[med-svn] [Git][med-team/graphlan][master] 7 commits: New upstream version 1.1.3

Andreas Tille gitlab at salsa.debian.org
Wed Sep 26 13:12:43 BST 2018


Andreas Tille pushed to branch master at Debian Med / graphlan


Commits:
44895364 by Andreas Tille at 2018-09-26T11:35:01Z
New upstream version 1.1.3
- - - - -
acbfc839 by Andreas Tille at 2018-09-26T11:35:27Z
Update upstream source from tag 'upstream/1.1.3'

Update to upstream version '1.1.3'
with Debian dir 01a232141bbd9e03b83ce4a03757be53b9f08a6d
- - - - -
70db3e12 by Andreas Tille at 2018-09-26T11:35:27Z
New upstream version

- - - - -
e629be31 by Andreas Tille at 2018-09-26T11:35:27Z
debhelper 11

- - - - -
de48d5d6 by Andreas Tille at 2018-09-26T11:35:32Z
Point Vcs fields to salsa.debian.org

- - - - -
42e4c864 by Andreas Tille at 2018-09-26T11:35:32Z
Standards-Version: 4.2.1

- - - - -
ed2e94fe by Andreas Tille at 2018-09-26T11:46:26Z
Upload to unstable

- - - - -


13 changed files:

- .hg_archival.txt
- .hgignore
- .hgsubstate
- .hgtags
- debian/changelog
- debian/compat
- debian/control
- examples/guide/annot_3.txt
- examples/metaref_fams/mr1.a.txt
- graphlan.py
- graphlan_annotate.py
- src/graphlan_lib.py
- src/pyphlan.py


Changes:

=====================================
.hg_archival.txt
=====================================
@@ -1,4 +1,4 @@
 repo: 0fdb21ec3cf53e710d679fbd7768f91510570ae7
-node: edea23ce7c21765cbd9ff601e1f91614241eae81
+node: c1fa530b9bcac13bbccacf8bfafd500536d17b7c
 branch: default
-tag: 1.1
+tag: 1.1.3


=====================================
.hgignore
=====================================
@@ -3,4 +3,10 @@ syntax: glob
 *.pyc
 *.DS_Store
 *.log
+examples/ade_pcopri
+examples/neisseriaceae/
+examples/caritro_fig6/
+examples/andrew_crc_cutc/
+examples/nic_erectale/
+examples/rand/
 examples/test/


=====================================
.hgsubstate
=====================================
@@ -1,2 +1,2 @@
-b2e0ba66718673ea28cb217c8e5dcd8e578fd033 export2graphlan
+c168a100f37e23e2c110849a8d91fac8da49f5bd export2graphlan
 eae40ebc0030c7179baed999c74de412ba696598 pyphlan


=====================================
.hgtags
=====================================
@@ -5,3 +5,6 @@ ba9c6f680022333b5b1bf0652748ab2db29e888a 0.9
 eaa3d2e05d74912da0f013bbfbb199764b180f05 0.9.5
 64570f7d4ae33f46ddd360101c13555396a0cab1 0.9.6
 7d483b7d34ccadb30f5c56f82b7aab19a820d1d6 1.0
+edea23ce7c21765cbd9ff601e1f91614241eae81 1.1
+17f32c8d85849d397884564680c145e5b8d28923 1.1.1
+3820c323e3c68d3d9e02bae2aefbc7d179df80bf 1.1.2


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+graphlan (1.1.3-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille at debian.org>  Wed, 26 Sep 2018 13:35:33 +0200
+
 graphlan (1.1-3) unstable; urgency=medium
 
   * Moved packaging from SVN to Git


=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python-all,
                dh-python
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/graphlan.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/graphlan.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/graphlan
+Vcs-Git: https://salsa.debian.org/med-team/graphlan.git
 Homepage: https://bitbucket.org/nsegata/graphlan/wiki/Home
 
 Package: graphlan


=====================================
examples/guide/annot_3.txt
=====================================
@@ -418,7 +418,7 @@ Staphylococcaceae.Staphylococcus.Swarneri	ring_height	5	2.39465498028
 
 Bacillaceae.Bacillus.Bsubtilis	clade_marker_label	65
 Staphylococcaceae.Staphylococcus.Saureus	clade_marker_label	17
-Bacillaceae.Bacillus.Banthracis	clade_marker_label	x	
+Bacillaceae.Bacillus.Banthracis	clade_marker_label	x
 Bacillaceae.Bacillus.Banthracis	clade_marker_font_color	w
 Bacillaceae.Bacillus.Banthracis	clade_marker_edge_color	b
 Bacillaceae.Lysinibacillus.Lfusiformis	clade_marker_label	156


=====================================
examples/metaref_fams/mr1.a.txt
=====================================
@@ -15,9 +15,9 @@ c2	clade_marker_color	#0000FF
 c2	clade_marker_size	35
 c3	clade_marker_color	#00FF00
 c3	clade_marker_size	35
-#class2	annotation_background_color	#0000FF	
+#class2	annotation_background_color	#0000FF
 #class2	class_label	Clades in which X is a core gene
-clade_marker_size	10	
+clade_marker_size	10
 branch_thickness	0.5
 Bacill.Bacillale	class	c3
 Bacill.Bacillale.Staphylococcaceae.Gemella	class	c1
@@ -48,7 +48,7 @@ Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium
 #Bacill.Bacillale	class	class2
 Bacill.Bacillale	annotation	Y
 Bacill.Bacillale.Staphylococcaceae	annotation	Y1
-Bacill.Bacillale.Thermoactinomycetaceae	annotation	Y2	
+Bacill.Bacillale.Thermoactinomycetaceae	annotation	Y2
 Bacill.Bacillale.unclassified	annotation	Y3
 Bacilli.Lactobacillales.Aerococcaceae	class	c2
 Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	class	c2
@@ -69,8 +69,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_shape	1	v
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_shape	1	v
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_shape	1	v
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_shape	1	v
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_shape	1	v
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_shape	1	v
@@ -78,7 +76,7 @@ Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	ring_shape	1	v
 Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	ring_shape	1	v
 Clostridi.Clostridiale.Veillonellaceae.Selenomonas	ring_shape	1	v
 Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	ring_shape	1	v
-Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_shape	1	v	
+Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_shape	1	v
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_shape	1	v
 Bacilli.Lactobacillales.Aerococcaceae.unclassified	ring_shape	1	v
 Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	ring_shape	1	v
@@ -96,8 +94,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_width	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_width	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_width	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_width	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_width	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_width	1	0.6
@@ -105,7 +101,7 @@ Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus	ring_width	1	0.6
 Clostridi.Clostridiales.Ruminococcaceae.Papillibacter	ring_width	1	0.6
 Clostridi.Clostridiale.Veillonellaceae.Selenomonas	ring_width	1	0.6
 Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium	ring_width	1	0.6
-Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_width	1	0.6	
+Bacilli.Lactobacillales.Aerococcaceae.Aerococcus	ring_width	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_width	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.unclassified	ring_width	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia	ring_width	1	0.6
@@ -123,8 +119,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_height	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_height	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_height	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_height	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_height	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_height	1	0.6


=====================================
graphlan.py
=====================================
@@ -2,9 +2,9 @@
 
