values)
+        else:
+            _color_scheme = ["#41c1c2", "#bdc3c7", "#f39c12", "#e74c3c"]
+            _label_legend = ["Genes", "Retained", "Duplicated", "Lost"]
+            _values_legend = [max_genes, max_genes, max_genes, max_genes]
+            w_legend = 40  # todo calculate base on len(_values)
+
+        def _layout(node):
+
+            if self.hog is None:
+                 _label = [str(node.nbr_genes),str(node.retained),str(node.dupl),str(node.gain),str(node.lost)]
+            else:
+                _label = [str(node.nbr_genes), str(node.retained), str(node.dupl), str(node.lost)]
+
+            def _add_face(name_feature, value_feature, cnum=1, pos="branch-right"):
+                node.add_face(TextFace("{}: {}".format(name_feature, value_feature)), column=cnum, position=pos)
+
+            def _add_faces(cNbr=1, posNbr="branch-right", cAttr=2, posAtt="branch-right"):
+
+                _add_face("#genes", node.nbr_genes, cnum=cNbr, pos=posNbr)
+
+                if node.retained is not None:
+                    _add_face("#Retained", node.retained, cnum=cAttr, pos=posAtt)
+
+                if node.dupl is not None:
+                    _add_face("#Duplicated", node.dupl, cnum=cAttr, pos=posAtt)
+
+                if node.gain is not None:
+                    _add_face("#Novel", node.gain, cnum=cAttr, pos=posAtt)
+
+                if node.lost is not None:
+                    _add_face("#Lost", node.lost, cnum=cAttr, pos=posAtt)
+
+            if node.is_leaf:
+                if display_internal_histogram:
+                    if self.hog is None:
+                        values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
+                        w_plot = 50
+                    else:
+                        values = [node.nbr_genes, node.retained, node.dupl, node.lost]
+                        w_plot = 40
+                    node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-right")
+                else:
+                    _add_faces()
+
+            else:
+
+                if display_internal_histogram:
+                    if node.is_root:
+                        node.add_face(BarChartFace([node.nbr_genes], deviations=None, width=10, height=25, colors=["#41c1c2"], labels=[str(node.nbr_genes)], min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0, position = "branch-bottom")
+                    else:
+                        if self.hog is None:
+                            values = [node.nbr_genes,node.retained,node.dupl,node.gain,node.lost]
+                            w_plot = 50
+                        else:
+                            values = [node.nbr_genes,node.retained,node.dupl,node.lost]
+                            w_plot = 40
+                        node.add_face(BarChartFace(values, deviations=None, width=w_plot, height=25, colors=_color_scheme, labels=_label, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=1, position = "branch-top")
+
+
+
+                else:
+                    _add_faces(cNbr=0, posNbr="branch-top", cAttr=0, posAtt="branch-bottom")
+
+        ts = TreeStyle()
+
+        if layout_function is not None:
+            ts.layout_fn = layout_function
+        else:
+            ts.layout_fn = _layout
+            ts.legend.add_face(BarChartFace(_values_legend, deviations=None, width=w_legend, height=25, colors=_color_scheme, labels=_label_legend, min_value=0, max_value=max_genes, label_fsize=6, scale_fsize=6),column=0)
+            ts.legend_position = 3
+
+        self.treemap.render(output, tree_style=ts)
+
+    def export_as_html(self, output):
+
+        """
+        Method to export the tree profile object as an interactive tool embedded into a html file.
+
+
+        Args:
+            | output (:obj:`str`): output file name. If filename finish by .html, a double click load the file into your default browser.
+        """
+
+        def visit_custom(node, data):
+
+            current = {
+                "name": node.props['name'],
+                "numberGenes": node.props['nbr_genes'],
+                "numberEvents": node.props['nbr_events'],
+
+                "length": 0.01,
+                "collapsed": "false",
+                "evolutionaryEvents": {
+                    "retained": None,
+                    "duplicated": None,
+                    "gained": None,
+                    "lost": None,
+                    "duplication": None
+                }
+            }
+
+            if node.is_root:
+                current['evolutionaryEvents'] = False
+
+            else:
+                current['evolutionaryEvents']["retained"] = node.props['retained']
+                current['evolutionaryEvents']["duplicated"] = node.props['dupl']
+                current['evolutionaryEvents']["gained"] = node.props['gain']
+                current['evolutionaryEvents']["lost"] = node.props['lost']
+                current['evolutionaryEvents']["duplication"] = node.props['duplication']
+
+            if not node.is_leaf:
