示例#1
0
def get_example_tree():

    # Set dashed blue lines in all leaves
    nst1 = NodeStyle()
    nst1["bgcolor"] = "LightSteelBlue"
    nst2 = NodeStyle()
    nst2["bgcolor"] = "Moccasin"
    nst3 = NodeStyle()
    nst3["bgcolor"] = "DarkSeaGreen"
    nst4 = NodeStyle()
    nst4["bgcolor"] = "Khaki"


    t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
    for n in t.traverse():
        n.dist = 0
    
    n1 = t.get_common_ancestor("a1", "a2", "a3")
    n1.set_style(nst1)
    n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
    n2.set_style(nst2)
    n3 = t.get_common_ancestor("c1", "c2", "c3")
    n3.set_style(nst3)
    n4 = t.get_common_ancestor("b3", "b4")
    n4.set_style(nst4)
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    ts.mode = "c"
    ts.root_opening_factor = 1
    return t, ts
示例#2
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文件: bubble_map.py 项目: tarah28/ete
def get_example_tree():
    # Random tree
    t = Tree()
    t.populate(20, random_branches=True)

    # Some random features in all nodes
    for n in t.traverse():
        n.add_features(weight=random.randint(0, 50))

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    ts.layout_fn = layout

    # Draw a tree
    ts.mode = "c"

    # We will add node names manually
    ts.show_leaf_name = False
    # Show branch data
    ts.show_branch_length = True
    ts.show_branch_support = True

    return t, ts
示例#3
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def get_example_tree():

    # Set dashed blue lines in all leaves
    nst1 = NodeStyle()
    nst1["bgcolor"] = "LightSteelBlue"
    nst2 = NodeStyle()
    nst2["bgcolor"] = "Moccasin"
    nst3 = NodeStyle()
    nst3["bgcolor"] = "DarkSeaGreen"
    nst4 = NodeStyle()
    nst4["bgcolor"] = "Khaki"

    t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
    for n in t.traverse():
        n.dist = 0

    n1 = t.get_common_ancestor("a1", "a2", "a3")
    n1.set_style(nst1)
    n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
    n2.set_style(nst2)
    n3 = t.get_common_ancestor("c1", "c2", "c3")
    n3.set_style(nst3)
    n4 = t.get_common_ancestor("b3", "b4")
    n4.set_style(nst4)
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    ts.mode = "c"
    ts.root_opening_factor = 1
    return t, ts
示例#4
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def get_example_tree():
    # Random tree
    t = Tree()
    t.populate(20, random_branches=True)

    # Some random features in all nodes
    for n in t.traverse():
        n.add_features(weight=random.randint(0, 50))

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    ts.layout_fn = layout

    # Draw a tree 
    ts.mode = "c"

    # We will add node names manually
    ts.show_leaf_name = False
    # Show branch data
    ts.show_branch_length = True
    ts.show_branch_support = True

    return t, ts
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "r"
    ts.show_leaf_name = False
    t.populate(10)
    return t, ts
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "r"
    ts.show_leaf_name = False
    t.populate(10)
    return t, ts
示例#7
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def get_example_tree():
        
    t = Tree()
    t.populate(8, reuse_names=False)

    ts = TreeStyle()
    ts.layout_fn = master_ly
    ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
    return t, ts
示例#8
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def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "c"
    ts.show_leaf_name = True
    ts.min_leaf_separation = 15
    t.populate(100)
    return t, ts
示例#9
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def get_example_tree():
    t = Tree()
    t.populate(10)
    ts = TreeStyle()
    ts.rotation = 45
    ts.show_leaf_name = False
    ts.layout_fn = rotation_layout
    
    return t, ts
示例#10
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文件: item_faces.py 项目: tarah28/ete
def get_example_tree():

    t = Tree()
    t.populate(8, reuse_names=False)

    ts = TreeStyle()
    ts.layout_fn = master_ly
    ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
    return t, ts
示例#11
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def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "c"
    ts.show_leaf_name = True
    ts.min_leaf_separation = 15
    t.populate(100)
    return t, ts
示例#12
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def get_example_tree():

    t = Tree()
    t.populate(8)

    # Node style handling is no longer limited to layout functions. You
    # can now create fixed node styles and use them many times, save them
    # or even add them to nodes before drawing (this allows to save and
    # reproduce an tree image design)

    # Set bold red branch to the root node
    style = NodeStyle()
    style["fgcolor"] = "#0f0f0f"
    style["size"] = 0
    style["vt_line_color"] = "#ff0000"
    style["hz_line_color"] = "#ff0000"
    style["vt_line_width"] = 8
    style["hz_line_width"] = 8
    style["vt_line_type"] = 0  # 0 solid, 1 dashed, 2 dotted
    style["hz_line_type"] = 0
    t.set_style(style)

    #Set dotted red lines to the first two branches
    style1 = NodeStyle()
    style1["fgcolor"] = "#0f0f0f"
    style1["size"] = 0
    style1["vt_line_color"] = "#ff0000"
    style1["hz_line_color"] = "#ff0000"
    style1["vt_line_width"] = 2
    style1["hz_line_width"] = 2
    style1["vt_line_type"] = 2  # 0 solid, 1 dashed, 2 dotted
    style1["hz_line_type"] = 2
    t.children[0].img_style = style1
    t.children[1].img_style = style1

    # Set dashed blue lines in all leaves
    style2 = NodeStyle()
    style2["fgcolor"] = "#000000"
    style2["shape"] = "circle"
    style2["vt_line_color"] = "#0000aa"
    style2["hz_line_color"] = "#0000aa"
    style2["vt_line_width"] = 2
    style2["hz_line_width"] = 2
    style2["vt_line_type"] = 1  # 0 solid, 1 dashed, 2 dotted
    style2["hz_line_type"] = 1
    for l in t.iter_leaves():
        l.img_style = style2

    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    return t, ts
示例#13
0
def get_example_tree():

    t = Tree()
    t.populate(8)

    # Node style handling is no longer limited to layout functions. You
    # can now create fixed node styles and use them many times, save them
    # or even add them to nodes before drawing (this allows to save and
    # reproduce an tree image design)

    # Set bold red branch to the root node
    style = NodeStyle()
    style["fgcolor"] = "#0f0f0f"
    style["size"] = 0
    style["vt_line_color"] = "#ff0000"
    style["hz_line_color"] = "#ff0000"
    style["vt_line_width"] = 8
    style["hz_line_width"] = 8
    style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
    style["hz_line_type"] = 0
    t.set_style(style)

    #Set dotted red lines to the first two branches
    style1 = NodeStyle()
    style1["fgcolor"] = "#0f0f0f"
    style1["size"] = 0
    style1["vt_line_color"] = "#ff0000"
    style1["hz_line_color"] = "#ff0000"
    style1["vt_line_width"] = 2
    style1["hz_line_width"] = 2
    style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
    style1["hz_line_type"] = 2
    t.children[0].img_style = style1
    t.children[1].img_style = style1