 #------------------------------------------------------------------------------
 # NAME: graphlan.py
-# DESCRIPTION:  GraPhlAn is a python program for creating images of circular 
-#               cladogram starting from a tree given in PhyloXML format. The 
-#               PhyloXML input tree can be formatted and annotated using the 
+# DESCRIPTION:  GraPhlAn is a python program for creating images of circular
+#               cladogram starting from a tree given in PhyloXML format. The
+#               PhyloXML input tree can be formatted and annotated using the
 #               graphlan_annotate.py script.
 #
 # Author:   Nicola Segata
@@ -14,10 +14,16 @@
 #------------------------------------------------------------------------------
 
 __author__ = 'Nicola Segata (nsegata at hsph.harvard.edu)'
-__version__ = '0.9.7'
-__date__ = '21 July 2014'
+__version__ = '1.1.3'
+__date__ = '5 June 2018'
 
 
+import sys
+
+if sys.version_info[0] > 2:
+    raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
+                    .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
+
 from sys import argv
 from argparse import ArgumentParser
 from src.graphlan_lib import CircTree as CTree
@@ -34,7 +40,7 @@ def read_params(args):
         help = "the output image, the format is guessed from the extension "
                "unless --format is given. Available file formats are: png, "
                "pdf, ps, eps, svg" )
-    arg('--format', choices=['png','pdf','ps','eps','svg'], default=None, 
+    arg('--format', choices=['png','pdf','ps','eps','svg'], default=None,
         type = str, metavar=['output_image_format'],
         help = "set the format of the output image (default none meaning that "
                "the format is guessed from the output file extension)")
@@ -53,7 +59,9 @@ def read_params(args):
     arg('--external_legends', default=False, action='store_true',
         help = "specify whether the two external legends should be put in separate file or keep them "
                "along with the image (default behavior)")
-    arg( '-v','--version', action='version', version="GraPhlAn version "+__version__+" ("+__date__+")", 
+    arg('--avoid_reordering', default=True, action='store_false',
+        help = "specify whether the tree will be reorder or not (default the tree will be reordered)")
+    arg( '-v','--version', action='version', version="GraPhlAn version "+__version__+" ("+__date__+")",
         help="Prints the current GraPhlAn version and exit" )
     return vars(parser.parse_args())
 
@@ -62,9 +70,10 @@ if __name__ == "__main__":
     args = read_params( argv )
     ctree = CTree( args['intree'], args['warnings'] )
     ctree.positions = args['positions']
-    ctree.draw( args['outimg'], 
-                out_format = args['format'], 
-                out_dpi = args['dpi'],
-                out_size = args['size'],
-                out_pad = args['pad'],
-                external_legends = args['external_legends'])
+    ctree.draw(args['outimg'],
+               out_format=args['format'],
+               out_dpi=args['dpi'],
+               out_size=args['size'],
+               out_pad=args['pad'],
+               external_legends=args['external_legends'],
+               reorder_tree=args['avoid_reordering'])


=====================================
graphlan_annotate.py
=====================================
@@ -11,10 +11,16 @@
 #------------------------------------------------------------------------------
 
 __author__ = 'Nicola Segata (nsegata at hsph.harvard.edu)'
-__version__ = '0.9'
-__date__ = '22 August 2012'
+__version__ = '1.1.3'
+__date__ = '5 June 2018'
 
 
+import sys
+
+if sys.version_info[0] > 2:
+    raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
+                    .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
+
 from sys import argv
 from argparse import ArgumentParser
 from src.graphlan_lib import CircTree as CTree


=====================================
src/graphlan_lib.py
=====================================
@@ -1,3 +1,9 @@
+import sys
+
+if sys.version_info[0] > 2:
+    raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
+                    .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
+
 from Bio import Phylo
 from Bio.Phylo import PhyloXML
 from Bio.Phylo import PhyloXMLIO
@@ -17,87 +23,79 @@ import matplotlib.patches as mpatches
 import matplotlib.lines as lines
 import matplotlib
 matplotlib.use('Agg')
+matplotlib.rcParams['svg.fonttype'] = 'none'
 from pylab import *
 from pyphlan import PpaTree
 
 
-clade_attr = ( ( 'clade_marker_size',               float,  20.0        ),
-               ( 'clade_marker_color',              str,    '#FFFFFF'   ),
-               ( 'clade_marker_edge_width',         float,  0.5         ),
-               ( 'clade_marker_shape',              str,    'o'         ),
-               ( 'clade_marker_edge_color',         str,    '#000000'   ),
-               ( 'clade_marker_label',              str,    ''          ),
-               ( 'clade_marker_font_size',          str,    '7'         ),
-               ( 'clade_marker_font_color',         str,    'k'         ),
-               ( 'class_label',                     str,    ""          ),  # to rem
-               ( 'annotation_font_size',            int,    7           ),
-               ( 'annotation_font_stretch',         int,    0           ),
-               ( 'annotation_background_color',     str,    '#FF0000'   ),
-               ( 'annotation_background_edge_color',str,    '#FF0000'   ),  # not implemented yet
-               ( 'annotation',                      str,    ''          ),
-               ( 'annotation_rotation',             int,    0           ),
-             )
+clade_attr = ( ( 'clade_marker_size',                float, 20.0      ),
+               ( 'clade_marker_color',               str,   '#FFFFFF' ),
+               ( 'clade_marker_edge_width',          float, 0.5       ),
+               ( 'clade_marker_shape',               str,   'o'       ),
+               ( 'clade_marker_edge_color',          str,   '#000000' ),
+               ( 'clade_marker_label',               str,   ''        ),
+               ( 'clade_marker_font_size',           str,   '7'       ),
+               ( 'clade_marker_font_color',          str,   'k'       ),
+               ( 'class_label',                      str,   ""        ),  # to rem
+               ( 'annotation_font_size',             int,   7         ),
+               ( 'annotation_font_stretch',          int,   0         ),
+               ( 'annotation_background_color',      str,   '#FF0000' ),
+               ( 'annotation_background_edge_color', str,   '#FF0000' ),  # not implemented yet
+               ( 'annotation',                       str,   ''        ),
+               ( 'annotation_rotation',              int,   0         ) )
 clade_attr_d = dict([(p,(t,d)) for p,t,d in clade_attr])
 
-ext_attr = ( ( 'ring_color',                        str,    '#000000'   ),
-             ( 'ring_width',                        float,   1.0        ),
-             ( 'ring_height',                       float,   -1.0       ),
-             ( 'ring_alpha',                        float,   1.0        ),
-             ( 'ring_shape',                        str,     "R"        ),
-             ( 'ring_label',                        str,     None       ),
-             ( 'ring_label_font_size',              int,     11         ),
-             ( 'ring_label_color',                  str,     'k'        ),
-             ( 'ring_edge_width',                   float,   0.1        ),
-             ( 'ring_edge_color',                   str,     None       ),
-             ( 'ring_internal_separator_thickness', float,   0.0        ),
-             ( 'ring_separator_color',              str,     'k'        ),
-             ( 'ring_external_separator_thickness', float,   0.0        ),
-           )
+ext_attr = ( ( 'ring_color',                        str,   '#000000' ),
+             ( 'ring_width',                        float, 1.0       ),
+             ( 'ring_height',                       float, -1.0      ),
+             ( 'ring_alpha',                        float, 1.0       ),
+             ( 'ring_shape',                        str,   "R"       ),
+             ( 'ring_label',                        str,   None      ),
+             ( 'ring_label_font_size',              int,   11        ),
+             ( 'ring_label_color',                  str,   'k'       ),
+             ( 'ring_edge_width',                   float, 0.1       ),
+             ( 'ring_edge_color',                   str,   None      ),
+             ( 'ring_internal_separator_thickness', float, 0.0       ),
+             ( 'ring_separator_color',              str,   'k'       ),
+             ( 'ring_external_separator_thickness', float, 0.0       ) )
 ext_attr_d = dict([(p,(t,d)) for p,t,d in ext_attr])
 
