[med-svn] [Git][med-team/python-ete3][master] 6 commits: New upstream version 3.1.3+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Nov 15 10:34:04 GMT 2023
Andreas Tille pushed to branch master at Debian Med / python-ete3
Commits:
b99004af by Andreas Tille at 2023-11-15T11:25:03+01:00
New upstream version 3.1.3+dfsg
- - - - -
17ebe75e by Andreas Tille at 2023-11-15T11:25:03+01:00
routine-update: New upstream version
- - - - -
ebc486cc by Andreas Tille at 2023-11-15T11:25:07+01:00
Update upstream source from tag 'upstream/3.1.3+dfsg'
Update to upstream version '3.1.3+dfsg'
with Debian dir 3ff1af71cde14edaf1cd6472390bbca337b700c7
- - - - -
daa807c1 by Andreas Tille at 2023-11-15T11:25:07+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
a678abb2 by Andreas Tille at 2023-11-15T11:25:11+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
fe52ec86 by Andreas Tille at 2023-11-15T11:29:03+01:00
routine-update: Ready to upload to unstable
- - - - -
22 changed files:
- PKG-INFO
- VERSION
- debian/changelog
- debian/control
- debian/rules
- ete3.egg-info/PKG-INFO
- ete3.egg-info/entry_points.txt
- ete3/coretype/tree.py
- ete3/evol/evoltree.py
- ete3/evol/model.py
- ete3/evol/parser/codemlparser.py
- ete3/ncbi_taxonomy/ncbiquery.py
- ete3/orthoxml/_orthoxml.py
- ete3/test/test_ncbiquery.py
- ete3/test/test_treeview/barchart_and_piechart_faces.py
- ete3/treeview/faces.py
- ete3/treeview/main.py
- ete3/treeview/qt.py
- ete3/treeview/qt4_face_render.py
- ete3/treeview/qt4_gui.py
- ete3/version.py
- setup.py
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,32 +1,16 @@
-Metadata-Version: 1.2
+Metadata-Version: 2.1
Name: ete3
-Version: 3.1.2
+Version: 3.1.3
Summary: A Python Environment for (phylogenetic) Tree Exploration
Home-page: http://etetoolkit.org
+Download-URL: http://etetoolkit.org/static/releases/ete3/
Author: Jaime Huerta-Cepas
Author-email: jhcepas at gmail.com
Maintainer: Jaime Huerta-Cepas
Maintainer-email: huerta at embl.de
License: GPLv3
-Download-URL: http://etetoolkit.org/static/releases/ete3/
-Description:
- The Environment for Tree Exploration (ETE) is a Python programming
- toolkit that assists in the recontruction, manipulation, analysis and
- visualization of phylogenetic trees (although clustering trees or any
- other tree-like data structure are also supported).
-
- ETE is currently developed as a tool for researchers working in
- phylogenetics and genomics. If you use ETE for a published work,
- please cite:
-
- ::
-
- Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
- analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
- 10.1093/molbev/msw046
-
- Visit http://etetoolkit.org for more info.
-
+Project-URL: Documentation, http://etetoolkit.org/docs/latest/tutorial/index.html
+Project-URL: Source, https://github.com/etetoolkit/ete
Keywords: tree,tree reconstruction,tree visualization,tree comparison,phylogeny,phylogenetics,phylogenomics
Platform: OS Independent
Classifier: Development Status :: 6 - Mature
@@ -46,3 +30,22 @@ Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires: six
Provides: ete3
+License-File: LICENSE
+
+
+The Environment for Tree Exploration (ETE) is a Python programming
+toolkit that assists in the recontruction, manipulation, analysis and
+visualization of phylogenetic trees (although clustering trees or any
+other tree-like data structure are also supported).
+
+ETE is currently developed as a tool for researchers working in
+phylogenetics and genomics. If you use ETE for a published work,
+please cite:
+
+::
+
+ Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
+ analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
+ 10.1093/molbev/msw046
+
+Visit http://etetoolkit.org for more info.
=====================================
VERSION
=====================================
@@ -1 +1 @@
-3.1.2
\ No newline at end of file
+3.1.3
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+python-ete3 (3.1.3+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Wed, 15 Nov 2023 11:26:38 +0100
+
python-ete3 (3.1.2+dfsg-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: python
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3-all,
python3-setuptools,
python3-numpy,
@@ -17,7 +17,7 @@ Build-Depends: debhelper-compat (= 13),
python3-six,
python3-skbio,
python3-pytest
-Standards-Version: 4.6.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-ete3
Vcs-Git: https://salsa.debian.org/med-team/python-ete3.git
Homepage: http://etetoolkit.org
=====================================
debian/rules
=====================================
@@ -6,7 +6,7 @@ export PYBUILD_NAME=ete3
#export PYBUILD_TEST_ARGS_python3=-k-XTest_ncbiquery
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_auto_install:
dh_auto_install -O--buildsystem=pybuild
rm -r debian/python3-ete3/usr/bin
=====================================
ete3.egg-info/PKG-INFO
=====================================
@@ -1,32 +1,16 @@
-Metadata-Version: 1.2
+Metadata-Version: 2.1
Name: ete3
-Version: 3.1.2
+Version: 3.1.3
Summary: A Python Environment for (phylogenetic) Tree Exploration
Home-page: http://etetoolkit.org
+Download-URL: http://etetoolkit.org/static/releases/ete3/
Author: Jaime Huerta-Cepas
Author-email: jhcepas at gmail.com
Maintainer: Jaime Huerta-Cepas
Maintainer-email: huerta at embl.de
License: GPLv3
-Download-URL: http://etetoolkit.org/static/releases/ete3/
-Description:
- The Environment for Tree Exploration (ETE) is a Python programming
- toolkit that assists in the recontruction, manipulation, analysis and
- visualization of phylogenetic trees (although clustering trees or any
- other tree-like data structure are also supported).
-
- ETE is currently developed as a tool for researchers working in
- phylogenetics and genomics. If you use ETE for a published work,
- please cite:
-
- ::
-
- Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
- analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
- 10.1093/molbev/msw046
-
- Visit http://etetoolkit.org for more info.
-
+Project-URL: Documentation, http://etetoolkit.org/docs/latest/tutorial/index.html
+Project-URL: Source, https://github.com/etetoolkit/ete
Keywords: tree,tree reconstruction,tree visualization,tree comparison,phylogeny,phylogenetics,phylogenomics
Platform: OS Independent
Classifier: Development Status :: 6 - Mature
@@ -46,3 +30,22 @@ Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires: six
Provides: ete3
+License-File: LICENSE
+
+
+The Environment for Tree Exploration (ETE) is a Python programming
+toolkit that assists in the recontruction, manipulation, analysis and
+visualization of phylogenetic trees (although clustering trees or any
+other tree-like data structure are also supported).