    # Set dashed blue lines in all leaves
    style2 = NodeStyle()
    style2["fgcolor"] = "#000000"
    style2["shape"] = "circle"
    style2["vt_line_color"] = "#0000aa"
    style2["hz_line_color"] = "#0000aa"
    style2["vt_line_width"] = 2
    style2["hz_line_width"] = 2
    style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
    style2["hz_line_type"] = 1
    for l in t.iter_leaves():
        l.img_style = style2

    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    return t, ts
示例#14
0
def get_example_tree():
    # Create a random tree and add to each leaf a random set of motifs
    # from the original set
    t = Tree()
    t.populate(10)
    # for l in t.iter_leaves():
    #     seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs))) 

    #     seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
    #                            seqtail_format="compactseq", scale_factor=1)
    #     seqFace.margin_bottom = 4
    #     f = l.add_face(seqFace, 0, "aligned")

    ts = TreeStyle()
    ts.layout_fn = layout
    t.show(tree_style=ts)
    return t, ts
示例#15
0
def get_example_tree():
    # Create a random tree and add to each leaf a random set of motifs
    # from the original set
    t = Tree()
    t.populate(10)
    # for l in t.iter_leaves():
    #     seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs)))

    #     seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
    #                            seqtail_format="compactseq", scale_factor=1)
    #     seqFace.margin_bottom = 4
    #     f = l.add_face(seqFace, 0, "aligned")

    ts = TreeStyle()
    ts.layout_fn = layout
    t.show(tree_style=ts)
    return t, ts
示例#16
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def draw(t, draw_alg=True):    
    def ly(node):
        node.img_style['vt_line_width'] = 1
        node.img_style['hz_line_width'] = 1
        if node.is_leaf():
            add_face_to_node(TextFace(' (%s)' %node.name.split()[0].replace("/exon2", ""), fsize=10, fgcolor='slategrey', tight_text=False), node, 1, position='branch-right')
            add_face_to_node(TextFace(node.species, fsize=12, fgcolor='black', fstyle='italic', tight_text=False), node, 0, position='branch-right')
            c = 1
            for tname in tracked_clades:
                if tname in node.named_lineage:
                    linF = TextFace(tname, fsize=10, fgcolor='white')
                    linF.margin_left = 3
                    linF.background.color = lin2color[tname]

                    add_face_to_node(linF, node, c, position='aligned')
                    c += 1
            for n in xrange(1, 20-(c-1)):
                add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
                c+=1

            if draw_alg and 'sequence' in node.features:
                #seqFace = SequenceFace(node.sequence,"aa",13)
                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
                            w = end-start
                            motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
                            last_lt = None

                    elif lt == '-':
                        if last_lt is not None:
                            start, end = last_lt, c-1
                            w = end-start
                            motifs.append([start, end, "[]", w, 13, "slategrey", "slategrey", None])
                            last_lt = None

                if not motifs:
                    print node, node.sequence

                seqFace = SeqMotifFace(node.sequence, motifs,
                                       intermotif_format="line",
                                       seqtail_format="line", scale_factor=1)
                add_face_to_node(seqFace, node, 20, aligned=True)

        else:
            if node.up: 
                add_face_to_node(TextFace('% 3g' %node.support, fsize=11, fgcolor='indianred'), node, 0, position='branch-top')
                
            if hasattr(node, "support2") and node.up:
                add_face_to_node(TextFace('% 3g' %float(node.support2), fsize=11, fgcolor='steelblue'), node, 0, position='branch-bottom')

        node.img_style['size'] = 0
        node.img_style['hz_line_color'] = 'black'
        node.img_style['vt_line_color'] = 'black'

    colors = random_color(num=len(tracked_clades))
    lin2color = dict([(ln, colors[i]) for i, ln in enumerate(tracked_clades)])
    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
    print 'Rendering tree.pdf'
    t.render('tree.svg', tree_style=ts)
    t.render('tree.png', tree_style=ts)
示例#17
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文件: visualize.py 项目: jhcepas/npr
def draw_tree(tree, conf, outfile):
    try:
        from ete_dev import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace,
                             SequenceFace, 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 xrange(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,
                                       intermotif_format="line",
                                       seqtail_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",]
    
    # ["Opisthokonta",  "Apicomplexa"]
    
    colors = random_color(num=len(TRACKED_CLADES), s=0.45)
    lin2color = dict([(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.scale = 160

    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)
        a = tree.search_nodes(species='Dictyostelium discoideum')[0]
        b = tree.search_nodes(species='Chondrus crispus')[0]
        #out = tree.get_common_ancestor([a, b])
        #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
        tree.set_outgroup(out)    
        tree.swap_children()
    except Exception:
        pass
    
    tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
示例#18
0
    parser.add_argument("--tax2track", dest="tax2track", type=str, help="")
    parser.add_argument("--dump_tax_info",
                        dest="dump_tax_info",
                        action="store_true",
                        help="")

    args = parser.parse_args()

    reftree_name = os.path.basename(args.ref_tree) if args.ref_tree else ""
    if args.explore:
        print "Reading tree from file:", args.explore
        t = cPickle.load(open(args.explore))
        ts = TreeStyle()
        ts.force_topology = True
        ts.show_leaf_name = False
        ts.layout_fn = ncbi_layout
        ts.mode = "r"
        t.show(tree_style=ts)
        print "dumping color config"
        cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))
        sys.exit()

    if args.output:
        OUT = open(args.output, "w")
    else:
        OUT = sys.stdout

    print "Dumping results into", OUT
    target_trees = []
    if args.tree_list_file:
        target_trees = [line.strip() for line in open(args.tree_list_file)]
示例#19
0
     >Chimp
     CAC GCC CGA TGG CTC AAC GAA AAG TTA AGA TGC GAA TTG AGA ACT CTG AAA AAA
     TTG GGA CTG GAC GGC TAC AAG GCA GTA AGT CAG TAC GTT AAA GGT CGT GCG
     >Orangutan
     GAT GCA CGC TGG ATC AAC GAA AAG TTA AGA TGC GTA TCG AGA ACT CTG AAA AAA
     TTG GGA CTG GAC GGC TAC AAG GGA GTA AGT CAA TAC GTT AAA GGT CGT CCG
     """)
     #try:
     #    tree.run_model("fb")
     #    tree.run_model("M2")
     #except:
     #    pass
     tree.dist = 0
     ts = TreeStyle()
     ts.title.add_face(TextFace("Example for EvolTree, interactivity shows codons", fsize=15), column=0)
     ts.layout_fn = test_layout_evol
     #try:
     #    tree.show(tree_style=ts, histfaces=["M2"])
     #except:
     tree.show(tree_style=ts)
 except:
     tree = PhyloTree('(Orangutan,Human,Chimp);')
     tree.link_to_alignment("""
                            >Chimp
                            HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
                            >Orangutan
                            DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
                            >Human
                            DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
                            """)
     nt_sequences = {"Human"    : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
示例#20
0
        f.border.width = 0
        