-int_attr = (
-             ( 'internal_label',                    str,     None       ),
-             ( 'internal_label_font_size',          int,     8          ),
-           )
+int_attr = ( ( 'internal_label',           str, None ),
+             ( 'internal_label_font_size', int, 8    ) )
 int_attr_d = dict([(p,(t,d)) for p,t,d in int_attr])
 
-structural_attr = ( ( 'ignore_branch_len',              int,    0       ),
-                    ( 'total_plotted_degrees',          float,  360.0   ),
-                    ( 'start_rotation',                 float,  180.0   ),
-                    ( 'clade_separation',               float,  0.0     ),
-                    ( 'branch_bracket_width',           float,  0.25    ),
-                    ( 'branch_bracket_depth',           float,  1.0     ),
-                  )
-
-global_graphical_attr = ( ( 'annotation_background_width',       float,  0.1    ),
-                          ( 'annotation_background_alpha',       float,  0.2    ),
-                          ( 'annotation_background_separation',  float,  0.02   ),
-                          ( 'annotation_background_offset',      float,  0.02   ),
-                          ( 'class_legend_font_size',            int,    7      ),
-                          ( 'title',                             str,    ""     ),
-                          ( 'title_font_size',                   int,    15     ),
-                          ( 'class_legend_marker_size',          float,  1.0    ),
-                          ( 'annotation_legend_font_size',       int,    7      ),
-                          ( 'internal_labels_rotation',          float,   None  ),
-                        )
-
-branch_attr = ( ( 'branch_thickness',           float,  0.75        ),
-                ( 'branch_color',               str,    '#000000'   ),
-                ( 'branch_color_from_ancestor', int,    1           ),
-              )
-
+structural_attr = ( ( 'ignore_branch_len',     int,   0     ),
+                    ( 'total_plotted_degrees', float, 360.0 ),
+                    ( 'start_rotation',        float, 180.0 ),
+                    ( 'clade_separation',      float, 0.0   ),
+                    ( 'branch_bracket_width',  float, 0.25  ),
+                    ( 'branch_bracket_depth',  float, 1.0   ) )
+
+global_graphical_attr = ( ( 'annotation_background_width',      float, 0.1   ),
+                          ( 'annotation_background_alpha',      float, 0.2   ),
+                          ( 'annotation_background_separation', float, 0.02  ),
+                          ( 'annotation_background_offset',     float, 0.02  ),
+                          ( 'class_legend_font_size',           int,   7     ),
+                          ( 'title',                            str,   ""    ),
+                          ( 'title_font_size',                  int,   15    ),
+                          ( 'class_legend_marker_size',         float, 1.0   ),
+                          ( 'annotation_legend_font_size',      int,   7     ),
+                          ( 'internal_labels_rotation',         float,  None ) )
+
+branch_attr = ( ( 'branch_thickness',           float, 0.75      ),
+                ( 'branch_color',               str,   '#000000' ),
+                ( 'branch_color_from_ancestor', int,   1         ) )
 
 leg_sep = '_._._'
-leg_attr    = ( ( 'annotation_background_color',        str,    "w"         ),
-                ( 'annotation_background_edge_color',   str,    "k"         ),
-                ( 'clade_marker_color',                 str,    "w"         ),
-                ( 'clade_marker_edge_width',            float,  0.5         ),
-                ( 'clade_marker_size',                  float,  20.0        ),
-                ( 'keys',                               str,    "?"         ),
-              )
+leg_attr = ( ( 'annotation_background_color',      str,   "w"  ),
+             ( 'annotation_background_edge_color', str,   "k"  ),
+             ( 'clade_marker_color',               str,   "w"  ),
+             ( 'clade_marker_edge_width',          float, 0.5  ),
+             ( 'clade_marker_size',                float, 20.0 ),
+             ( 'clade_marker_shape',               str,   'o' ),
+             ( 'keys',                             str,   "?"  ) )
 
 lev_sep = '.'
-
 legal_options = set(zip(*clade_attr+ext_attr+int_attr+structural_attr+global_graphical_attr+branch_attr+leg_attr)[0]) | set(['class'])
 
 def random_keys(used_keys):
@@ -115,8 +113,8 @@ class CircTree(PpaTree):
 
     def annotate(   self, inp_file, out_file = None,
                     c = None, p = None, v = None ):
-        term_names = set([t.name for t in self.tree.get_terminals()])
-        nterm_names = set([t.name for t in self.tree.get_nonterminals()])
+        term_names = set([t.name for t in self.tree.get_terminals() if t.name])
+        nterm_names = set([t.name for t in self.tree.get_nonterminals() if t.name])
         clade_names = term_names | nterm_names
         props, gprops, classes = ddict(dict), {}, ddict(dict)
 
@@ -147,8 +145,14 @@ class CircTree(PpaTree):
 
         self._tmp_levs = set()
         for line in (l.strip().split('\t') for l in lines if l[0] != '#'):
+            if not ''.join(line): # skip empty lines
+                continue
             ll = len(line)
-            if ll == 2:
+            if (ll < 2) or (ll > 4):
+                sys.stderr.write('Unrecognized annotation "{}", maybe spaces '
+                                 'instead of tabs?\n'.format(line))
+                exit(1)
+            elif ll == 2:
                 legal( line[0] ) #  in legal_options, "%s is not a valid option" % line[1]
                 gprops[line[0]] = line[1]
             elif ll == 3:
@@ -159,7 +163,12 @@ class CircTree(PpaTree):
                 elif clade in ext_attr_d:
                     prop,lev = clade,prop
                     legal( prop )
-                    ilev = int(lev)
+                    try:
+                        ilev = int(lev)
+                    except:
+                        print(line)
+                        asdasdasd
+
                     if prop not in gprops:
                         gprops[prop] = {}
                     if ilev not in gprops[prop]:
@@ -203,9 +212,21 @@ class CircTree(PpaTree):
                     else:
                         gprops[prop] = {ilev:val}
                 elif clade.split(lev_sep)[-1] in clade_names:
-                    ilev = int(lev)
+                    try:
+                        ilev = int(lev)
+                    except:
+                        print(line)
+                        asdasdasd
+
                     self._tmp_levs.add( ilev )
                     if prop in props[clade]:
+                        # print "clade", clade
+                        # print "prop", prop
+                        # print "props[clade]", props[clade]
+                        # print "val", val
+                        # print "ilev", ilev
+                        # print
+
                         props[clade][prop][ilev] = val
                     else:
                         props[clade][prop] = {ilev:val}
@@ -214,12 +235,11 @@ class CircTree(PpaTree):
                     if ilev not in gprops[prop]:
                         gprops[prop][ilev] = ext_attr_d[prop][1]
                 else:
-                    print ll
-                    print clade.split(lev_sep)[-1]
-                    print clade_names
-                    print line
-                    sys.stderr.write( "Classes not implemented for external "
-                                       "annotations\n" )
+                    # print ll
+                    # print clade.split(lev_sep)[-1]
+                    # print clade_names
+                    # print line
+                    sys.stderr.write( "Classes not implemented for external annotations\n" )
                     exit(1)
 