+
+ETE is currently developed as a tool for researchers working in
+phylogenetics and genomics. If you use ETE for a published work,
+please cite:
+
+::
+
+ Jaime Huerta-Cepas, François Serra and Peer Bork. "ETE 3: Reconstruction,
+ analysis and visualization of phylogenomic data." Mol Biol Evol (2016) doi:
+ 10.1093/molbev/msw046
+
+Visit http://etetoolkit.org for more info.
=====================================
ete3.egg-info/entry_points.txt
=====================================
@@ -1,3 +1,2 @@
[console_scripts]
ete3 = ete3.tools.ete:main
-
=====================================
ete3/coretype/tree.py
=====================================
@@ -1658,7 +1658,7 @@ class TreeNode(object):
:param name attr_t2: Compare trees using a custom node
attribute as a node name in target tree.
- :param False attr_t2: If True, consider trees as unrooted.
+ :param False unrooted_trees: If True, consider trees as unrooted.
:param False expand_polytomies: If True, all polytomies in the reference
and target tree will be expanded into all possible binary
=====================================
ete3/evol/evoltree.py
=====================================
@@ -44,12 +44,20 @@ the coretype PhyloNode and add some speciall features to the the node
instances.
"""
from __future__ import absolute_import
+from ..tools.utils import which
+from .utils import translate
+from .model import Model, PARAMS, AVAIL
+from ..parser.newick import write_newick
+from .. import PhyloNode, SeqGroup
+from warnings import warn
+import sys
+import os
from six.moves import map
-__author__ = "Francois-Jose Serra"
-__email__ = "francois at barrabin.org"
-__licence__ = "GPLv3"
-__version__ = "0.0"
+__author__ = "Francois-Jose Serra"
+__email__ = "francois at barrabin.org"
+__licence__ = "GPLv3"
+__version__ = "0.0"
__references__ = '''
Yang, Z., Nielsen, R., Goldman, N., & Pedersen, A. M. 2000.
Codon-substitution models for heterogeneous selection pressure at amino acid sites.
@@ -73,18 +81,10 @@ Yang, Z. 2007.
Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/17483113
'''
-import os
-import sys
-from warnings import warn
-from .. import PhyloNode, SeqGroup
-from ..parser.newick import write_newick
-from .model import Model, PARAMS, AVAIL
-from .utils import translate
-from ..tools.utils import which
try:
from scipy.stats import chi2
- chi_high = lambda x, y: 1 - chi2.cdf(x, y)
+ def chi_high(x, y): return 1 - chi2.cdf(x, y)
except ImportError:
from .utils import chi_high
@@ -97,12 +97,14 @@ else:
__all__ = ["EvolNode", "EvolTree"]
+
def _parse_species(name):
'''
just to return specie name from fasta description
'''
return name[:3]
+
class EvolNode(PhyloNode):
""" Re-implementation of the standart TreeNode instance. It adds
attributes and methods to work with phylogentic trees.
@@ -118,7 +120,7 @@ class EvolNode(PhyloNode):
def __init__(self, newick=None, alignment=None, alg_format="fasta",
sp_naming_function=_parse_species, format=0,
- binpath='', **kwargs):
+ binpath='', **kwargs):
'''
freebranch: path to find codeml output of freebranch model.
'''
@@ -167,11 +169,12 @@ class EvolNode(PhyloNode):
nid = 1
# check we do not have dupplicated names in tree
if (len(self)) != len(set(self.get_leaf_names())):
- duplis = [n for n in self.get_leaf_names() if self.get_leaf_names().count(n)>1]
+ duplis = [n for n in self.get_leaf_names(
+ ) if self.get_leaf_names().count(n) > 1]
raise Exception('EvolTree require unique names for leaves', duplis)
# put ids
for leaf in sorted(self, key=lambda x: x.name):
- leaf.add_feature ('node_id', nid)
+ leaf.add_feature('node_id', nid)
nid += 1
self.add_feature('node_id', nid)
self._label_internal_nodes([nid])
@@ -187,7 +190,7 @@ class EvolNode(PhyloNode):
if self.node_id == idname:
return self
except AttributeError:
- warn('Should be first labelled as paml ' + \
+ warn('Should be first labelled as paml ' +
'(automatically done when alignemnt is loaded)')
def _write_algn(self, fullpath):
@@ -196,12 +199,11 @@ class EvolNode(PhyloNode):
"""
seq_group = SeqGroup()
for n in self:
- seq_group.id2seq [n.node_id] = n.nt_sequence
- seq_group.id2name [n.node_id] = n.name
- seq_group.name2id [n.name ] = n.node_id
+ seq_group.id2seq[n.node_id] = n.nt_sequence
+ seq_group.id2name[n.node_id] = n.name
+ seq_group.name2id[n.name] = n.node_id
seq_group.write(outfile=fullpath, format='paml')
-
def run_model(self, model_name, ctrl_string='', keep=True, **kwargs):
'''
To compute evolutionnary models. e.g.: b_free_lala.vs.lele, will launch one free branch model, and store
@@ -226,21 +228,22 @@ class EvolNode(PhyloNode):
* model-name is compulsory, is the name of the model (see table above for the full list)
* the second part is accessory, it is to avoid over-writing models with the same name.
:argument ctrl_string: list of parameters that can be used as control file.
+ :argument True keep: links the model to the tree (equivalen of running `EVOL_TREE.link_to_evol_model(MODEL_NAME)`)
:argument kwargs: extra parameters should be one of: %s.