        node.img_style["size"] = 10
        node.img_style["shape"] = "square"
    node.img_style["bgcolor"] = random_color()
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
    #if node.is_leaf():
    #    f = faces.CircleFace(50, "red")
    #    faces.add_face_to_node(f, node, 0, position="aligned")
        

ts = TreeStyle()
ts.mode = "c"
ts.arc_span = 360
ts.layout_fn = layout 
ts.show_leaf_name = False
ts.show_border = True
ts.draw_guiding_lines = False
ts.show_scale = True
#ts.scale = 60
t = Tree()
t.dist = 0

t.size = 0,0
for x in xrange(100):
    n = t.add_child()
    n = n.add_child()
    n = n.add_child()
    n2 = n.add_child()
    n3 = n.add_child()
示例#21
0
def main(argv):
    parser = argparse.ArgumentParser(description=__DESCRIPTION__, 
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    # name or flags - Either a name or a list of option strings, e.g. foo or -f, --foo.
    # action - The basic type of action to be taken when this argument is encountered at the command line. (store, store_const, store_true, store_false, append, append_const, version)
    # nargs - The number of command-line arguments that should be consumed. (N, ? (one or default), * (all 1 or more), + (more than 1) )
    # const - A constant value required by some action and nargs selections. 
    # default - The value produced if the argument is absent from the command line.
    # type - The type to which the command-line argument should be converted.
    # choices - A container of the allowable values for the argument.
    # required - Whether or not the command-line option may be omitted (optionals only).
    # help - A brief description of what the argument does.
    # metavar - A name for the argument in usage messages.
    # dest - The name of the attribute to be added to the object returned by parse_args().
    
    parser.add_argument("--show", dest="show_tree",
                        action="store_true", 
                        help="""Display tree after the analysis.""")
    
    parser.add_argument("--render", dest="render",
                        action="store_true", 
                        help="""Render tree.""")

    parser.add_argument("--dump", dest="dump",
                        action="store_true", 
                        help="""Dump analysis""")

    parser.add_argument("--explore", dest="explore",
                        type=str,
                        help="""Reads a previously analyzed tree and visualize it""")
    
    input_args = parser.add_mutually_exclusive_group()
    input_args.required=True
    input_args.add_argument("-t", "--tree", dest="target_tree",  nargs="+",
                        type=str,
                        help="""Tree file in newick format""")

    input_args.add_argument("-tf", dest="tree_list_file",
                        type=str, 
                        help="File with the list of tree files")
    
    parser.add_argument("--tax", dest="tax_info", type=str,
                        help="If the taxid attribute is not set in the"
                        " newick file for all leaf nodes, a tab file file"
                        " with the translation of name and taxid can be"
                        " provided with this option.")

    parser.add_argument("--sp_delimiter", dest="sp_delimiter", type=str,
                        help="If taxid is part of the leaf name, delimiter used to split the string")

    parser.add_argument("--sp_field", dest="sp_field", type=int, default=0,
                        help="field position for taxid after splitting leaf names")
    
    parser.add_argument("--ref", dest="ref_tree", type=str,
                        help="Uses ref tree to compute robinson foulds"
                        " distances of the different subtrees")

    parser.add_argument("--rf-only", dest="rf_only",
                        action = "store_true",
                        help="Skip ncbi consensus analysis")

    parser.add_argument("--outgroup", dest="outgroup",
                        type=str, nargs="+",
                        help="A list of node names defining the trees outgroup")
    
    parser.add_argument("--is_sptree", dest="is_sptree",
                        action = "store_true",
                        help="Assumes no duplication nodes in the tree")
    
    parser.add_argument("-o", dest="output", type=str,
                        help="Writes result into a file")

    parser.add_argument("--tax2name", dest="tax2name", type=str,
                        help="")
    
    parser.add_argument("--tax2track", dest="tax2track", type=str,
                        help="")
    
    parser.add_argument("--dump_tax_info", dest="dump_tax_info", action="store_true",
                        help="")
    
    args = parser.parse_args(argv)

    if args.sp_delimiter:
        GET_TAXID = lambda x: x.split(args.sp_delimiter)[args.sp_field]
    else:
        GET_TAXID = None
    
    reftree_name = os.path.basename(args.ref_tree) if args.ref_tree else ""
    if args.explore:
        print >>sys.stderr, "Reading tree from file:", args.explore
        t = cPickle.load(open(args.explore))
        ts = TreeStyle()
        ts.force_topology = True
        ts.show_leaf_name = False
        ts.layout_fn = ncbi_layout 
        ts.mode = "r"
        t.show(tree_style=ts)
        print >>sys.stderr, "dumping color config"
        cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))
        sys.exit()
    
    if args.output:
        OUT = open(args.output, "w")
    else:
        OUT = sys.stdout

    print >>sys.stderr, "Dumping results into", OUT
    target_trees = []
    if args.tree_list_file:
        target_trees = [line.strip() for line in open(args.tree_list_file)]
    if args.target_tree:
        target_trees += args.target_tree
    prev_tree = None
    if args.tax2name:
        tax2name = cPickle.load(open(args.tax2name))
    else:
        tax2name = {}

    if args.tax2track:
        tax2track = cPickle.load(open(args.tax2track))
    else:
        tax2track = {}
    print len(tax2track), len(tax2name)
    header = ("TargetTree", "Subtrees", "Ndups", "Broken subtrees", "Broken clades", "Clade sizes", "RF (avg)", "RF (med)", "RF (std)", "RF (max)", "Shared tips")
    print >>OUT, '|'.join([h.ljust(15) for h in header])
    if args.ref_tree:
        print >>sys.stderr, "Reading ref tree from", args.ref_tree
        reft = Tree(args.ref_tree, format=1)
    else:
        reft = None

    SHOW_TREE = False
    if args.show_tree or args.render:
        SHOW_TREE = True

        
    prev_broken = set()
    ENTRIES = []
    ncbi.connect_database()
    for tfile in target_trees:
        #print tfile
        t = PhyloTree(tfile, sp_naming_function=None)
        if GET_TAXID:
            for n in t.iter_leaves():
                n.name = GET_TAXID(n.name)
        
        if args.outgroup:
            if len(args.outgroup) == 1:
                out = t & args.outgroup[0]
            else:
                out = t.get_common_ancestor(args.outgroup)
                if set(out.get_leaf_names()) ^ set(args.outgroup):
                    raise ValueError("Outgroup is not monophyletic")
                
            t.set_outgroup(out)
        t.ladderize()

        if prev_tree:
            tree_compare(t, prev_tree)
        prev_tree = t
       
        
        if args.tax_info:
            tax2name, tax2track = annotate_tree_with_taxa(t, args.tax_info, tax2name, tax2track)
            if args.dump_tax_info:
                cPickle.dump(tax2track, open("tax2track.pkl", "w"))
                cPickle.dump(tax2name, open("tax2name.pkl", "w"))
                print "Tax info written into pickle files"
        else:
            for n in t.iter_leaves():
                spcode = n.name
                n.add_features(taxid=spcode)
                n.add_features(species=spcode)
            tax2name, tax2track = annotate_tree_with_taxa(t, None, tax2name, tax2track)
            