 
@@ -249,7 +269,13 @@ class CircTree(PpaTree):
                         value = v
                         if k == 'annotation':
                             if v.count(":"):
-                                kkk,vvv = v.split(":")
+
+                                try:
+                                    kkk,vvv = v.split(":")
+                                except:
+                                    print(v)
+                                    asdasdasd
+
                                 if kkk == '*':
                                     if fn is None:
                                         kkk = rkeys_gen.next()
@@ -258,7 +284,7 @@ class CircTree(PpaTree):
                                     fn = kkk
                                 if vvv == '*':
                                     vvv = clade.name
-                                value = kkk + ":" + vvv
+                                value = kkk + ": " + vvv
                             elif v == '*':
                                 value = clade.name
                         cp.append(  Prop( value=value, ref='A:1', id_ref=k,
@@ -333,6 +359,8 @@ class CircTree(PpaTree):
         # visual separation between subtrees.
         # This is executed if the user sets clade_separatio > 0.0
         self._ord_leaves = []
+
+
         def compute_tot_add( clade ):
             if clade.is_terminal():
                 self._ord_leaves.append( clade )
@@ -349,8 +377,8 @@ class CircTree(PpaTree):
                 last = t
 
         coffset = self.start_rotation + (rpi2 - self.total_plotted_degrees) * 0.5
-        circ_step = self.total_plotted_degrees*(1.0-self.clade_separation) / self._n_terminals
-        self.circ_pos = coffset+circ_step/2
+        circ_step = self.total_plotted_degrees * (1.0 - self.clade_separation) / self._n_terminals
+        self.circ_pos = coffset - circ_step
         self._last_leaf = self.tree.root
         self._varf = circ_step
 
@@ -359,6 +387,7 @@ class CircTree(PpaTree):
         self._ext_levs = set()
         #self._ext_max_height = {}
 
+
         def set_clade_data_rec( clade ):
             if self.ignore_branch_len:
                 clade.branch_length = 1.0
@@ -464,6 +493,7 @@ class CircTree(PpaTree):
                     self._ext_levs[l] = default
         self._all_ext_attr = [v[0] for v in ext_attr]
 
+
         def rec_set_exts( clade ):
             if hasattr( clade, "ext" ):
                 ext = clade.ext
@@ -570,7 +600,6 @@ class CircTree(PpaTree):
         gprops = dict([(p.id_ref,p.value)
                     for p in self.tree.properties if not p.id_ref.startswith("ext__") ])
 
-
         eggrops = [( int(p.id_ref.split('__')[1]),p.id_ref.split('__')[2], p.value)
                         for p in self.tree.properties if p.id_ref.startswith("ext__")]
         iggrops = [( float(p.id_ref.split('__')[1]),p.id_ref.split('__')[2], p.value)
@@ -622,7 +651,6 @@ class CircTree(PpaTree):
             if attr == 'ring_height':
                 self._ext_max_height[int(lev)] = float(val) if float(val) >= 0.0 else 0.0
 
-
         self._n_terminals = self.tree.count_terminals()
         # with few leaves, the total rotation is lowered (unless the user set it)
         if self._n_terminals < 16 and 'total_plotted_degrees' not in gprops:
@@ -630,6 +658,7 @@ class CircTree(PpaTree):
         self.total_plotted_degrees = self.total_plotted_degrees * rpi / 180.0
         self.start_rotation = self.start_rotation * rpi / 180.0
 
+
     def set_branches( self ):
         def set_branches_rec( clade, fcol ):
             if clade == self.tree.root:
@@ -674,82 +703,146 @@ class CircTree(PpaTree):
 
         set_branches_rec( self.tree.root, self.branch_color )
 
+
     def set_wings( self ):
         if not self._wing_levs:
+            # print "not self._wing_levs", not self._wing_levs
+
             self._wing_tot_offset = 1.0 # self._max_depth
             self._tot_offset = 1.0
             return
+
         if self.ignore_branch_len:
+            # print "self.ignore_branch_len", self.ignore_branch_len
+
             self._wing_levs.sort(reverse=True)
-            nlevs = len( self._wing_levs )
-            minl, maxl = min(self._wing_levs),max(self._wing_levs)
+            nlevs = len(self._wing_levs)
+            minl, maxl = min(self._wing_levs), max(self._wing_levs)
+
+            # print "nlevs", nlevs
+            # print "minl", minl
+            # print "maxl", maxl
+
         lthetas = [l.theta for l in self.tree.get_terminals()]
         rad_offset = self.annotation_background_separation
         lev_width = self.annotation_background_width
 
+        # print "lthetas", lthetas
+        # print "rad_offset", rad_offset
+        # print "lev_width", lev_width
+
         def set_wings_rec( clade ):
-            if hasattr( clade, 'annotation') and not hasattr( clade, 'annotation_background_color'):
+            if hasattr(clade, 'annotation') and not hasattr(clade, 'annotation_background_color'):
                 if self.warnings:
-                    sys.stderr.write("Warning: label "
-                                     "\""+clade.annotation+"\" has "
-                                     "a default gray background because no color is found for "
-                                     "the corresponding \"annotation\"\n")
-                clade.annotation_background_color = [0.3,0.3,0.3]
-            if hasattr( clade, 'annotation_background_color'):
+                    sys.stderr.write('Warning: label "{}" has a default gray background because no color is found for the corresponding "annotation"\n'.format(clade.annotation))
+
+                clade.annotation_background_color = [0.3, 0.3, 0.3]
+
+            if hasattr(clade, 'annotation_background_color'):
                 if clade.is_terminal(): # same as non-terminal ??
+                    # print "clade.theta", clade.theta
+                    # print ''
+                    # print "clade.pc", clade.pc
+                    # print "clade.nc", clade.nc
+                    # print ''
+                    # print "clade.pc.theta", clade.pc.theta
+                    # print "clade.nc.theta", clade.nc.theta
+
                     cpc = clade.theta + (clade.theta-clade.nc.theta) if clade.pc is None else clade.pc.theta
                     cnc = clade.theta - (clade.pc.theta-clade.theta) if clade.nc is None else clade.nc.theta
+
                     if cpc > clade.theta:
                         cpc -= rpi2
+
                     if cnc < clade.theta:
                         cnc += rpi2
-                    lsm = ( clade.theta + cpc ) * 0.5
-                    lgr = ( clade.theta + cnc ) * 0.5
 