'''
from subprocess import Popen, PIPE
model_obj = Model(model_name, self, **kwargs)
- fullpath = os.path.join (self.workdir, model_obj.name)
- os.system("mkdir -p %s" %fullpath)
+ fullpath = os.path.join(self.workdir, model_obj.name)
+ os.system("mkdir -p %s" % fullpath)
# write tree file
self._write_algn(fullpath + '/algn')
if model_obj.properties['exec'] == 'Slr':
- self.write(outfile=fullpath+'/tree', format = (11))
+ self.write(outfile=fullpath+'/tree', format=(11))
else:
self.write(outfile=fullpath+'/tree',
- format = (10 if model_obj.properties['allow_mark'] else 9))
+ format=(10 if model_obj.properties['allow_mark'] else 9))
# write algn file
- ## MODEL MODEL MDE
+ # MODEL MODEL MDE
if ctrl_string == '':
ctrl_string = model_obj.get_ctrl_string(fullpath+'/tmp.ctl')
else:
@@ -249,34 +252,31 @@ class EvolNode(PhyloNode):
os.chdir(fullpath)
bin_ = os.path.join(self.execpath, model_obj.properties['exec'])
try:
- proc = Popen([bin_, 'tmp.ctl'], stdout=PIPE, stdin=PIPE)
+ proc = Popen([bin_, 'tmp.ctl'], stdout=PIPE,
+ stdin=PIPE, stderr=PIPE)
except OSError:
raise Exception(('ERROR: {} not installed, ' +
'or wrong path to binary\n').format(bin_))
- run, err = proc.communicate(b'\n') # send \n via stdin in case codeml/slr asks something (note on py3, stdin needs bytes)
+ # send \n via stdin in case codeml/slr asks something (note on py3, stdin needs bytes)
+ run, err = proc.communicate(b'\n')
run = run.decode(sys.stdout.encoding)
- if err is not None:
- warn("ERROR: codeml not found!!!\n" +
- " define your variable EvolTree.execpath")
- return 1
- if 'error' in run or 'Error' in run:
- warn("ERROR: inside codeml!!\n" + run)
- return 1
os.chdir(hlddir)
+ if err:
+ warn("ERROR: inside codeml!!\n" + err)
+ return 1
if keep:
setattr(model_obj, 'run', run)
- self.link_to_evol_model(os.path.join(fullpath,'out'), model_obj)
+ self.link_to_evol_model(os.path.join(fullpath, 'out'), model_obj)
sep = '\n'
run_model.__doc__ = run_model.__doc__ % \
- (sep.join([' %-8s %-27s %-15s ' % \
- ('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) for x in sorted (sorted (AVAIL.keys()), key=lambda x: \
- AVAIL[x]['typ'],
- reverse=True)]),
- ', '.join(list(PARAMS.keys())))
-
+ (sep.join([' %-8s %-27s %-15s ' %
+ ('%s' % (x), AVAIL[x]['evol'], AVAIL[x]['typ']) for x in sorted(sorted(AVAIL.keys()), key=lambda x:
+ AVAIL[x]['typ'],
+ reverse=True)]),
+ ', '.join(list(PARAMS.keys())))
- #def test_codon_model(self):
+ # def test_codon_model(self):
# for c_frq in range(4):
# self.run_model('M0.model_test-'+str(c_frq), CodonFreq=c_frq)
# if self.get_most_likely('M0.model_test-1', 'M0.model_test-0') > 0.05:
@@ -288,7 +288,7 @@ class EvolNode(PhyloNode):
# self.get_most_likely('M0.model_test-3', 'M0.model_test-2')
def link_to_alignment(self, alignment, alg_format="paml",
- nucleotides=True, **kwargs):
+ nucleotides=True, **kwargs):
'''
same function as for phyloTree, but translate sequences if nucleotides
nucleotidic sequence is kept under node.nt_sequence
@@ -332,11 +332,11 @@ class EvolNode(PhyloNode):
except AttributeError:
warn('model %s not computed' % (hist))
if not 'histface' in mdl.properties:
- if len(histfaces)>1 and histfaces.index(hist)!=0:
+ if len(histfaces) > 1 and histfaces.index(hist) != 0:
mdl.set_histface(up=False)
else:
mdl.set_histface()
- if mdl.properties ['histface'].up:
+ if mdl.properties['histface'].up:
ts.aligned_header.add_face(
mdl.properties['histface'], 1)
else:
@@ -346,7 +346,6 @@ class EvolNode(PhyloNode):
else:
raise ValueError("Treeview module is disabled")
-
def render(self, file_name, layout=None, w=None, h=None,
tree_style=None, header=None, histfaces=None):
'''
@@ -369,11 +368,11 @@ class EvolNode(PhyloNode):
except AttributeError:
warn('model %s not computed' % (hist))
if not 'histface' in mdl.properties:
- if len(histfaces)>1 and histfaces.index(hist)!=0:
+ if len(histfaces) > 1 and histfaces.index(hist) != 0:
mdl.set_histface(up=False)
else:
mdl.set_histface()
- if mdl.properties ['histface'].up:
+ if mdl.properties['histface'].up:
ts.aligned_header.add_face(
mdl.properties['histface'], 1)
else:
@@ -385,7 +384,6 @@ class EvolNode(PhyloNode):
else:
raise ValueError("Treeview module is disabled")
-
def mark_tree(self, node_ids, verbose=False, **kargs):
'''
function to mark branches on tree in order that paml could interpret it.
@@ -401,11 +399,11 @@ class EvolNode(PhyloNode):
'''
from re import match
- node_ids = list(map(int , node_ids))
+ node_ids = list(map(int, node_ids))
if 'marks' in kargs:
marks = list(kargs['marks'])
else:
- marks = ['#1']*len (node_ids)
+ marks = ['#1']*len(node_ids)
for node in self.traverse():
if not hasattr(node, 'node_id'):
continue
@@ -415,7 +413,8 @@ class EvolNode(PhyloNode):
marks[node_ids.index(node.node_id)]) is None) and verbose:
warn('WARNING: marks should be "#" sign directly ' +
'followed by integer\n' + self.mark_tree.__doc__)
- node.add_feature('mark', ' '+marks[node_ids.index(node.node_id)])
+ node.add_feature(
+ 'mark', ' '+marks[node_ids.index(node.node_id)])
elif not 'mark' in node.features:
node.add_feature('mark', '')
@@ -430,7 +429,7 @@ class EvolNode(PhyloNode):
:argument model: either the name of a model, or a Model object (usually empty)
'''
- if type(model) == str :
+ if isinstance(model, str):
model = Model(model, self, path)
else:
model._load(path)
@@ -443,7 +442,7 @@ class EvolNode(PhyloNode):
if not os.path.isfile(path):
warn("ERROR: not a file: " + path)
return 1
- if len(self._models) == 1 and model.properties['exec']=='codeml':
+ if len(self._models) == 1 and model.properties['exec'] == 'codeml':
self.change_dist_to_evol('bL', model, fill=True)
def get_evol_model(self, modelname):
@@ -456,8 +455,7 @@ class EvolNode(PhyloNode):
try:
return self._models[modelname]
except KeyError:
- warn("Model %s not found." % (modelname))
-
+ Exception("ERROR: Model %s not found." % (modelname))
def write(self, features=None, outfile=None, format=10):
"""
@@ -465,15 +463,15 @@ class EvolNode(PhyloNode):
TODO: internal writting format need to be something like 0
"""
from re import sub
- if int(format)==11:
+ if int(format) == 11:
nwk = ' %s 1\n' % (len(self))
- nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
- write_newick(self, features=['mark'],format=9))
- elif int(format)==10:
- nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1', \
- write_newick(self, features=['mark'],format=9))
+ nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
+ write_newick(self, features=['mark'], format=9))
+ elif int(format) == 10:
+ nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
+ write_newick(self, features=['mark'], format=9))
else:
- nwk = write_newick(self, features=features,format=format)
+ nwk = write_newick(self, features=features, format=format)
if outfile is not None:
open(outfile, "w").write(nwk)
return nwk
@@ -482,7 +480,6 @@ class EvolNode(PhyloNode):
write.__doc__ += super(PhyloNode, PhyloNode()).write.__doc__.replace(
'argument format', 'argument 10 format')
-
def get_most_likely(self, altn, null):
'''
Returns pvalue of LRT between alternative model and null model.