        # Split tree into species trees
        #subtrees =  t.get_speciation_trees()
        if not args.rf_only:
            #print "Calculating tree subparts..."
            t1 = time.time()
            if not args.is_sptree:
                subtrees =  t.split_by_dups()
                #print "Subparts:", len(subtrees), time.time()-t1
            else:
                subtrees = [t]

          
            valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = analyze_subtrees(t, subtrees, show_tree=SHOW_TREE)
            
            #print valid_subtrees, broken_subtrees, ncbi_mistakes, total_rf
        else:
            subtrees = []
            valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = 0, 0, 0, 0, 0, 0
            
        ndups = 0
        nsubtrees = len(subtrees)
           
        rf = 0
        rf_max = 0
        rf_std = 0
        rf_med = 0
        common_names = 0
        max_size = 0
        if reft and len(subtrees) == 1:
            rf = t.robinson_foulds(reft, attr_t1="realname")
            rf_max = rf[1]
            rf = rf[0]
            rf_med = rf
            
        elif reft:
            #print "Calculating avg RF..."
            nsubtrees, ndups, subtrees = t.get_speciation_trees(map_features=["taxid"])
            #print len(subtrees), "Sub-Species-trees found"
            avg_rf = []
            rf_max = 0.0 # reft.robinson_foulds(reft)[1]
            sum_size = 0.0
            print nsubtrees, "subtrees", ndups, "duplications"

            for ii, subt in enumerate(subtrees):
                print "\r%d" %ii,
                sys.stdout.flush()
                try:
                    partial_rf = subt.robinson_foulds(reft, attr_t1="taxid")
                except ValueError:
                    pass
                else:
                    sptree_size = len(set([n.taxid for n in subt.iter_leaves()]))
                    sum_size += sptree_size
                    avg_rf.append((partial_rf[0]/float(partial_rf[1])) * sptree_size)
                    common_names = len(partial_rf[3])
                    max_size = max(max_size, sptree_size)
                    rf_max = max(rf_max, partial_rf[1])
                #print  partial_rf[:2]
            rf = numpy.sum(avg_rf) / float(sum_size) # Treeko dist
            rf_std = numpy.std(avg_rf)
            rf_med = numpy.median(avg_rf)

        sizes_info = "%0.1f/%0.1f +- %0.1f" %( numpy.mean(broken_sizes), numpy.median(broken_sizes), numpy.std(broken_sizes))
        iter_values = [os.path.basename(tfile), nsubtrees, ndups,
                        broken_subtrees, ncbi_mistakes, broken_branches, sizes_info, rf, rf_med,
                       rf_std, rf_max, common_names] 
        print >>OUT, '|'.join(map(lambda x: str(x).strip().ljust(15), iter_values)) 
        fixed = sorted([n for n in prev_broken if n not in broken_clades])
        new_problems =  sorted(broken_clades - prev_broken)
        fixed_string = color(', '.join(fixed), "green") if fixed else ""
        problems_string = color(', '.join(new_problems), "red") if new_problems else ""
        OUT.write("    Fixed clades: %s\n" %fixed_string) if fixed else None
        OUT.write("    New broken:   %s\n" %problems_string) if new_problems else None
        prev_broken = broken_clades
        ENTRIES.append([os.path.basename(tfile), nsubtrees, ndups,
                        broken_subtrees, ncbi_mistakes, broken_branches, sizes_info, fixed_string, problems_string])
        OUT.flush()
        if args.show_tree or args.render:
            ts = TreeStyle()
            ts.force_topology = True
            #ts.tree_width = 500
            ts.show_leaf_name = False
            ts.layout_fn = ncbi_layout 
            ts.mode = "r"
            t.dist = 0
            if args.show_tree:
                #if args.hide_monophyletic:
                #    tax2monophyletic = {}
                #    n2content = t.get_node2content()
                #    for node in t.traverse():
                #        term2count = defaultdict(int)
                #        for leaf in n2content[node]:
                #            if leaf.lineage:
                #                for term in leaf.lineage:
                #                    term2count[term] += 1
                #        expected_size = len(n2content)
                #        for term, count in term2count.iteritems():
                #            if count > 1
                    
                print "Showing tree..."
                t.show(tree_style=ts)
            else:
                t.render("img.svg", tree_style=ts, dpi=300)
            print "dumping color config"
            cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))

        if args.dump:
            cPickle.dump(t, open("ncbi_analysis.pkl", "w"))
            
    print
    print
    HEADER = ("TargetTree", "Subtrees", "Ndups", "Broken subtrees", "Broken clades", "Broken branches", "Clade sizes", "Fixed Groups", "New Broken Clades")
    print_table(ENTRIES, max_col_width = 50, row_line=True, header=HEADER)
            
    if args.output:
        OUT.close()
示例#22
0
                col += 1
            # Add the corresponding face to the node
            if name.startswith("Dme"):
                faces.add_face_to_node(flyFace, node, column=col)
            elif name.startswith("Dre"):
                faces.add_face_to_node(fishFace, node, column=col)
            elif name.startswith("Mms"):
                faces.add_face_to_node(mouseFace, node, column=col)
            elif name.startswith("Ptr"):
                faces.add_face_to_node(chimpFace, node, column=col)
            elif name.startswith("Hsa"):
                faces.add_face_to_node(humanFace, node, column=col)
            elif name.startswith("Cfa"):
                faces.add_face_to_node(dogFace, node, column=col)

            # Modifies this node's style
            node.img_style["size"] = 16
            node.img_style["shape"] = "sphere"
            node.img_style["fgcolor"] = "#AA0000"

    # If leaf is "Hsa" (h**o sapiens), highlight it using a
    # different background.
    if node.is_leaf() and node.name.startswith("Hsa"):
        node.img_style["bgcolor"] = "#9db0cf"


# And, finally, Visualize the tree using my own layout function
ts = TreeStyle()
ts.layout_fn = mylayout
t.render("img_faces.png", w=600, tree_style=ts)
示例#23
0
    global CONT
    if CONT >= len(chars):
        CONT = 0
    if node.is_leaf():
        node.img_style["size"] = 0
        F2= AttrFace("name", tight_text=True)
        F= TextFace(chars[CONT], tight_text=True)
        F.inner_border.width = 0
        F2.inner_border.width = 0
        #faces.add_face_to_node(F ,node, 0, position="branch-right")
        faces.add_face_to_node(F2 ,node, 1, position="branch-right")
        CONT += 1
t = Tree()
t.populate(20, random_branches=True)
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "c"
ts.show_leaf_name = False

temp_tface = TreeFace(t, ts)
n = main_tree.add_child()
n.add_face(temp_tface, 0, "aligned")

# MAIN TREE

ms = TreeStyle()
ms.mode = "r"
ms.show_leaf_name = False
main_tree.show(tree_style=ms)        