+                    lsm = (clade.theta + cpc) * 0.5
+                    lgr = (clade.theta + cnc) * 0.5
                 else:
-                    f,t = clade.fc.theta, clade.fc.pc.theta if clade.fc.pc else clade.fc.nc.theta
-                    cpc = min(abs(f-t),abs(f+rpi2-t),abs(t+rpi2-f))
-                    f,t = clade.lc.theta, clade.lc.nc.theta if clade.lc.nc else clade.lc.pc.theta
-                    cnc = min(abs(f-t),abs(f+rpi2-t),abs(t+rpi2-f))
+                    # print "clade.fc.pc", clade.fc.pc
+                    # print "clade.lc.nc", clade.lc.nc
+                    # print ''
+                    # print "clade.fc.theta", clade.fc.theta
+                    # print "clade.lc.theta", clade.lc.theta
+                    # print ''
+                    # print "clade.fc.pc.theta", clade.fc.pc.theta
+                    # print "clade.fc.nc.theta", clade.fc.nc.theta
+                    # print ''
+                    # print "clade.lc.pc.theta", clade.lc.pc.theta
+                    # print "clade.lc.nc.theta", clade.lc.nc.theta
+
+                    f, t = clade.fc.theta, clade.fc.pc.theta if clade.fc.pc else clade.fc.nc.theta
+                    cpc = min(abs(f-t), abs(f+rpi2-t), abs(t+rpi2-f))
+                    f, t = clade.lc.theta, clade.lc.nc.theta if clade.lc.nc else clade.lc.pc.theta
+                    cnc = min(abs(f-t), abs(f+rpi2-t), abs(t+rpi2-f))
 
                     lsm = clade.fc.theta - cpc * 0.5
                     lgr = clade.lc.theta + cnc * 0.5
 
-                self._wing_thetas.append( lsm )
+                # print ''
+                # print "cpc", cpc
+                # print "cnc", cnc
+                # print "lsm", lsm
+                # print "lgr", lgr
+
+                self._wing_thetas.append(lsm)
+
                 if self.ignore_branch_len:
-                    rad = 1.0 + lev_width * ( 1 + self._wing_levs.index(int(self._depths[clade.name]))  ) - clade.r
+                    rad = 1.0 + lev_width * ( 1 + self._wing_levs.index(int(self._depths[clade.name])) ) - clade.r
                 else:
                     rad = (1.0 - clade.r) + lev_width
-                self._wing_radii.append( rad + rad_offset )
-                width = abs( lgr - lsm)
-                self._wing_widths.append( width )
-                self._wing_bottoms.append( clade.r )
-                self._wing_colors.append( clade.annotation_background_color )
+
+                # print "rad", rad
+
+                self._wing_radii.append(rad + rad_offset)
+                width = abs(lgr - lsm)
+
+                # print "width", width
+
+                self._wing_widths.append(width)
+                self._wing_bottoms.append(clade.r)
+                self._wing_colors.append(clade.annotation_background_color)
+
                 if clade.r + rad + rad_offset > self._wing_tot_offset:
                     self._wing_tot_offset = clade.r + rad + rad_offset
                     self._tot_offset = self._wing_tot_offset
 
+                    # print ''
+                    # print "self._wing_tot_offset", self._wing_tot_offset
+                    # print "self._tot_offset", self._tot_offset
+
                 if hasattr( clade, 'annotation') and clade.annotation:
                     lab, ext_key = clade.annotation, None
+
                     if lab.count(":"):
                         ext_key, lab = lab, lab.split(":")[0]
-                    self._label.append( lab )
+
+                    self._label.append(lab)
+
                     if ext_key:
                         self._ext_key.append( ext_key )
+
                     avgtheta = (lgr + lsm)*0.5
                     self._label_theta.append( avgtheta )
 
-                    rot90 = hasattr( clade, 'annotation_rotation') and clade.annotation_rotation
+                    rot90 = hasattr(clade, 'annotation_rotation') and clade.annotation_rotation
                     fract = 0.05 if rot90 else 0.5
+
                     if self.ignore_branch_len:
                         rad = 1.0 + lev_width * ( 1 + self._wing_levs.index(int(self._depths[clade.name]))  ) - lev_width * fract
                     else:
                         rad = 1.0 + lev_width * fract
 
+                    # print "rad", rad
+
                     self._label_r.append( rad + rad_offset )
                     rot = avgtheta * 180.0 / rpi + 90.0 if rpi < clade.theta%rpi2 < rpi2 else avgtheta * 180.0 / rpi - 90.0
                     rot = (rot + 360.0) % 360.0 + 1e-10
                     rot = -rot if rot90 else rot
+
+                    # print "rot", rot
+
                     self._label_rot.append( rot )
                     lfs = clade.annotation_font_size if hasattr(clade,"annotation_font_size") else self.default_annotation_font_size
                     self._annotation_font_size.append( lfs )
@@ -761,6 +854,7 @@ class CircTree(PpaTree):
 
         set_wings_rec( self.tree.root )
 
+
     def disambiguate_names(self):
         def disambiguate_names_rec( clade, cnames = set() ):
             if not hasattr(clade,'name'):
@@ -771,34 +865,41 @@ class CircTree(PpaTree):
 
             for c in clade.clades:
                 disambiguate_names_rec( c, cnames )
+
         disambiguate_names_rec( self.tree.root )
 
 
     def get_legend( self ):
         ax1 = plt.subplot(111, visible=False)
+        keys = getattr(self, "leg_keys")
 
-        keys = getattr( self, "leg_keys")
-
-        clade_marker_color        = getattr( self, "leg_clade_marker_color")
+        clade_marker_color = getattr(self, "leg_clade_marker_color")
         if not clade_marker_color:
             clade_marker_color = [self.default_clade_marker_color] * len(keys)
-        clade_marker_size              = getattr( self, "leg_clade_marker_size")
+
+        clade_marker_size  = getattr(self, "leg_clade_marker_size")
         if not clade_marker_size:
             clade_marker_size = [self.default_clade_marker_size] * len(keys)
-        clade_marker_edge_width   = getattr( self, "leg_clade_marker_edge_width")
+
+        clade_marker_edge_width = getattr(self, "leg_clade_marker_edge_width")
         if not clade_marker_edge_width:
             clade_marker_edge_width = [self.default_clade_marker_edge_width] * len(keys)
 
+        clade_marker_shape = getattr(self, "leg_clade_marker_shape")
+        if not clade_marker_shape:
+            clade_marker_shape = [self.default_clade_marker_shape] * len(keys)
+
         ll = []
-        for s,c,lw in zip(clade_marker_size,clade_marker_color,clade_marker_edge_width):
-            l = ax1.scatter(   0.0, 0.0, s = s, c = c,
-                                linewidths = lw )
+        for s,c,lw,m in zip(clade_marker_size, clade_marker_color, clade_marker_edge_width, clade_marker_shape):
+            l = ax1.scatter( 0.0, 0.0, s=s, c=c, linewidths=lw, marker=m )
             ll.append(l)
+
         ax1.set_xlim((0,1))
         ax1.set_ylim((0,1))
 
         return ll , keys, 'upper right'
 
+
     def _init_attr( self ):
         self._depths = dict([(c.name,dist) for c,dist in
             self.tree.depths(self.ignore_branch_len).items()])
@@ -834,17 +935,13 @@ class CircTree(PpaTree):
         self._ext_patches = []
         self._ext_lines = []
 
-    def draw( self, out_img, out_format = None, out_dpi = 72, out_size = 7.0, out_pad = 0.5, external_legends = False ):
 
-        self.reorder_tree()
+    def draw(self, out_img, out_format=None, out_dpi=72, out_size=7.0, out_pad=0.5, external_legends=False, reorder_tree=True):
+        self.reorder_tree(reorder_tree)
         #self.tree.ladderize()
-
         self.load_set_attr()
-
         self.disambiguate_names()
-
         self._init_attr()
-
         self.set_clade_data()
         self.set_branches()
         self.set_wings()
@@ -859,7 +956,6 @@ class CircTree(PpaTree):
         xticks([])
         yticks([])
 
