Esempio n. 1
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 def ly_condensed_alg(self, node):
     if node.is_leaf():
         if 'sequence' in node.features:
             seqFace = SeqMotifFace(node.sequence, [],
                                    intermotif_format="line",
                                    seqtail_format="line", scale_factor=1)
             add_face_to_node(seqFace, node, 10, aligned=True)
Esempio n. 2
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 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')
Esempio n. 3
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    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)
Esempio n. 4
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 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
Esempio n. 5
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 def ly_tax_labels(self, node):
     if node.is_leaf():
         c = self.LABEL_START_COL
         node_lin = getattr(node, "named_lineage", [])
         for tname in node_lin:
              if tname.lower() in self.TRACKED_CLADES:
                   linF = self.LIN2FACE[tname.lower()]
                   # linF = TextFace(tname, fsize=10, fgcolor='white')
                   # linF.margin_left = 3
                   # linF.margin_right = 2
                   # linF.background.color = self.LIN2COLOR[tname.lower()]
                   add_face_to_node(linF, node, c, position='aligned')
                   c += 1
        
         for n in xrange(c, len(self.TRACKED_CLADES)):
              add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
              c+=1
Esempio n. 6
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    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
Esempio n. 7
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     def ly_block_alg(self, node):
          if node.is_leaf():
             if 'sequence' in node.features:
                 # [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=1)
                 add_face_to_node(seqFace, node, 10, aligned=True)
Esempio n. 8
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def rotation_layout(node):
    if node.is_leaf():
        F = TextFace(node.name, tight_text=True)
        F.rotation = randint(0, 360)
        add_face_to_node(TextFace("third" ), node, column=8, position="branch-right")
        add_face_to_node(TextFace("second" ), node, column=2, position="branch-right")
        add_face_to_node(F, node, column=0, position="branch-right")

        F.border.width = 1
        F.inner_border.width = 1
Esempio n. 9
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 def ly_leaf_names(self, node):
     if node.is_leaf():
         if node.species != 0 and self.ncbitaxa:
             spF = TextFace("%s" %getattr(node, "spname", ""), fsize=8, fgcolor='#777777', ftype='Helvetica')
             geneF = TextFace("(%s)" %node.name[:50], fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
             
             add_face_to_node(spF, node, column=0, position='branch-right')
             add_face_to_node(geneF, node, column=1, position='branch-right')
             
         else:
             geneF = TextFace("%s" %node.name, fsize=8, fgcolor='#777777', ftype='Helvetica')
             add_face_to_node(geneF, node, column=0, position='branch-right')
Esempio n. 10
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def layout(node):
    if node.is_leaf():
        seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
        add_face_to_node(seqFace, node, 0, position="aligned")
Esempio n. 11
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 def ly_supports(self, node):
     if not node.is_leaf():
         supFace = TextFace("%0.3g" %(node.support), fsize=7, fgcolor='indianred')
         add_face_to_node(supFace, node, column=0, position='branch-top')
Esempio n. 12
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    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'
Esempio n. 13
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 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')
Esempio n. 14
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    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'
Esempio n. 15
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def layout(node):
    if node.is_leaf():
        seqFace = SeqMotifFace(seq, motifs, scale_factor=1)
        add_face_to_node(seqFace, node, 0, position="aligned")