@@ -530,7 +527,7 @@ class EvolNode(PhyloNode):
return 1.0
try:
if hasattr(altn, 'lnL') and hasattr(null, 'lnL'):
- if null.lnL - altn.lnL < 0:
+ if null.lnL - altn.lnL < 0:
return chi_high(2 * abs(altn.lnL - null.lnL),
float(altn.np - null.np))
else:
@@ -563,7 +560,7 @@ class EvolNode(PhyloNode):
node.dist = model.branches[node.node_id][evol]
if fill:
for e in ['dN', 'dS', 'w', 'bL']:
- node.add_feature(e, model.branches [node.node_id][e])
+ node.add_feature(e, model.branches[node.node_id][e])
# cosmetic alias
=====================================
ete3/evol/model.py
=====================================
@@ -217,8 +217,7 @@ class Model:
if not 'ylim' in kwargs:
kwargs['ylim'] = (0, 2)
if errors:
- errors = self.sites[val]['se'] if 'se' in self.sites[val]\
- else None
+ errors = self.sites[val].get('se', None)
if TREEVIEW:
try:
hist = SequencePlotFace(self.sites[val]['w'], hlines=hlines,
@@ -336,7 +335,7 @@ class Model:
self.sites[val]['class']):
if pval < 0.95:
categories.append('NS')
- elif curr_class != self.n_classes[val] and not ps_model:
+ elif curr_class == self.n_classes[val] and not ps_model:
if pval < 0.99:
categories.append('RX')
else:
=====================================
ete3/evol/parser/codemlparser.py
=====================================
@@ -107,16 +107,16 @@ def parse_rst(path):
sites[typ].setdefault ('aa', []).append (line[1])
# get site class probability
probs = []
- for i in range (k):
+ for i in range(k):
probs.append (float (line[2+i]))
- sites [typ].setdefault ('p'+str(i), []).append (float (line[2+i]))
- sites [typ].setdefault ('pv', []).append (max (probs))
+ sites [typ].setdefault('p' + str(i), []).append(float(line[2+i]))
+ sites [typ].setdefault ('pv', []).append (max(probs))
# get most likely site class
classe = int (line [3 + i])
- sites[typ].setdefault ('class', []).append (classe)
+ sites[typ].setdefault ('class', []).append(classe)
# if there, get omega and error
try:
- sites [typ].setdefault ('w' , []).append (float (line [4 + i]))
+ sites [typ].setdefault('w' , []).append(float (line [4 + i]))
except IndexError:
# in this case we are with branch-site A or A1 and we should sum
# probabilities of categories 2a and 2b
@@ -218,7 +218,7 @@ def parse_paml (pamout, model):
model._tree._label_as_paml()
# starts parsing
for i, line in enumerate (all_lines):
- if line is '\n':
+ if line == '\n':
continue
# codon frequency
if line.startswith('Codon frequencies under model'):
=====================================
ete3/ncbi_taxonomy/ncbiquery.py
=====================================
@@ -97,7 +97,7 @@ class NCBITaxa(object):
Provides a local transparent connector to the NCBI taxonomy database.
"""
- def __init__(self, dbfile=None, taxdump_file=None):
+ def __init__(self, dbfile=None, taxdump_file=None, update=True):
if not dbfile:
self.dbfile = DEFAULT_TAXADB
@@ -107,7 +107,7 @@ class NCBITaxa(object):
if taxdump_file:
self.update_taxonomy_database(taxdump_file)
- if dbfile is None and not os.path.exists(self.dbfile):
+ if dbfile != DEFAULT_TAXADB and not os.path.exists(self.dbfile):
print('NCBI database not present yet (first time used?)', file=sys.stderr)
self.update_taxonomy_database(taxdump_file)
@@ -117,7 +117,7 @@ class NCBITaxa(object):
self.db = None
self._connect()
- if not is_taxadb_up_to_date(self.dbfile):
+ if not is_taxadb_up_to_date(self.dbfile) and update:
print('NCBI database format is outdated. Upgrading', file=sys.stderr)
self.update_taxonomy_database(taxdump_file)
@@ -371,7 +371,7 @@ class NCBITaxa(object):
elif intermediate_nodes:
return list(map(int, [n.name for n in tree.get_descendants()]))
else:
- return map(int, [n.name for n in tree])
+ return list(map(int, [n.name for n in tree]))
elif intermediate_nodes:
return [tid for tid, count in six.iteritems(descendants)]
@@ -410,11 +410,11 @@ class NCBITaxa(object):
visited = set()
start = prepostorder.index(root_taxid)
try:
- end = prepostorder.index(root_taxid, start+1)
- subtree = prepostorder[start:end+1]
+ end = prepostorder.index(root_taxid, start+1)
+ subtree = prepostorder[start:end+1]
except ValueError:
# If root taxid is not found in postorder, must be a tip node
- subtree = [root_taxid]
+ subtree = [root_taxid]
leaves = set([v for v, count in Counter(subtree).items() if count == 1])
nodes[root_taxid] = PhyloTree(name=str(root_taxid))
current_parent = nodes[root_taxid]
=====================================
ete3/orthoxml/_orthoxml.py
=====================================
@@ -447,13 +447,13 @@ class orthoXML(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='orthoXML'):
if self.origin is not None and 'origin' not in already_processed:
already_processed.append('origin')
- outfile.write(' origin=%s' % (self.gds_format_string(quote_attrib(self.origin).encode(ExternalEncoding), input_name='origin'), ))
+ outfile.write(' origin=%s' % (self.gds_format_string(quote_attrib(self.origin), input_name='origin'), ))
if self.version is not None and 'version' not in already_processed:
already_processed.append('version')
outfile.write(' version="%s"' % self.gds_format_float(self.version, input_name='version'))
if self.originVersion is not None and 'originVersion' not in already_processed:
already_processed.append('originVersion')
- outfile.write(' originVersion=%s' % (self.gds_format_string(quote_attrib(self.originVersion).encode(ExternalEncoding), input_name='originVersion'), ))