-
         if len(self._t) > 0 and len(self._r) > 0:
             ax.scatter( self._t, self._r,
                         marker = self.default_clade_marker_shape,
@@ -889,19 +985,13 @@ class CircTree(PpaTree):
                                             color=self._br_colors,
                                             linewidth= self.branch_thickness )
 
-
         if len( self._wing_thetas ) < 2:
             self._wing_thetas.append(0)
             self._wing_radii.append(0)
             self._wing_widths.append(0)
             self._wing_bottoms.append(0)
-        wbar = ax.bar( self._wing_thetas, self._wing_radii,
-                       width = self._wing_widths,
-                       bottom = self._wing_bottoms,
-                       alpha = self.annotation_background_alpha,
-                       color = self._wing_colors,
-                       edgecolor = self._wing_colors,
-                       )
+
+        wbar = ax.bar(self._wing_thetas, self._wing_radii, width=self._wing_widths, bottom=self._wing_bottoms, alpha=self.annotation_background_alpha, color=self._wing_colors, edgecolor=self._wing_colors, align='edge')
 
         for lev,d in self.int_levs.items():
             if 'internal_label' in d:
@@ -970,6 +1060,10 @@ class CircTree(PpaTree):
         for l,v in self.ext_levs.items():
             for p in ['ring_internal_separator_thickness','ring_external_separator_thickness']:
                 if p in v and float(v[p]) > 0.0:
+                    if l not in self._ext_bottoms.keys():
+                        print('[e] External ring #'+str(l), 'defined, but not used. Please check your annotations file')
+                        continue
+
                     bot = offset + self._ext_bottoms[l]
                     if p == 'ring_external_separator_thickness':
                         bot += self._ext_max_height[l]*0.1 if l in self._ext_max_height else 0.1
@@ -981,12 +1075,12 @@ class CircTree(PpaTree):
             if 'ring_label' in v and v['ring_label']:
                 bot = offset + self._ext_bottoms[l]
                 bot1 = offset + ( self._ext_bottoms[l+1] if l+1 in self._ext_bottoms else self._ext_bottoms[l] +
-                            (self._ext_max_height[l]*0.1 if l in self._ext_max_height else 0.1) )
-                off = (rpi2-self.total_plotted_degrees)*0.5
+                                 (self._ext_max_height[l]*0.1 if l in self._ext_max_height else 0.1) )
+
+                off = self.start_rotation + (rpi2 - self.total_plotted_degrees) * 0.5
                 b = (bot+bot1)*0.5
-                s = -90 if 0.5*rpi < self.start_rotation < 1.5*rpi else 90
-                #rot = (self.start_rotation*360.0/rpi2 + s + off*360.0/rpi2 )%360.0
-                rot = (self.start_rotation*360.0/rpi2 + s )%360.0
+                s = 180.0 if self.start_rotation == rpi else 0.0
+                rot = (self.start_rotation*360.0/rpi2)%180.0 - 90 + s
                 fs = v['ring_label_font_size']
                 lcol = v['ring_label_color']
                 ax.text( self.start_rotation, b, v['ring_label'], rotation = rot,
@@ -1004,31 +1098,19 @@ class CircTree(PpaTree):
         #ax.text( 0, 1, t )
 
         if self._ext_key:
-            #a = ax.legend( bbox_to_anchor=(.0, 1), loc = 'upper left', shadow=False, frameon = False,
-            #           scatterpoints = 1, borderpad = 0, handlelength = 0,
-            #           handletextpad = 0, markerscale = 0.0, ncol = 1,
-            #           labelspacing = 0.05,
-            #           prop = {'size':self.annotation_legend_font_size}
-            #        )
-
             if external_legends:
-                if self._ext_key:
-                    lengths = [len(s) for s in self._ext_key]
-                    charsize = self.annotation_legend_font_size * 0.0138889
-                    width = round(max(lengths) * charsize * 10.) / 10.
-                    height = round(self._tot_offset * len(self._ext_key) * charsize * 10.) / 10.
-                    fig_annot = plt.figure(figsize=(width, height))
-                    ax = fig_annot.add_subplot(111, frame_on=False, xticks=[], yticks=[])
-                else:
-                    print '[W] External annotation not created, no annotated labels!'
+                lengths = [len(s) for s in self._ext_key]
+                charsize = self.annotation_legend_font_size * 0.0138889
+                width = round(max(lengths) * charsize * 10.) / 10.
+                height = round(self._tot_offset * len(self._ext_key) * charsize * 10.) / 10.
+                fig_annot = plt.figure(figsize=(width, height))
+                ax = fig_annot.add_subplot(111, frame_on=False, xticks=[], yticks=[])
 
             ll = [ax.scatter(0.0, 0.0, s=0.0)] * len(self._ext_key)
-
-            if self._ext_key:
-                plt.figlegend(ll, sorted(self._ext_key), 'upper left', frameon=False,
-                    shadow=False, scatterpoints=1, handlelength=0, markerscale=0.0,
-                    handletextpad=0.2, ncol=1, labelspacing=0.1,
-                    prop={'size': self.annotation_legend_font_size})
+            plt.figlegend(ll, sorted(self._ext_key), 'upper left', frameon=False,
+                shadow=False, scatterpoints=1, handlelength=0, markerscale=0.0,
+                handletextpad=0.2, ncol=1, labelspacing=0.1,
+                prop={'size': self.annotation_legend_font_size})
 
             if external_legends: # add '_annot' to the filename
                 if out_format:
@@ -1036,10 +1118,11 @@ class CircTree(PpaTree):
                 else:
                     img_name = out_img[:out_img.rfind('.')] + "_annot" + out_img[out_img.rfind('.'):]
 
-                if self._ext_key:
-                    plt.savefig(img_name, dpi=out_dpi, bbox_inches='tight',
-                        bbox_extra_artists=handles, pad_inches=out_pad, format=out_format)
-                    plt.close()
+                plt.savefig(img_name, dpi=out_dpi, bbox_inches='tight',
+                    bbox_extra_artists=handles, pad_inches=out_pad, format=out_format)
+                plt.close()
+        # else:
+        #     print '[w] External annotation not created, no annotated labels!'
 
         if external_legends:
             if labels: # need to check if there are annotated labels!
@@ -1048,7 +1131,7 @@ class CircTree(PpaTree):
                 height = round(self._tot_offset * len(labels) * charsize * self.class_legend_marker_size * 10.) / 10.
                 plt.figure(figsize=(width, height))
             else:
-                print '[W] External legend not created, no annotated labels!'
+                print('[w] External legend not created, no annotated labels!')
 
         if labels:
             plt.figlegend(handles, labels, loc, labelspacing=0.1, frameon=False,
@@ -1073,7 +1156,6 @@ class CircTree(PpaTree):
                 pad_inches=out_pad, format=out_format,
                 # edgecolor=fc
             )
-
             plt.close()
         else:
             plt.show()