+                current['children'] = []
+
+            for child in node.children:
+                current['children'].append(visit_custom(child, data))
+
+            return current
+
+        template = '''
+        <!DOCTYPE html>
+        <html>
+        <head>
+            <title>Phylo.io</title>
+            <meta charset="UTF-8">
+            <script src="https://peterolson.github.com/BigInteger.js/BigInteger.min.js"></script>
+            <script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/jquery-2.1.4.min.js"></script>
+            <script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/9eae3d2af33f1f75bff78e393909dccfdd400650/www/js/treecompare.js"></script>
+            <script type="text/javascript" src="https://underscorejs.org/underscore-min.js"></script>
+            <script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/d3.min.js"></script>
+            <script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/bootstrap.min.js"></script>
+            <script type="text/javascript" src="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/js/FileSaver.min.js"></script>
+            <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/solid.css" integrity="sha384-v2Tw72dyUXeU3y4aM2Y0tBJQkGfplr39mxZqlTBDUZAb9BGoC40+rdFCG0m10lXk" crossorigin="anonymous">
+            <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.0.8/css/fontawesome.css" integrity="sha384-q3jl8XQu1OpdLgGFvNRnPdj5VIlCvgsDQTQB6owSOHWlAurxul7f+JpUOVdAiJ5P" crossorigin="anonymous">
+            <link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/bootstrap.min.css">
+            <link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/bootstrap-theme.min.css">
+            <link rel="stylesheet" type="text/css" href="https://cdn.rawgit.com/DessimozLab/phylo-io/5e89fafc3b1746b22da33c20b2af621d5807b6fb/www/css/style.css">
+            <style>
+
+            text {{stroke: none;}}
+
+            #help_modal_button {{
+                position: fixed;
+                right: 10px;
+                margin-right: 10px; /*magic number */
+                bottom: 10px;
+                z-index: 99;
+            }}
+
+            </style>
+        </head>
+        <body id="phylo">
+
+        <!-- Modal -->
+        <div class="modal  fade bs-example-modal-lg" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel">
+            <div class="modal-dialog modal-lg" role="document">
+                <div class="modal-content">
+                    <div class="modal-header">
+                        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+                        <h4 class="modal-title" id="myModalLabel">Tree profile help</h4>
+                    </div>
+                    <div class="modal-body">
+
+                        <embed src="https://cdn.rawgit.com/DessimozLab/pyham/fc01fb94/help.pdf" frameborder="0" width="100%" height="400px">
+                    </div>
+                    <div class="modal-footer">
+                        <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+                    </div>
+                </div>
+            </div>
+        </div>
+
+
+        <!-- Button trigger modal -->
+        <button id="help_modal_button" type="button" class="btn btn-sm" data-toggle="modal" data-target="#myModal">
+            Help
+        </button>
+
+
+
+        <div id="vis-container1" style="width: 100%; height: 100%;">
+        <div id="scale-1"> </div>
+        </div>
+        <script type="text/javascript">
+            var treecomp = TreeCompare().init({{
+                enableScale: true,
+                scaleColor: "black",
+                showHistogramValues: true,
+                showHistogramSummaryValue: true
+            }});
+            treeData = '{json_data}';
+            var tree1 = treecomp.addTree(treeData, undefined, "single");
+            treecomp.viewTree(tree1.name, "vis-container1", "scale-1");
+            treecomp.addMainLegend(tree1.name);
+        </script>
+        </body>
+        </html>
+        '''
+
+        data = {}
+
+        data = visit_custom(self.treemap, data)
+
+        data = json.dumps(data)
+
+        template = template.format(json_data=data)
+
+        with open(output, 'w') as outfile:
+            outfile.write(template)

pyham/__init__.py

@@ -0,0 +1,20 @@
+from .parsers import *
+from .ham import *
+from .abstractgene import *
+from .taxonomy import *
+from .genome import *
+from .utils import *
+from .mapper import *
+from .TreeProfile import *
+from .iham import *
+from .validation import *
+
+try:
+    from ._version import version as __version__
+except ImportError:
+    from importlib.metadata import version, PackageNotFoundError
+
+    try:
+        __version__ = version("pyham")
+    except PackageNotFoundError:
+        __version__ = "unknown"

pyham/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '2.0.0'
+__version_tuple__ = version_tuple = (2, 0, 0)
+
+__commit_id__ = commit_id = 'g3ae35e1c8'