+ outfile.write(' originVersion=%s' % (self.gds_format_string(quote_attrib(self.originVersion), input_name='originVersion'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='orthoXML', fromsubclass_=False):
if self.notes:
self.notes.export(outfile, level, namespace_, name_='notes')
@@ -609,7 +609,7 @@ class species(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='species'):
if self.name is not None and 'name' not in already_processed:
already_processed.append('name')
- outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name).encode(ExternalEncoding), input_name='name'), ))
+ outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
if self.NCBITaxId is not None and 'NCBITaxId' not in already_processed:
already_processed.append('NCBITaxId')
outfile.write(' NCBITaxId="%s"' % self.gds_format_integer(self.NCBITaxId, input_name='NCBITaxId'))
@@ -740,19 +740,19 @@ class database(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='database'):
if self.transcriptLink is not None and 'transcriptLink' not in already_processed:
already_processed.append('transcriptLink')
- outfile.write(' transcriptLink=%s' % (self.gds_format_string(quote_attrib(self.transcriptLink).encode(ExternalEncoding), input_name='transcriptLink'), ))
+ outfile.write(' transcriptLink=%s' % (self.gds_format_string(quote_attrib(self.transcriptLink), input_name='transcriptLink'), ))
if self.protLink is not None and 'protLink' not in already_processed:
already_processed.append('protLink')
- outfile.write(' protLink=%s' % (self.gds_format_string(quote_attrib(self.protLink).encode(ExternalEncoding), input_name='protLink'), ))
+ outfile.write(' protLink=%s' % (self.gds_format_string(quote_attrib(self.protLink), input_name='protLink'), ))
if self.geneLink is not None and 'geneLink' not in already_processed:
already_processed.append('geneLink')
- outfile.write(' geneLink=%s' % (self.gds_format_string(quote_attrib(self.geneLink).encode(ExternalEncoding), input_name='geneLink'), ))
+ outfile.write(' geneLink=%s' % (self.gds_format_string(quote_attrib(self.geneLink), input_name='geneLink'), ))
if self.name is not None and 'name' not in already_processed:
already_processed.append('name')
- outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name).encode(ExternalEncoding), input_name='name'), ))
+ outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
if self.version is not None and 'version' not in already_processed:
already_processed.append('version')
- outfile.write(' version=%s' % (self.gds_format_string(quote_attrib(self.version).encode(ExternalEncoding), input_name='version'), ))
+ outfile.write(' version=%s' % (self.gds_format_string(quote_attrib(self.version), input_name='version'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='database', fromsubclass_=False):
if self.genes:
self.genes.export(outfile, level, namespace_, name_='genes', )
@@ -962,16 +962,16 @@ class gene(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='gene'):
if self.protId is not None and 'protId' not in already_processed:
already_processed.append('protId')
- outfile.write(' protId=%s' % (self.gds_format_string(quote_attrib(self.protId).encode(ExternalEncoding), input_name='protId'), ))
+ outfile.write(' protId=%s' % (self.gds_format_string(quote_attrib(self.protId), input_name='protId'), ))
if self.id is not None and 'id' not in already_processed:
already_processed.append('id')
outfile.write(' id="%s"' % self.gds_format_integer(self.id, input_name='id'))
if self.geneId is not None and 'geneId' not in already_processed:
already_processed.append('geneId')
- outfile.write(' geneId=%s' % (self.gds_format_string(quote_attrib(self.geneId).encode(ExternalEncoding), input_name='geneId'), ))
+ outfile.write(' geneId=%s' % (self.gds_format_string(quote_attrib(self.geneId), input_name='geneId'), ))
if self.transcriptId is not None and 'transcriptId' not in already_processed:
already_processed.append('transcriptId')
- outfile.write(' transcriptId=%s' % (self.gds_format_string(quote_attrib(self.transcriptId).encode(ExternalEncoding), input_name='transcriptId'), ))
+ outfile.write(' transcriptId=%s' % (self.gds_format_string(quote_attrib(self.transcriptId), input_name='transcriptId'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='gene', fromsubclass_=False):
pass
def hasContent_(self):
@@ -1277,7 +1277,7 @@ class group(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='group'):
if self.id is not None and 'id' not in already_processed:
already_processed.append('id')
- outfile.write(' id=%s' % (self.gds_format_string(quote_attrib(self.id).encode(ExternalEncoding), input_name='id'), ))
+ outfile.write(' id=%s' % (self.gds_format_string(quote_attrib(self.id), input_name='id'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='group', fromsubclass_=False):
for score_ in self.score:
score_.export(outfile, level, namespace_, name_='score')
@@ -1576,7 +1576,7 @@ class scoreDef(GeneratedsSuper):
outfile.write(' id=%s' % (quote_attrib(self.id), ))
if self.desc is not None and 'desc' not in already_processed:
already_processed.append('desc')
- outfile.write(' desc=%s' % (self.gds_format_string(quote_attrib(self.desc).encode(ExternalEncoding), input_name='desc'), ))
+ outfile.write(' desc=%s' % (self.gds_format_string(quote_attrib(self.desc), input_name='desc'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='scoreDef', fromsubclass_=False):