=====================================
src/pyphlan.py
=====================================
@@ -9,7 +9,7 @@ from Bio.Phylo.BaseTree import Clade as BClade
 import string
 from numpy import pi as rpi
 rpi2 = 2.0*rpi
-import numpy as np 
+import numpy as np
 import array as arr
 import collections as colls
 import sys
@@ -115,7 +115,7 @@ def reroot_mid_fat_edge( tree, node ):
 def clades2terms( tree, startswith = None ):
     c2t = {}
     def clades2terms_rec( c ):
-        if startswith: 
+        if startswith:
             if c.name and c.name.startswith( startswith ):
                 c2t[c] = c.get_terminals()
         else:
@@ -127,11 +127,11 @@ def clades2terms( tree, startswith = None ):
 
 def dist_matrix( tree ):
     terminals = list(tree.get_terminals())
-    term_names = [t.name for t in terminals] 
+    term_names = [t.name for t in terminals]
     # can be made faster with recursion
     for n in tree.get_nonterminals():
         n.ids = set( [nn.name for nn in n.get_terminals()]  )
-    
+
     dists = dict([(n,dict([(nn,0.0) for nn in term_names])) for n in term_names])
 
     def dist_matrix_rec( clade ):
@@ -160,18 +160,21 @@ class PpaTree:
     def __load_tree_txt__( self, fn ):
         tree = Phylo.BaseTree.Tree()
         try:
-            rows = [l.decode('utf-8').rstrip().split("\t")[0] for l in 
+            rows = [l.decode('utf-8').rstrip().split("\t")[0] for l in
                         open(fn, 'rb')]
         except IOError:
             raise IOError()
-      
+
         clades = [r.split(lev_sep) for r in rows]
 
         tree = BTree()
         tree.root = BClade()
-       
+
         def add_clade_rec( father, txt_tree ):
-            fl = set([t[0] for t in txt_tree])
+            fl = []
+            for c in [t[0] for t in txt_tree]:
+                if c in fl: continue
+                else: fl.append(c)
             father.clades = []
             for c in fl:
                 nclade = BClade( branch_length = 1.0,
@@ -184,7 +187,7 @@ class PpaTree:
         add_clade_rec( tree.root, clades )
         self.ignore_branch_len = 1
         return tree.as_phyloxml()
-        
+
 
     def __read_tree__( self, fn ):
         for ff in ['phyloxml','newick','nexus',"txt"]:
@@ -199,25 +202,25 @@ class PpaTree:
                 continue
             except IOError:
                 sys.stderr.write("Error: No tree file found: "+fn+"\n")
-                raise IOError 
+                raise IOError
             except Exception:
                 continue
             else:
                 return tree.as_phyloxml()
         sys.stderr.write("Error: unrecognized input format "+fn+"\n")
-        raise ValueError 
+        raise ValueError
 
 
     def __init__( self, filename, warnings = False ):
         self.warnings = warnings
         if filename is None:
             self.tree = None
-            return 
+            return
         try:
-            self.tree = self.__read_tree__(filename) 
+            self.tree = self.__read_tree__(filename)
             self.add_full_paths()
         except:
-            sys.exit(0) 
+            sys.exit(0)
 
 
     def core_test( self, ok, tot, pr ):
@@ -242,7 +245,7 @@ class PpaTree:
         add = 0
         for subclade in clade.clades:
             if "?" in subclade.name:
-                out = subclade.imgids - intersection # targs  
+                out = subclade.imgids - intersection # targs
                 add += len(out)
         if add and len_intersection >= add:
             len_intersection += int(round(add/1.99))
@@ -259,10 +262,10 @@ class PpaTree:
                 if len(subclade.imgids & targs) == 0:
                     nsubclades_absent += 1
                 continue
-            
+
             sc_intersection = subclade.imgids & targs
             sc_len_intersection = len(sc_intersection)
-           
+
             sc_add = 0
             for sc_subclade in subclade.clades:
                 if "?" in sc_subclade.name:
@@ -271,7 +274,7 @@ class PpaTree:
             if add and sc_len_intersection >= sc_add:
                 sc_len_intersection += int(round(sc_add/1.99))
 
-            subcore = self.core_test( sc_len_intersection, subclade.nterminals, er )    
+            subcore = self.core_test( sc_len_intersection, subclade.nterminals, er )
             if subcore < 0.05:
                 return False, core, None
         if nsubclades > 0 and nsubclades == nsubclades_absent:
@@ -295,7 +298,7 @@ class PpaTree:
                                 1.0)]
                 return []
             if skip_qm and clade.name and "?" in clade.name:
-                return [] 
+                return []
             if len(clade.imgids) == 1:
                 cimg = list(clade.imgids)[0]
                 if cimg in terminals:
@@ -320,7 +323,7 @@ class PpaTree:
 
 
     def add_full_paths( self ):
-        
+
         def _add_full_paths_( clade, path ):
             lpath = path + ([clade.name] if clade.name else [])
             clade.full_name = ".".join( lpath )
@@ -330,7 +333,7 @@ class PpaTree:
 
     def find_cores( self, cl_taxa_file, min_core_size = 1, error_rate = 0.95, subtree = None, skip_qm = True ):
         if subtree:
-            self.subtree( 'name', subtree ) 
+            self.subtree( 'name', subtree )
         self.ctc = {}
         imgids2terminals = {}
         for t in self.tree.get_terminals():
@@ -343,7 +346,7 @@ class PpaTree:
             n.imgids = set( [nn.imgid for nn in n.get_terminals()]  )
             n.nterminals = len( n.imgids )
 
-        self.add_full_paths() # unnecessary 
+        self.add_full_paths() # unnecessary
 
         ret = {}
         for vec in (l.strip().split('\t') for l in open(cl_taxa_file)):
@@ -357,7 +360,7 @@ class PpaTree:
                 ret[sid] = self._find_core( tgts, er = error_rate, root_name = subtree, skip_qm = skip_qm )
                 #print sid #, ret[sid]
         return ret
-   
+
     def markerness( self, coreness, uniqueness, cn_min, cn_max, cn_avg ):
         return coreness * uniqueness * (1.0 / float(cn_max-cn_min+1)) * 1.0 / cn_avg
 
@@ -376,9 +379,9 @@ class PpaTree:
             n.imgids = set( [nn.imgid for nn in n.get_terminals()]  )
             n.nterminals = len( n.imgids )
 
-        self.add_full_paths() # unnecessary 
-        
-        cus = dict([(int(l[0]),[int(ll) for ll in l[1:]]) for l in 
+        self.add_full_paths() # unnecessary
+
+        cus = dict([(int(l[0]),[int(ll) for ll in l[1:]]) for l in
                         (line.strip().split('\t') for line in open(cu_file))])
         cinfo = dict([(int(v[0]),[v[1]] + [int(vv) for vv in v[2:6]] + [float(vv) for vv in v[6:]])
                         for v in (line.strip().split('\t') for line in open(core_file))])
@@ -390,7 +393,7 @@ class PpaTree:
             lca = self.lca( cus[sid], ids2clades )
             if lca.is_terminal():
                 tin = set([lca.imgid])
-                tout = tgts_l - tin 
+                tout = tgts_l - tin
             else:
                 tout = tgts_l - lca.imgids
                 tin = lca.imgids & tgts_l
@@ -403,15 +406,15 @@ class PpaTree:
             gtax = ci[0]
             cobs, ctot = int(ci[1]), int(ci[2])
             markerness = self.markerness( coreness, uniqueness, cn_min, cp_max, cn_avg )
-            
+
             res_lin = [ gtax, markerness, coreness, uniqueness, cobs, ctot, cn_min, cp_max, cn_avg,
                         ltin, ltout, "|".join([str(s) for s in tin]), "|".join([str(s) for s in tout]) ]
-            ret[sid] = res_lin 
+            ret[sid] = res_lin
         return ret
-       
+
 