示例#24
0
def main(argv):
    parser = argparse.ArgumentParser(
        description=__DESCRIPTION__,
        formatter_class=argparse.RawDescriptionHelpFormatter)
    # name or flags - Either a name or a list of option strings, e.g. foo or -f, --foo.
    # action - The basic type of action to be taken when this argument is encountered at the command line. (store, store_const, store_true, store_false, append, append_const, version)
    # nargs - The number of command-line arguments that should be consumed. (N, ? (one or default), * (all 1 or more), + (more than 1) )
    # const - A constant value required by some action and nargs selections.
    # default - The value produced if the argument is absent from the command line.
    # type - The type to which the command-line argument should be converted.
    # choices - A container of the allowable values for the argument.
    # required - Whether or not the command-line option may be omitted (optionals only).
    # help - A brief description of what the argument does.
    # metavar - A name for the argument in usage messages.
    # dest - The name of the attribute to be added to the object returned by parse_args().

    parser.add_argument("--show",
                        dest="show_tree",
                        action="store_true",
                        help="""Display tree after the analysis.""")

    parser.add_argument("--render",
                        dest="render",
                        action="store_true",
                        help="""Render tree.""")

    parser.add_argument("--dump",
                        dest="dump",
                        action="store_true",
                        help="""Dump analysis""")

    parser.add_argument(
        "--explore",
        dest="explore",
        type=str,
        help="""Reads a previously analyzed tree and visualize it""")

    input_args = parser.add_mutually_exclusive_group()
    input_args.required = True
    input_args.add_argument("-t",
                            "--tree",
                            dest="target_tree",
                            nargs="+",
                            type=str,
                            help="""Tree file in newick format""")

    input_args.add_argument("-tf",
                            dest="tree_list_file",
                            type=str,
                            help="File with the list of tree files")

    parser.add_argument("--tax",
                        dest="tax_info",
                        type=str,
                        help="If the taxid attribute is not set in the"
                        " newick file for all leaf nodes, a tab file file"
                        " with the translation of name and taxid can be"
                        " provided with this option.")

    parser.add_argument(
        "--sp_delimiter",
        dest="sp_delimiter",
        type=str,
        help=
        "If taxid is part of the leaf name, delimiter used to split the string"
    )

    parser.add_argument(
        "--sp_field",
        dest="sp_field",
        type=int,
        default=0,
        help="field position for taxid after splitting leaf names")

    parser.add_argument("--ref",
                        dest="ref_tree",
                        type=str,
                        help="Uses ref tree to compute robinson foulds"
                        " distances of the different subtrees")

    parser.add_argument("--rf-only",
                        dest="rf_only",
                        action="store_true",
                        help="Skip ncbi consensus analysis")

    parser.add_argument(
        "--outgroup",
        dest="outgroup",
        type=str,
        nargs="+",
        help="A list of node names defining the trees outgroup")

    parser.add_argument("--is_sptree",
                        dest="is_sptree",
                        action="store_true",
                        help="Assumes no duplication nodes in the tree")

    parser.add_argument("-o",
                        dest="output",
                        type=str,
                        help="Writes result into a file")

    parser.add_argument("--tax2name", dest="tax2name", type=str, help="")

    parser.add_argument("--tax2track", dest="tax2track", type=str, help="")

    parser.add_argument("--dump_tax_info",
                        dest="dump_tax_info",
                        action="store_true",
                        help="")

    args = parser.parse_args(argv)

    if args.sp_delimiter:
        GET_TAXID = lambda x: x.split(args.sp_delimiter)[args.sp_field]
    else:
        GET_TAXID = None

    reftree_name = os.path.basename(args.ref_tree) if args.ref_tree else ""
    if args.explore:
        print >> sys.stderr, "Reading tree from file:", args.explore
        t = cPickle.load(open(args.explore))
        ts = TreeStyle()
        ts.force_topology = True
        ts.show_leaf_name = False
        ts.layout_fn = ncbi_layout
        ts.mode = "r"
        t.show(tree_style=ts)
        print >> sys.stderr, "dumping color config"
        cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))
        sys.exit()

    if args.output:
        OUT = open(args.output, "w")
    else:
        OUT = sys.stdout

    print >> sys.stderr, "Dumping results into", OUT
    target_trees = []
    if args.tree_list_file:
        target_trees = [line.strip() for line in open(args.tree_list_file)]
    if args.target_tree:
        target_trees += args.target_tree
    prev_tree = None
    if args.tax2name:
        tax2name = cPickle.load(open(args.tax2name))
    else:
        tax2name = {}

    if args.tax2track:
        tax2track = cPickle.load(open(args.tax2track))
    else:
        tax2track = {}
    print len(tax2track), len(tax2name)
    header = ("TargetTree", "Subtrees", "Ndups", "Broken subtrees",
              "Broken clades", "Clade sizes", "RF (avg)", "RF (med)",
              "RF (std)", "RF (max)", "Shared tips")
    print >> OUT, '|'.join([h.ljust(15) for h in header])
    if args.ref_tree:
        print >> sys.stderr, "Reading ref tree from", args.ref_tree
        reft = Tree(args.ref_tree, format=1)
    else:
        reft = None

    SHOW_TREE = False
    if args.show_tree or args.render:
        SHOW_TREE = True

    prev_broken = set()
    ENTRIES = []
    ncbi.connect_database()
    for tfile in target_trees:
        #print tfile
        t = PhyloTree(tfile, sp_naming_function=None)
        if GET_TAXID:
            for n in t.iter_leaves():
                n.name = GET_TAXID(n.name)

        if args.outgroup:
            if len(args.outgroup) == 1:
                out = t & args.outgroup[0]
            else:
                out = t.get_common_ancestor(args.outgroup)
                if set(out.get_leaf_names()) ^ set(args.outgroup):
                    raise ValueError("Outgroup is not monophyletic")

            t.set_outgroup(out)
        t.ladderize()

        if prev_tree:
            tree_compare(t, prev_tree)
        prev_tree = t

        if args.tax_info:
            tax2name, tax2track = annotate_tree_with_taxa(
                t, args.tax_info, tax2name, tax2track)
            if args.dump_tax_info:
                cPickle.dump(tax2track, open("tax2track.pkl", "w"))
                cPickle.dump(tax2name, open("tax2name.pkl", "w"))
                print "Tax info written into pickle files"
        else:
            for n in t.iter_leaves():
                spcode = n.name
                n.add_features(taxid=spcode)
                n.add_features(species=spcode)
            tax2name, tax2track = annotate_tree_with_taxa(
                t, None, tax2name, tax2track)

        # Split tree into species trees
        #subtrees =  t.get_speciation_trees()
        if not args.rf_only:
            #print "Calculating tree subparts..."
            t1 = time.time()
            if not args.is_sptree:
                subtrees = t.split_by_dups()
                #print "Subparts:", len(subtrees), time.time()-t1
            else:
                subtrees = [t]

            valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = analyze_subtrees(
                t, subtrees, show_tree=SHOW_TREE)