pass
def hasContent_(self):
@@ -1744,10 +1744,10 @@ class property(GeneratedsSuper):
def exportAttributes(self, outfile, level, already_processed, namespace_='ortho:', name_='property'):
if self.name is not None and 'name' not in already_processed:
already_processed.append('name')
- outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name).encode(ExternalEncoding), input_name='name'), ))
+ outfile.write(' name=%s' % (self.gds_format_string(quote_attrib(self.name), input_name='name'), ))
if self.value is not None and 'value' not in already_processed:
already_processed.append('value')
- outfile.write(' value=%s' % (self.gds_format_string(quote_attrib(self.value).encode(ExternalEncoding), input_name='value'), ))
+ outfile.write(' value=%s' % (self.gds_format_string(quote_attrib(self.value), input_name='value'), ))
def exportChildren(self, outfile, level, namespace_='ortho:', name_='property', fromsubclass_=False):
pass
def hasContent_(self):
=====================================
ete3/test/test_ncbiquery.py
=====================================
@@ -56,13 +56,13 @@ class Test_ncbiquery(unittest.TestCase):
self.assertEqual(set(name2id['Bacteria']), set([2]))
out = ncbi.get_descendant_taxa("9605", intermediate_nodes=True)
- #Out[9]: [9606, 63221, 741158, 2665952, 2665953, 1425170]
+ #Out[9]: [9606, 63221, 741158, 2665952, 2665953, 1425170, 2813598, 2813599]
# New Taxonomies of Homo in NCBI, {2665952: 'environmental samples', 2665953: 'Homo sapiens environmental sample'}
- self.assertEqual(set(out), set([9606, 63221, 741158, 2665952, 2665953, 1425170]))
+ self.assertEqual(set(out), set([9606, 63221, 741158, 2665952, 2665953, 1425170, 2813598, 2813599]))
out = ncbi.get_descendant_taxa("9605", intermediate_nodes=False)
#Out[10]: [63221, 741158, 2665953, 1425170]
- self.assertEqual(set(out), set([63221, 741158, 2665953, 1425170]))
+ self.assertEqual(set(out), set([63221, 741158, 2665953, 1425170, 2813599]))
out = ncbi.get_descendant_taxa("9596", intermediate_nodes=False, rank_limit="species")
#Out[11]: [9597, 9598]
=====================================
ete3/test/test_treeview/barchart_and_piechart_faces.py
=====================================
@@ -2,7 +2,7 @@ import sys
import random
from ... import Tree, faces, TreeStyle, COLOR_SCHEMES
-schema_names = COLOR_SCHEMES.keys()
+schema_names = sorted(COLOR_SCHEMES.keys())
def layout(node):
if node.is_leaf():
=====================================
ete3/treeview/faces.py
=====================================
@@ -63,9 +63,9 @@ from six.moves import zip
from .qt import (QGraphicsRectItem, QGraphicsLineItem,
QGraphicsPolygonItem, QGraphicsEllipseItem,
QPen, QColor, QBrush, QPolygonF, QFont,
- QPixmap, QFontMetrics, QPainter,
+ QPixmap, QFontMetrics, QPainter, QPainterPath,
QRadialGradient, QGraphicsSimpleTextItem, QGraphicsTextItem,
- QGraphicsItem, Qt, QPointF, QRect, QRectF, QGraphicsSvgItem)
+ QGraphicsItem, Qt, QLineF, QPointF, QRect, QRectF, QGraphicsSvgItem)
from .main import add_face_to_node, _Background, _Border, COLOR_SCHEMES
@@ -560,19 +560,19 @@ class ProfileFace(Face):
# Draw axis and scale
p.setPen(QColor("black"))
- p.drawRect(x2,y,profile_width, profile_height-1)
+ p.drawRect(QRectF(x2,y,profile_width, profile_height-1))
p.setFont(QFont("Verdana",8))
- p.drawText(profile_width,y+10,"%0.3f" %self.max_value)
- p.drawText(profile_width,y+profile_height,"%0.3f" %self.min_value)
+ p.drawText(QPointF(profile_width,y+10), "%0.3f" %self.max_value)
+ p.drawText(QPointF(profile_width,y+profile_height), "%0.3f" %self.min_value)
dashedPen = QPen(QBrush(QColor("#ddd")), 0)
dashedPen.setStyle(Qt.DashLine)
# Draw hz grid
p.setPen(dashedPen)
- p.drawLine(x2+1, mean_line_y, profile_width-2, mean_line_y )
- p.drawLine(x2+1, line2_y, profile_width-2, line2_y )
- p.drawLine(x2+1, line3_y, profile_width-2, line3_y )
+ p.drawLine(QLineF(x2+1, mean_line_y, profile_width-2, mean_line_y ))
+ p.drawLine(QLineF(x2+1, line2_y, profile_width-2, line2_y ))
+ p.drawLine(QLineF(x2+1, line3_y, profile_width-2, line3_y ))
# Draw bars
@@ -603,17 +603,17 @@ class ProfileFace(Face):
# Draw bar border
p.setPen(QColor("black"))
- #p.drawRect(x1+2,mean_y1, x_alpha-3, profile_height-mean_y1+1)
+ #p.drawRect(QRectF(x1+2,mean_y1, x_alpha-3, profile_height-mean_y1+1))
# Fill bar with custom color
- p.fillRect(x1+3,profile_height-mean_y1, x_alpha-4, mean_y1-1, QBrush(customColor))
+ p.fillRect(QRectF(x1+3,profile_height-mean_y1, x_alpha-4, mean_y1-1), QBrush(customColor))
# Draw error bars
if dev1 != 0:
dev_up_y1 = int((mean1+dev1 - self.min_value) * y_alpha)
dev_down_y1 = int((mean1-dev1 - self.min_value) * y_alpha)
- p.drawLine(x1+x_alpha/2, profile_height-dev_up_y1 ,x1+x_alpha/2, profile_height-dev_down_y1 )
- p.drawLine(x1-1+x_alpha/2, profile_height-dev_up_y1, x1+1+x_alpha/2, profile_height-dev_up_y1 )
- p.drawLine(x1-1+x_alpha/2, profile_height-dev_down_y1, x1+1+x_alpha/2, profile_height-dev_down_y1 )
+ p.drawLine(QLineF(1+x_alpha/2, profile_height-dev_up_y1 ,x1+x_alpha/2, profile_height-dev_down_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, profile_height-dev_up_y1, x1+1+x_alpha/2, profile_height-dev_up_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, profile_height-dev_down_y1, x1+1+x_alpha/2, profile_height-dev_down_y1 ))
def draw_centered_bar_profile(self):