     def select_markers( self, marker_file, markerness_th = 0.0, max_markers = 200 ):
-        cl2markers = colls.defaultdict( list ) 
+        cl2markers = colls.defaultdict( list )
         for line in (l.strip().split('\t') for l in open( marker_file )):
             gid = line[1]
             markerness = float(line[2])
@@ -433,7 +436,7 @@ class PpaTree:
             for c in clade.clades:
                 _get_c2t_( c )
         _get_c2t_( self.tree.root )
-        return tc2t 
+        return tc2t
 
     def ltcs( self, terminals, tc2t = None, terminals2clades = None, lca_precomputed = None ):
         set_terminals = set( terminals )
@@ -444,7 +447,7 @@ class PpaTree:
             terms = tc2t[clade] if tc2t else set([cc.name for cc in clade.get_terminals()])
             if len(terms) < cur_max:
                 return None,0
-            if terms <= set_terminals: 
+            if terms <= set_terminals:
                 return clade,len(terms)
             rets = []
             for c in clade.clades:
@@ -456,7 +459,7 @@ class PpaTree:
             if rets:
                 return sorted(rets,key=lambda x:x[1])[-1][0],cur_max
             else:
-                return None,None 
+                return None,None
         return _ltcs_rec_( lca, cur_max = 0 )[0]
 
     def lca( self, terminals, terminals2clades = None ):
@@ -476,7 +479,7 @@ class PpaTree:
         lca = self.tree.common_ancestor( clade_targets )
         return lca
 
-    
+
     def lcca( self, t, t2c ):
         node_path = list(self.tree.get_path(t))
         if not node_path or len(node_path) < 2:
@@ -520,7 +523,7 @@ class PpaTree:
             outs = [c]
             if len(out_terms):
                 diam = sum(sorted(ltcs.depths().values())[-2:])
-                outs += [":".join([t.name,str( self.tree.distance(ltcs,t)/diam )]) 
+                outs += [":".join([t.name,str( self.tree.distance(ltcs,t)/diam )])
                              for t in out_terms]
             res.append( outs )
         return res
@@ -528,7 +531,7 @@ class PpaTree:
     def tax_resolution( self, terminals ):
         pass
 
-    
+
     def prune( self, strategy = 'lca', n = None, fn = None, name = None, newname = None ):
         prune = None
         if strategy == 'root_name':
@@ -557,7 +560,7 @@ class PpaTree:
             toprune = node_path[-n]
             fat = node_path[-n-1]
             fat.clades = [cc for cc in fat.clades if cc != toprune]
-            prune = None 
+            prune = None
         else:
             sys.stderr.write( strategy + " not supported yet." )
             sys.exit(-1)
@@ -620,8 +623,8 @@ class PpaTree:
 
     def reroot( self, strategy = 'lca', tf = None, n = None ):
         if strategy in [ 'lca', 'ltcs' ]:
-            targets = self.read_targets( tf ) 
-          
+            targets = self.read_targets( tf )
+
             lca = self.lca( targets ) if strategy == 'lca' else self.ltcs( targets )
             reroot_mid_fat_edge( self.tree, lca)
 
@@ -641,46 +644,55 @@ class PpaTree:
             #self.tree.reroot_at_midpoint(update_splits=True)
         elif strategy == 'longest_edge':
             nodes = list(self.tree.get_nonterminals()) + list(self.tree.get_terminals())
-            longest = max( nodes, key=lambda x:x.branch_length ) 
+            longest = max( nodes, key=lambda x:x.branch_length )
             reroot_mid_fat_edge( self.tree, longest )
             #longest_edge = max( self.ntree.get_edge_set(),
             #                    key=lambda x:x.length)
             #self.tree.reroot_at_edge(longest_edge, update_splits=True)
         elif strategy == 'longest_internal_edge':
             nodes = list(self.tree.get_nonterminals())
-            longest = max( nodes, key=lambda x:x.branch_length ) 
+            longest = max( nodes, key=lambda x:x.branch_length )
             if self.tree.root != longest:
                 reroot_mid_fat_edge( self.tree, longest )
             #longest = get_lensorted_int_edges( self.tree )
             #self.tree.reroot_at_edge( list(longest)[-1], update_splits=True )
         elif strategy == 'longest_internal_edge_n':
             nodes = list(self.tree.get_nonterminals())
-            longest = max( nodes, key=lambda x:x.branch_length 
-                    if len(x.get_terminals()) >= n else -1.0) 
+            longest = max( nodes, key=lambda x:x.branch_length
+                    if len(x.get_terminals()) >= n else -1.0)
             reroot_mid_fat_edge( self.tree, longest )
             #longest = get_lensorted_int_edges( self.tree, n )
             #self.tree.reroot_at_edge( list(longest)[-1], update_splits=True )
 
 
-    def reorder_tree( self ):
+    def reorder_tree( self, reorder_tree ):
         self._ord_terms = []
-        def reorder_tree_rec( clade ):
+
+
+        def reorder_tree_rec( clade, reorder_tree ):
             if clade.is_terminal():
                 self._ord_terms.append( clade )
                 return clade,clade
-            clade.clades.sort( key=lambda x:len(x.get_terminals()), reverse = True)
+
+            if reorder_tree:
+                clade.clades.sort(key=lambda x:len(x.get_terminals()), reverse = True)
+
             for c in clade.clades:
-                c.fc,c.lc = reorder_tree_rec( c ) 
-            return clade.clades[0].fc,clade.clades[-1].lc 
+                c.fc,c.lc = reorder_tree_rec( c, reorder_tree )
+
+            return clade.clades[0].fc,clade.clades[-1].lc
             #clade.fc, clade.lc = clade.clades[0], clade.clades[-1]
-        
-        reorder_tree_rec( self.tree.root )
+
+
+        reorder_tree_rec( self.tree.root, reorder_tree )
         last = None # self._ord_terms[-1]
+
         for c in self._ord_terms:
             c.pc = last
             if last:
                 last.nc = c
             last = c
+
         c.nc = None
         #self._ord_terms[-1].nc = None # self._ord_terms[0]
 
@@ -696,7 +708,7 @@ class PpaTree:
                 leaves += rec_subtree_leaves( c )
             leaves = [l for l in leaves if l]
             subtrees.append( (clade.name if clade.name else "",leaves)  )
-            return leaves 
+            return leaves
 
         rec_subtree_leaves( self.tree.root )
         return subtrees
@@ -713,14 +725,14 @@ class PpaTree:
                 if not nam and not clade.name:
                     lnam = ""
                 elif not nam:
-                    lnam = clade.name 
+                    lnam = clade.name
                 elif not clade.name:
                     lnam = nam
                 else:
-                    lnam = lev_sep.join( [nam, clade.name if clade.name else ""] ) 
-                ret += [lnam] if lnam else [] 
+                    lnam = lev_sep.join( [nam, clade.name if clade.name else ""] )
+                ret += [lnam] if lnam else []
                 for c in clade.clades:
-                    ret += rec_name(c,lnam) 
+                    ret += rec_name(c,lnam)
                 return ret
             names = set(rec_name(self.tree.root))
         else:



View it on GitLab: https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad

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View it on GitLab: https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad
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