            #print valid_subtrees, broken_subtrees, ncbi_mistakes, total_rf
        else:
            subtrees = []
            valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = 0, 0, 0, 0, 0, 0

        ndups = 0
        nsubtrees = len(subtrees)

        rf = 0
        rf_max = 0
        rf_std = 0
        rf_med = 0
        common_names = 0
        max_size = 0
        if reft and len(subtrees) == 1:
            rf = t.robinson_foulds(reft, attr_t1="realname")
            rf_max = rf[1]
            rf = rf[0]
            rf_med = rf

        elif reft:
            #print "Calculating avg RF..."
            nsubtrees, ndups, subtrees = t.get_speciation_trees(
                map_features=["taxid"])
            #print len(subtrees), "Sub-Species-trees found"
            avg_rf = []
            rf_max = 0.0  # reft.robinson_foulds(reft)[1]
            sum_size = 0.0
            print nsubtrees, "subtrees", ndups, "duplications"

            for ii, subt in enumerate(subtrees):
                print "\r%d" % ii,
                sys.stdout.flush()
                try:
                    partial_rf = subt.robinson_foulds(reft, attr_t1="taxid")
                except ValueError:
                    pass
                else:
                    sptree_size = len(
                        set([n.taxid for n in subt.iter_leaves()]))
                    sum_size += sptree_size
                    avg_rf.append(
                        (partial_rf[0] / float(partial_rf[1])) * sptree_size)
                    common_names = len(partial_rf[3])
                    max_size = max(max_size, sptree_size)
                    rf_max = max(rf_max, partial_rf[1])
                #print  partial_rf[:2]
            rf = numpy.sum(avg_rf) / float(sum_size)  # Treeko dist
            rf_std = numpy.std(avg_rf)
            rf_med = numpy.median(avg_rf)

        sizes_info = "%0.1f/%0.1f +- %0.1f" % (numpy.mean(broken_sizes),
                                               numpy.median(broken_sizes),
                                               numpy.std(broken_sizes))
        iter_values = [
            os.path.basename(tfile), nsubtrees, ndups, broken_subtrees,
            ncbi_mistakes, broken_branches, sizes_info, rf, rf_med, rf_std,
            rf_max, common_names
        ]
        print >> OUT, '|'.join(
            map(lambda x: str(x).strip().ljust(15), iter_values))
        fixed = sorted([n for n in prev_broken if n not in broken_clades])
        new_problems = sorted(broken_clades - prev_broken)
        fixed_string = color(', '.join(fixed), "green") if fixed else ""
        problems_string = color(', '.join(new_problems),
                                "red") if new_problems else ""
        OUT.write("    Fixed clades: %s\n" % fixed_string) if fixed else None
        OUT.write("    New broken:   %s\n" %
                  problems_string) if new_problems else None
        prev_broken = broken_clades
        ENTRIES.append([
            os.path.basename(tfile), nsubtrees, ndups, broken_subtrees,
            ncbi_mistakes, broken_branches, sizes_info, fixed_string,
            problems_string
        ])
        OUT.flush()
        if args.show_tree or args.render:
            ts = TreeStyle()
            ts.force_topology = True
            #ts.tree_width = 500
            ts.show_leaf_name = False
            ts.layout_fn = ncbi_layout
            ts.mode = "r"
            t.dist = 0
            if args.show_tree:
                #if args.hide_monophyletic:
                #    tax2monophyletic = {}
                #    n2content = t.get_node2content()
                #    for node in t.traverse():
                #        term2count = defaultdict(int)
                #        for leaf in n2content[node]:
                #            if leaf.lineage:
                #                for term in leaf.lineage:
                #                    term2count[term] += 1
                #        expected_size = len(n2content)
                #        for term, count in term2count.iteritems():
                #            if count > 1

                print "Showing tree..."
                t.show(tree_style=ts)
            else:
                t.render("img.svg", tree_style=ts, dpi=300)
            print "dumping color config"
            cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))

        if args.dump:
            cPickle.dump(t, open("ncbi_analysis.pkl", "w"))

    print
    print
    HEADER = ("TargetTree", "Subtrees", "Ndups", "Broken subtrees",
              "Broken clades", "Broken branches", "Clade sizes",
              "Fixed Groups", "New Broken Clades")
    print_table(ENTRIES, max_col_width=50, row_line=True, header=HEADER)

    if args.output:
        OUT.close()
示例#25
0
        f.border.width = 0

        node.img_style["size"] = 10
        node.img_style["shape"] = "square"
    node.img_style["bgcolor"] = random_color()
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
    #if node.is_leaf():
    #    f = faces.CircleFace(50, "red")
    #    faces.add_face_to_node(f, node, 0, position="aligned")


ts = TreeStyle()
ts.mode = "c"
ts.arc_span = 360
ts.layout_fn = layout
ts.show_leaf_name = False
ts.show_border = True
ts.draw_guiding_lines = False
ts.show_scale = True
#ts.scale = 60
t = Tree()
t.dist = 0

t.size = 0, 0
for x in xrange(100):
    n = t.add_child()
    n = n.add_child()
    n = n.add_child()
    n2 = n.add_child()
    n3 = n.add_child()
示例#26
0
                        help="")
    parser.add_argument("--tax2track", dest="tax2track", type=str,
                        help="")
    parser.add_argument("--dump_tax_info", dest="dump_tax_info", action="store_true",
                        help="")
    
    args = parser.parse_args()

    reftree_name = os.path.basename(args.ref_tree) if args.ref_tree else ""
    if args.explore:
        print "Reading tree from file:", args.explore
        t = cPickle.load(open(args.explore))
        ts = TreeStyle()
        ts.force_topology = True
        ts.show_leaf_name = False
        ts.layout_fn = ncbi_layout 
        ts.mode = "r"
        t.show(tree_style=ts)
        print "dumping color config"
        cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))
        sys.exit()
    
    if args.output:
        OUT = open(args.output, "w")
    else:
        OUT = sys.stdout

    print "Dumping results into", OUT
    target_trees = []
    if args.tree_list_file:
        target_trees = [line.strip() for line in open(args.tree_list_file)]
示例#27
0
文件: item_faces.py 项目: xguse/ete
    # Center text according to masterItem size
    tw = text.boundingRect().width()
    th = text.boundingRect().height()
    center = masterItem.boundingRect().center()
    text.setPos(center.x()-tw/2, center.y()-th/2)
    
    return masterItem

def master_ly(node):
    if node.is_leaf():
        # Create an ItemFAce. First argument must be the pointer to
        # the constructor function that returns a QGraphicsItem. It
        # will be used to draw the Face. Next arguments are arbitrary,
        # and they will be forwarded to the constructor Face function.
        F = faces.DynamicItemFace(ugly_name_face, 100, 50)
        faces.add_face_to_node(F, node, 0, position="aligned")
  

t = Tree()
t.populate(8, reuse_names=False)

ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)


t.render("item_faces.png", h=400, tree_style=ts)
# The interactive features are only available using the GUI
t.show(tree_style=ts)
示例#28
0
def draw(t, draw_alg=True):
    def ly(node):
        node.img_style['vt_line_width'] = 1
        node.img_style['hz_line_width'] = 1
        if node.is_leaf():
            add_face_to_node(TextFace(
                ' (%s)' % node.name.split()[0].replace("/exon2", ""),
                fsize=10,
                fgcolor='slategrey',
                tight_text=False),
                             node,
                             1,
                             position='branch-right')
            add_face_to_node(TextFace(node.species,
                                      fsize=12,
                                      fgcolor='black',
                                      fstyle='italic',
                                      tight_text=False),
                             node,
                             0,
                             position='branch-right')
            c = 1
            for tname in tracked_clades:
                if tname in node.named_lineage:
                    linF = TextFace(tname, fsize=10, fgcolor='white')
                    linF.margin_left = 3
                    linF.background.color = lin2color[tname]

                    add_face_to_node(linF, node, c, position='aligned')
                    c += 1
            for n in xrange(1, 20 - (c - 1)):
                add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
                                 node,
                                 c,
                                 position='aligned')
                c += 1

            if draw_alg and 'sequence' in node.features:
                #seqFace = SequenceFace(node.sequence,"aa",13)
                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
                            w = end - start
                            motifs.append([
                                start, end, "[]", w, 13, "slategrey",
                                "slategrey", None
                            ])
                            last_lt = None

                    elif lt == '-':
                        if last_lt is not None:
                            start, end = last_lt, c - 1
                            w = end - start
                            motifs.append([
                                start, end, "[]", w, 13, "slategrey",
                                "slategrey", None
                            ])
                            last_lt = None

                if not motifs:
                    print node, node.sequence

                seqFace = SeqMotifFace(node.sequence,
                                       motifs,
                                       intermotif_format="line",
                                       seqtail_format="line",
                                       scale_factor=1)
                add_face_to_node(seqFace, node, 20, aligned=True)

        else:
            if node.up:
                add_face_to_node(TextFace('% 3g' % node.support,
                                          fsize=11,
                                          fgcolor='indianred'),
                                 node,
                                 0,
                                 position='branch-top')

            if hasattr(node, "support2") and node.up:
                add_face_to_node(TextFace('% 3g' % float(node.support2),
                                          fsize=11,
                                          fgcolor='steelblue'),
                                 node,
                                 0,
                                 position='branch-bottom')

        node.img_style['size'] = 0
        node.img_style['hz_line_color'] = 'black'
        node.img_style['vt_line_color'] = 'black'

    colors = random_color(num=len(tracked_clades))
    lin2color = dict([(ln, colors[i]) for i, ln in enumerate(tracked_clades)])
    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
    print 'Rendering tree.pdf'
    t.render('tree.svg', tree_style=ts)
    t.render('tree.png', tree_style=ts)
示例#29
0
import sys
from ete_dev import Tree, faces, TreeStyle, COLOR_SCHEMES

sys.path.insert(0, "./")
def layout(node):
    if node.is_leaf():
        F= faces.PieChartFace([10,10,10,10,10,10,10,10,10,4,6], colors=COLOR_SCHEMES["set3"], width=100, height=100)
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F,node, 0, position="branch-right")
        F.background.color = "indianred"
        x = faces.TextFace("hola")
        faces.add_face_to_node(x,node, 1, position="branch-right")
        x.background.color = "blue"
    else:
        F= faces.BarChartFace([40,20,70,100,30,40,50,40,70,12], min_value=0, colors=COLOR_SCHEMES["spectral"])
        faces.add_face_to_node(F,node, 0, position="branch-top")
        
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False

t.populate(10)
t.show(tree_style=ts)
示例#30
0
文件: utils.py 项目: jhcepas/npr
    if "improve" in node.features:
        color = "orange" if float(node.improve) < 0 else "green"
        if float(node.improve) == 0:
            color = "blue"

        support_face = faces.CircleFace(200, color)
        faces.add_face_to_node(support_face, node, 0, position="float-behind")


try:
    from ete_dev import TreeStyle, NodeStyle, faces
    from ete_dev.treeview import random_color

    NPR_TREE_STYLE = TreeStyle()
    NPR_TREE_STYLE.layout_fn = npr_layout
    NPR_TREE_STYLE.show_leaf_name = False
except ImportError:
    TreeStyle, NodeStyle, faces, random_color = [None] * 4
    NPR_TREE_STYLE = None


# CONVERT shell colors to the same curses palette
COLORS = {
    "wr": "\033[1;37;41m",  # white on red
    "wo": "\033[1;37;43m",  # white on orange
    "wm": "\033[1;37;45m",  # white on magenta
    "wb": "\033[1;37;46m",  # white on blue
    "bw": "\033[1;37;40m",  # black on white
    "lblue": "\033[1;34m",  # light blue
    "lred": "\033[1;31m",  # light red
示例#31
0
     TTG GGA CTG GAC GGC TAC AAG GCA GTA AGT CAG TAC GTT AAA GGT CGT GCG
     >Orangutan
     GAT GCA CGC TGG ATC AAC GAA AAG TTA AGA TGC GTA TCG AGA ACT CTG AAA AAA
     TTG GGA CTG GAC GGC TAC AAG GGA GTA AGT CAA TAC GTT AAA GGT CGT CCG
     """)
     #try:
     #    tree.run_model("fb")
     #    tree.run_model("M2")
     #except:
     #    pass
     tree.dist = 0
     ts = TreeStyle()
     ts.title.add_face(TextFace(
         "Example for EvolTree, interactivity shows codons", fsize=15),
                       column=0)
     ts.layout_fn = test_layout_evol
     #try:
     #    tree.show(tree_style=ts, histfaces=["M2"])
     #except:
     tree.show(tree_style=ts)
 except:
     tree = PhyloTree('(Orangutan,Human,Chimp);')
     tree.link_to_alignment("""
                            >Chimp
                            HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
                            >Orangutan
                            DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
                            >Human
                            DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
                            """)
     nt_sequences = {
示例#32
0
def ncbi_consensus(self, ):
    nsubtrees, ndups, subtrees = self.get_speciation_trees(map_features=["taxid"])

    valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = analyze_subtrees(t, subtrees, show_tree=SHOW_TREE)


    avg_rf = []
    rf_max = 0.0 # reft.robinson_foulds(reft)[1]
    sum_size = 0.0

    #reftree = 


    for tn, subt in enumerate(subtrees):
        partial_rf = subt.robinson_foulds(reft, attr_t1="taxid")

        sptree_size = len(set([n.taxid for n in subt.iter_leaves()]))
        sum_size += sptree_size
        avg_rf.append((partial_rf[0]/float(partial_rf[1])) * sptree_size)
        common_names = len(partial_rf[3])
        max_size = max(max_size, sptree_size)
        rf_max = max(rf_max, partial_rf[1])