# Calculate vector
@@ -649,20 +649,20 @@ class ProfileFace(Face):
# Draw axis and scale
p.setPen(QColor("black"))
- p.drawRect(x2,y,profile_width, profile_height-1)
+ p.drawRect(QRectF(x2,y,profile_width), profile_height-1)
p.setFont(QFont("Verdana",8))
- p.drawText(profile_width,y+10,"%0.3f" %self.max_value)
- p.drawText(profile_width,y+profile_height,"%0.3f" %self.min_value)
- p.drawText(profile_width,mean_line_y,"%0.3f" %self.center_v)
+ p.drawText(QPointF(profile_width,y+10), "%0.3f" %self.max_value)
+ p.drawText(QPointF(profile_width,y+profile_height), "%0.3f" %self.min_value)
+ p.drawText(QPointF(profile_width,mean_line_y), "%0.3f" %self.center_v)
dashedPen = QPen(QBrush(QColor("#ddd")), 0)
dashedPen.setStyle(Qt.DashLine)
# Draw hz grid
p.setPen(dashedPen)
- p.drawLine(x2+1, mean_line_y, profile_width-2, mean_line_y )
- p.drawLine(x2+1, line2_y, profile_width-2, line2_y )
- p.drawLine(x2+1, line3_y, profile_width-2, line3_y )
+ p.drawLine(QLineF(x2+1, mean_line_y, profile_width-2, mean_line_y ))
+ p.drawLine(QLineF(x2+1, line2_y, profile_width-2, line2_y ))
+ p.drawLine(QLineF(x2+1, line3_y, profile_width-2, line3_y ))
# Draw bars
@@ -704,24 +704,24 @@ class ProfileFace(Face):
#p.drawRect(x1+2,mean_y1, x_alpha-3, profile_height-mean_y1+1)
# Fill bar with custom color
if mean1<self.center_v:
- p.fillRect(x1+3, mean_line_y, x_alpha-4, mean_y1, QBrush(customColor))
+ p.fillRect(QRectF(x1+3, mean_line_y, x_alpha-4, mean_y1), QBrush(customColor))
else:
- p.fillRect(x1+3, mean_line_y-mean_y1, x_alpha-4, mean_y1+1, QBrush(customColor))
+ p.fillRect(QRectF(x1+3, mean_line_y-mean_y1, x_alpha-4, mean_y1+1), QBrush(customColor))
# Draw error bars
if dev1 != 0:
if mean1<self.center_v:
dev_up_y1 = int((mean1+dev1 - self.center_v) * y_alpha_down)
dev_down_y1 = int((mean1-dev1 - self.center_v) * y_alpha_down)
- p.drawLine(x1+x_alpha/2, mean_line_y+dev_up_y1 ,x1+x_alpha/2, mean_line_y+dev_down_y1 )
- p.drawLine(x1-1+x_alpha/2, mean_line_y+dev_up_y1 ,x1+1+x_alpha/2, mean_line_y+dev_up_y1 )
- p.drawLine(x1-1+x_alpha/2, mean_line_y+dev_down_y1 ,x1+1+x_alpha/2, mean_line_y+dev_down_y1 )
+ p.drawLine(QLineF(x1+x_alpha/2, mean_line_y+dev_up_y1 ,x1+x_alpha/2, mean_line_y+dev_down_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, mean_line_y+dev_up_y1 ,x1+1+x_alpha/2, mean_line_y+dev_up_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, mean_line_y+dev_down_y1 ,x1+1+x_alpha/2, mean_line_y+dev_down_y1 ))
else:
dev_up_y1 = int((mean1+dev1 - self.center_v) * y_alpha_up)
dev_down_y1 = int((mean1-dev1 - self.center_v) * y_alpha_up)
- p.drawLine(x1+x_alpha/2, mean_line_y-dev_up_y1 ,x1+x_alpha/2, mean_line_y-dev_down_y1 )
- p.drawLine(x1-1+x_alpha/2, mean_line_y-dev_up_y1 ,x1+1+x_alpha/2, mean_line_y-dev_up_y1 )
- p.drawLine(x1-1+x_alpha/2, mean_line_y-dev_down_y1 ,x1+1+x_alpha/2, mean_line_y-dev_down_y1 )
+ p.drawLine(QLineF(x1+x_alpha/2, mean_line_y-dev_up_y1 ,x1+x_alpha/2, mean_line_y-dev_down_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, mean_line_y-dev_up_y1 ,x1+1+x_alpha/2, mean_line_y-dev_up_y1 ))
+ p.drawLine(QLineF(x1-1+x_alpha/2, mean_line_y-dev_down_y1 ,x1+1+x_alpha/2, mean_line_y-dev_down_y1 ))
def draw_line_profile(self):
# Calculate vector
@@ -754,20 +754,20 @@ class ProfileFace(Face):
# Draw axis and scale
p.setPen(QColor("black"))
- p.drawRect(x2,y,profile_width, profile_height-1)
+ p.drawRect(QRectF(x2,y,profile_width, profile_height-1))
p.setFont(QFont("Verdana",8))
- p.drawText(profile_width,y+10,"%0.3f" %self.max_value)
- p.drawText(profile_width,y+profile_height,"%0.3f" %self.min_value)
- p.drawText(profile_width,mean_line_y+5,"%0.3f" %self.center_v)
+ p.drawText(QPointF(profile_width,y+10), "%0.3f" %self.max_value)
+ p.drawText(QPointF(profile_width,y+profile_height), "%0.3f" %self.min_value)
+ p.drawText(QPointF(profile_width,mean_line_y+5), "%0.3f" %self.center_v)
dashedPen = QPen(QBrush(QColor("#ddd")), 0)
dashedPen.setStyle(Qt.DashLine)
# Draw hz grid
p.setPen(dashedPen)
- p.drawLine(x2+1, mean_line_y, profile_width-2, mean_line_y )
- p.drawLine(x2+1, line2_y, profile_width-2, line2_y )
- p.drawLine(x2+1, line3_y, profile_width-2, line3_y )
+ p.drawLine(QLineF(x2+1, mean_line_y, profile_width-2, mean_line_y ))
+ p.drawLine(QLineF(x2+1, line2_y, profile_width-2, line2_y ))
+ p.drawLine(QLineF(x2+1, line3_y, profile_width-2, line3_y ))
# Draw lines
for pos in range(0,vlength-1):
@@ -782,7 +782,7 @@ class ProfileFace(Face):
# Draw vt grid
if x2 < profile_width:
p.setPen(dashedPen)
- p.drawLine(x2, y+1, x2, profile_height-2)
+ p.drawLine(QLineF(x2, y+1, x2, profile_height-2))
# If nan values, continue
if not isfinite(mean1) or not isfinite(mean2):
@@ -799,11 +799,11 @@ class ProfileFace(Face):
dev_y2 = (dev2 - self.min_value) * y_alpha
# Draw red deviation lines
p.setPen(QColor("red"))
- p.drawLine(x1, profile_height-dev_y1, x2, profile_height-dev_y2)
- p.drawLine(x1, profile_height+dev_y1, x2, profile_height+dev_y2)
+ p.drawLine(QLineF(x1, profile_height-dev_y1, x2, profile_height-dev_y2))
+ p.drawLine(QLineF(x1, profile_height+dev_y1, x2, profile_height+dev_y2))
# Draw blue mean line
p.setPen(QColor("blue"))
- p.drawLine(x1, profile_height-mean_y1, x2, profile_height-mean_y2)
+ p.drawLine(QLineF(x1, profile_height-mean_y1, x2, profile_height-mean_y2))
def draw_heatmap_profile(self):
@@ -857,11 +857,11 @@ class ProfileFace(Face):
customColor = colors[100]
