# #START_LICENSE########################################################### # # # This file is part of the Environment for Tree Exploration program # (ETE). http://etetoolkit.org # # ETE is free software: you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # ETE is distributed in the hope that it will be useful, but WITHOUT # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY # or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public # License for more details. # # You should have received a copy of the GNU General Public License # along with ETE. If not, see . # # # ABOUT THE ETE PACKAGE # ===================== # # ETE is distributed under the GPL copyleft license (2008-2015). # # If you make use of ETE in published work, please cite: # # Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon. # ETE: a python Environment for Tree Exploration. Jaime BMC # Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24 # # Note that extra references to the specific methods implemented in # the toolkit may be available in the documentation. # # More info at http://etetoolkit.org. Contact: huerta@embl.de # # # #END_LICENSE############################################################# from __future__ import absolute_import from __future__ import print_function import re from six.moves import range def draw_tree(tree, conf, outfile): try: from ... import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace, random_color, SeqMotifFace) except ImportError as e: print(e) return def ly_basic(node): if node.is_leaf(): node.img_style['size'] = 0 else: node.img_style['size'] = 0 node.img_style['shape'] = 'square' if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"): if node.tree_seqtype == "nt": node.img_style["bgcolor"] = "#CFE6CA" ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica') add_face_to_node(ntF, node, 10, position="branch-bottom") if len(NPR_TREES) > 1 and hasattr(node, "tree_type"): node.img_style['size'] = 4 node.img_style['fgcolor'] = "steelblue" node.img_style['hz_line_width'] = 1 node.img_style['vt_line_width'] = 1 def ly_leaf_names(node): if node.is_leaf(): spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica') add_face_to_node(spF, node, column=0, position='branch-right') if hasattr(node, 'genename'): geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica') add_face_to_node(geneF, node, column=1, position='branch-right') def ly_supports(node): if not node.is_leaf() and node.up: supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred') add_face_to_node(supFace, node, column=0, position='branch-top') def ly_tax_labels(node): if node.is_leaf(): c = LABEL_START_COL largest = 0 for tname in TRACKED_CLADES: if hasattr(node, "named_lineage") and tname in node.named_lineage: linF = TextFace(tname, fsize=10, fgcolor='white') linF.margin_left = 3 linF.margin_right = 2 linF.background.color = lin2color[tname] add_face_to_node(linF, node, c, position='aligned') c += 1 for n in range(c, len(TRACKED_CLADES)): add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned') c+=1 def ly_full_alg(node): pass def ly_block_alg(node): if node.is_leaf(): if 'sequence' in node.features: seqFace = SeqMotifFace(node.sequence, []) # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"], motifs = [] last_lt = None for c, lt in enumerate(node.sequence): if lt != '-': if last_lt is None: last_lt = c if c+1 == len(node.sequence): start, end = last_lt, c motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None]) last_lt = None elif lt == '-': if last_lt is not None: start, end = last_lt, c-1 motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None]) last_lt = None seqFace = SeqMotifFace(node.sequence, motifs, gap_format="line", scale_factor=ALG_SCALE) add_face_to_node(seqFace, node, ALG_START_COL, aligned=True) TRACKED_CLADES = ["Eukaryota", "Viridiplantae", "Fungi", "Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta", "Amoebozoa", "Crypthophyta", "Bacteria", "Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria", "Gammaproteobacteria",] colors = random_color(num=len(TRACKED_CLADES), s=0.45) lin2color = {ln: colors[i] for i, ln in enumerate(TRACKED_CLADES)} NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444') LABEL_START_COL = 10 ALG_START_COL = 40 ts = TreeStyle() ts.draw_aligned_faces_as_table = False ts.draw_guiding_lines = False ts.show_leaf_name = False ts.show_branch_support = False ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels] MIXED_RES = set() MAX_SEQ_LEN = 0 NPR_TREES = [] for n in tree.traverse(): if hasattr(n, "tree_seqtype"): MIXED_RES.add(n.tree_seqtype) if hasattr(n, "tree_type"): NPR_TREES.append(n.tree_type) seq = getattr(n, "sequence", "") MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN) if MAX_SEQ_LEN: ALG_SCALE = min(1, 1000./MAX_SEQ_LEN) ts.layout_fn.append(ly_block_alg) if len(NPR_TREES) > 1: rF = RectFace(4, 4, "steelblue", "steelblue") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" NPR node"), 1) ts.legend_position = 3 if len(MIXED_RES) > 1: rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA") rF.margin_right = 10 rF.margin_left = 10 ts.legend.add_face(rF, 0) ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1) ts.legend_position = 3 try: tree.set_species_naming_function(spname) annotate_tree_with_ncbi(tree) tree.set_outgroup(out) tree.swap_children() except Exception: pass tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=300) tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=300) tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=300) def annotate_tree_with_ncbi(tree): from ...ncbi_taxonomy import ncbiquery as ncbi ncbi.connect_database() name2sp = ncbi.get_name_translator(tree.get_species()) for lf in tree.iter_leaves(): lf.add_features(taxid=name2sp.get(lf.species, [0])[0]) lf.add_features(genename=re.sub('\{[^}]+\}', '', lf.name).strip()) ncbi.annotate_tree(tree, attr_name='taxid') def spname(name): m = re.search('\{([^}]+)\}', name) if m: return m.groups()[0] else: return name.split('|')[0].strip().replace('_', ' ') taxid = name.split('.', 1)[0] tax2name = ncbi.get_taxid_translator([taxid]) if int(taxid) not in tax2name: print('name', name, taxid, tax2name) return tax2name.get(int(taxid), taxid)