        rf = numpy.sum(avg_rf) / float(sum_size) # Treeko dist
        rf_std = numpy.std(avg_rf)
        rf_med = numpy.median(avg_rf)

        sizes_info = "%0.1f/%0.1f +- %0.1f" %( numpy.mean(broken_sizes), numpy.median(broken_sizes), numpy.std(broken_sizes))
        iter_values = [os.path.basename(tfile), nsubtrees, ndups,
                        broken_subtrees, ncbi_mistakes, broken_branches, sizes_info, rf, rf_med,
                       rf_std, rf_max, common_names] 
        print >>OUT, '|'.join(map(lambda x: str(x).strip().ljust(15), iter_values)) 
        fixed = sorted([n for n in prev_broken if n not in broken_clades])
        new_problems =  sorted(broken_clades - prev_broken)
        fixed_string = color(', '.join(fixed), "green") if fixed else ""
        problems_string = color(', '.join(new_problems), "red") if new_problems else ""
        OUT.write("    Fixed clades: %s\n" %fixed_string) if fixed else None
        OUT.write("    New broken:   %s\n" %problems_string) if new_problems else None
        prev_broken = broken_clades
        ENTRIES.append([os.path.basename(tfile), nsubtrees, ndups,
                        broken_subtrees, ncbi_mistakes, broken_branches, sizes_info, fixed_string, problems_string])
        OUT.flush()
        if args.show_tree or args.render:
            ts = TreeStyle()
            ts.force_topology = True
            #ts.tree_width = 500
            ts.show_leaf_name = False
            ts.layout_fn = ncbi_layout 
            ts.mode = "r"
            t.dist = 0
            if args.show_tree:
                #if args.hide_monophyletic:
                #    tax2monophyletic = {}
                #    n2content = t.get_node2content()
                #    for node in t.traverse():
                #        term2count = defaultdict(int)
                #        for leaf in n2content[node]:
                #            if leaf.lineage:
                #                for term in leaf.lineage:
                #                    term2count[term] += 1
                #        expected_size = len(n2content)
                #        for term, count in term2count.iteritems():
                #            if count > 1
                    
                print "Showing tree..."
                t.show(tree_style=ts)
            else:
                t.render("img.svg", tree_style=ts, dpi=300)
            print "dumping color config"
            cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))

        if args.dump:
            cPickle.dump(t, open("ncbi_analysis.pkl", "w"))
示例#33
0
                col += 1
            # Add the corresponding face to the node
            if name.startswith("Dme"):
                faces.add_face_to_node(flyFace, node, column=col)
            elif name.startswith("Dre"):
                faces.add_face_to_node(fishFace, node, column=col)
            elif name.startswith("Mms"):
                faces.add_face_to_node(mouseFace, node, column=col)
            elif name.startswith("Ptr"):
                faces.add_face_to_node(chimpFace, node, column=col)
            elif name.startswith("Hsa"):
                faces.add_face_to_node(humanFace, node, column=col)
            elif name.startswith("Cfa"):
                faces.add_face_to_node(dogFace, node, column=col)

            # Modifies this node's style
            node.img_style["size"] = 16
            node.img_style["shape"] = "sphere"
            node.img_style["fgcolor"] = "#AA0000"

    # If leaf is "Hsa" (h**o sapiens), highlight it using a
    # different background.
    if node.is_leaf() and node.name.startswith("Hsa"):
        node.img_style["bgcolor"] = "#9db0cf"

# And, finally, Visualize the tree using my own layout function
ts = TreeStyle()
ts.layout_fn = mylayout
t.render("img_faces.png", w=600, tree_style = ts)

示例#34
0
def ncbi_consensus(self, ):
    nsubtrees, ndups, subtrees = self.get_speciation_trees(
        map_features=["taxid"])

    valid_subtrees, broken_subtrees, ncbi_mistakes, broken_branches, total_rf, broken_clades, broken_sizes = analyze_subtrees(
        t, subtrees, show_tree=SHOW_TREE)

    avg_rf = []
    rf_max = 0.0  # reft.robinson_foulds(reft)[1]
    sum_size = 0.0

    #reftree =

    for tn, subt in enumerate(subtrees):
        partial_rf = subt.robinson_foulds(reft, attr_t1="taxid")

        sptree_size = len(set([n.taxid for n in subt.iter_leaves()]))
        sum_size += sptree_size
        avg_rf.append((partial_rf[0] / float(partial_rf[1])) * sptree_size)
        common_names = len(partial_rf[3])
        max_size = max(max_size, sptree_size)
        rf_max = max(rf_max, partial_rf[1])

        rf = numpy.sum(avg_rf) / float(sum_size)  # Treeko dist
        rf_std = numpy.std(avg_rf)
        rf_med = numpy.median(avg_rf)

        sizes_info = "%0.1f/%0.1f +- %0.1f" % (numpy.mean(broken_sizes),
                                               numpy.median(broken_sizes),
                                               numpy.std(broken_sizes))
        iter_values = [
            os.path.basename(tfile), nsubtrees, ndups, broken_subtrees,
            ncbi_mistakes, broken_branches, sizes_info, rf, rf_med, rf_std,
            rf_max, common_names
        ]
        print >> OUT, '|'.join(
            map(lambda x: str(x).strip().ljust(15), iter_values))
        fixed = sorted([n for n in prev_broken if n not in broken_clades])
        new_problems = sorted(broken_clades - prev_broken)
        fixed_string = color(', '.join(fixed), "green") if fixed else ""
        problems_string = color(', '.join(new_problems),
                                "red") if new_problems else ""
        OUT.write("    Fixed clades: %s\n" % fixed_string) if fixed else None
        OUT.write("    New broken:   %s\n" %
                  problems_string) if new_problems else None
        prev_broken = broken_clades
        ENTRIES.append([
            os.path.basename(tfile), nsubtrees, ndups, broken_subtrees,
            ncbi_mistakes, broken_branches, sizes_info, fixed_string,
            problems_string
        ])
        OUT.flush()
        if args.show_tree or args.render:
            ts = TreeStyle()
            ts.force_topology = True
            #ts.tree_width = 500
            ts.show_leaf_name = False
            ts.layout_fn = ncbi_layout
            ts.mode = "r"
            t.dist = 0
            if args.show_tree:
                #if args.hide_monophyletic:
                #    tax2monophyletic = {}
                #    n2content = t.get_node2content()
                #    for node in t.traverse():
                #        term2count = defaultdict(int)
                #        for leaf in n2content[node]:
                #            if leaf.lineage:
                #                for term in leaf.lineage:
                #                    term2count[term] += 1
                #        expected_size = len(n2content)
                #        for term, count in term2count.iteritems():
                #            if count > 1

                print "Showing tree..."
                t.show(tree_style=ts)
            else:
                t.render("img.svg", tree_style=ts, dpi=300)
            print "dumping color config"
            cPickle.dump(name2color, open("ncbi_colors.pkl", "w"))

        if args.dump:
            cPickle.dump(t, open("ncbi_analysis.pkl", "w"))