# Fill bar with custom color
- p.fillRect(x1, y, x_alpha, y_step, QBrush(customColor))
+ p.fillRect(QRectF(x1, y, x_alpha, y_step), QBrush(customColor))
y+= y_step
x2 = 0
p.end()
-
+
def fit_to_scale(self,v):
if v<self.min_value:
return float(self.min_value)
@@ -944,8 +944,8 @@ class OLD_SequenceFace(Face):
letter_pen = QPen(QColor(self.aafg.get(letter,"black" )))
p.setPen(letter_pen)
- p.fillRect(x,0,width, height,letter_brush)
- p.drawText(x, y, letter)
+ p.fillRect(QRectF(x,0,width, height,letter_brush))
+ p.drawText(QPointF(x, y), letter)
x += float(width)/len(self.seq)
p.end()
@@ -1225,7 +1225,7 @@ class _PieChartItem(QGraphicsRectItem):
col = self.colors[i]
painter.setBrush(QBrush(QColor(col)))
angle_span = (p/100.) * a
- painter.drawPie(self.rect(), angle_start, angle_span )
+ painter.drawPie(self.rect(), int(angle_start), int(angle_span) )
angle_start += angle_span
@@ -1478,26 +1478,26 @@ class _BarChartItem(QGraphicsRectItem):
if self.draw_border:
p.setPen(QColor("black"))
- p.drawRect(x, y + 1, plot_width, plot_height)
+ p.drawRect(QRectF(x, y + 1, plot_width, plot_height))
if self.draw_scale:
p.setFont(QFont("Verdana", self.scale_fsize))
font_height = QFontMetrics(p.font()).height()
max_string = "% 7.2f" %max_value
min_string = "% 7.2f" %min_value
- p.drawText(plot_width + margin, font_height-2, max_string)
- p.drawText(plot_width + margin, plot_height - 2, min_string)
- p.drawLine(plot_width + margin - 1, 1, plot_width + margin - 1, plot_height+1)
- p.drawLine(plot_width + margin - 1, 1, plot_width + margin + 2, 1)
- p.drawLine(plot_width + margin - 1, plot_height+1, plot_width + margin + 2, plot_height+1)
+ p.drawText(QPointF(plot_width + margin, font_height-2), max_string)
+ p.drawText(QPointF(plot_width + margin, plot_height - 2), min_string)
+ p.drawLine(QLineF(plot_width + margin - 1, 1, plot_width + margin - 1, plot_height+1))
+ p.drawLine(QLineF(plot_width + margin - 1, 1, plot_width + margin + 2, 1))
+ p.drawLine(QLineF(plot_width + margin - 1, plot_height+1, plot_width + margin + 2, plot_height+1))
if self.draw_grid:
dashedPen = QPen(QBrush(QColor("#ddd")), 0)
dashedPen.setStyle(Qt.DashLine)
p.setPen(dashedPen)
- p.drawLine(x+1, mean_line_y, plot_width - 2, mean_line_y)
- p.drawLine(x+1, line2_y, plot_width - 2, line2_y )
- p.drawLine(x+1, line3_y, plot_width - 2, line3_y )
+ p.drawLineQLineF((x+1, mean_line_y, plot_width - 2, mean_line_y))
+ p.drawLine(QLineF(x+1, line2_y, plot_width - 2, line2_y ))
+ p.drawLine(QLineF(x+1, line3_y, plot_width - 2, line3_y ))
# Draw bars
p.setFont(QFont("Verdana", self.label_fsize))
@@ -1515,8 +1515,8 @@ class _BarChartItem(QGraphicsRectItem):
p.save()
p.translate(x1, plot_height+2)
p.rotate(90)
- p.drawText(0, -x_alpha, label_height, x_alpha, Qt.AlignVCenter, str(self.labels[pos]))
- #p.drawRect(0, -x_alpha, label_height, x_alpha)
+ p.drawText(QRectF(0, -x_alpha, label_height, x_alpha), Qt.AlignVCenter, str(self.labels[pos]))
+ #p.drawRect(QRectF(0, -x_alpha, label_height, x_alpha))
p.restore()
# If nan value, skip
@@ -1530,16 +1530,16 @@ class _BarChartItem(QGraphicsRectItem):
p.setPen(QColor("black"))
# Fill bar with custom color
- p.fillRect(x1, height - mean_y1, x_alpha, mean_y1, QBrush(color))
+ p.fillRect(QRectF(x1, height - mean_y1, x_alpha, mean_y1), QBrush(color))
# Draw error bars
if std != 0:
dev_up_y1 = int((val + std - min_value) * y_alpha)
dev_down_y1 = int((val - std - min_value) * y_alpha)
center_x = x1 + (x_alpha / 2)
- p.drawLine(center_x, plot_height - dev_up_y1, center_x, plot_height - dev_down_y1)
- p.drawLine(center_x + 1, plot_height - dev_up_y1, center_x -1, plot_height - dev_up_y1)
- p.drawLine(center_x + 1, plot_height - dev_down_y1, center_x -1, plot_height - dev_down_y1)
+ p.drawLine(QLineF(center_x, plot_height - dev_up_y1, center_x, plot_height - dev_down_y1))
+ p.drawLine(QLineF(center_x + 1, plot_height - dev_up_y1, center_x -1, plot_height - dev_up_y1))
+ p.drawLine(QLineF(center_x + 1, plot_height - dev_down_y1, center_x -1, plot_height - dev_down_y1))
@@ -1617,20 +1617,20 @@ class SequenceItem(QGraphicsRectItem):
if self.draw_text and self.poswidth >= 8:
br = QBrush(QColor(self.bg.get(letter, "white")))
p.setPen(blackPen)
- p.fillRect(x, 0, self.poswidth, self.posheight, br)
+ p.fillRect(QRectF(x, 0, self.poswidth, self.posheight), br)
qfont.setPixelSize(min(self.posheight, self.poswidth))
p.setFont(qfont)
p.setBrush(QBrush(QColor("black")))
- p.drawText(x, 0, self.poswidth, self.posheight,
+ p.drawText(QRectF(x, 0, self.poswidth, self.posheight),
Qt.AlignCenter | Qt.AlignVCenter,
letter)
elif letter == "-" or letter == ".":
p.setPen(blackPen)
- p.drawLine(x, self.posheight/2, x+self.poswidth, self.posheight/2)
+ p.drawLine(QLineF(x, self.posheight/2, x+self.poswidth, self.posheight/2))
else:
br = QBrush(QColor(self.bg.get(letter, "white")))
- p.fillRect(x, 0, max(1, self.poswidth), self.posheight, br)
+ p.fillRect(QRectF(x, 0, max(1, self.poswidth), self.posheight), br)
#p.setPen(QPen(QColor(self.bg.get(letter, "black"))))
#p.drawLine(x, 0, x, self.posheight)
current_pixel = int(x)
@@ -2420,3 +2420,68 @@ class DiamondFace(StaticItemFace, Face):
def _height(self):
return self.height
+
+class ArrowFace(Face):
+
+ """
+
+ Creates a color-stripped arrow representation for synteny visualization
+
+ :param width: width of the arrow (min of 10)
+ :param height: height of arrow (min of 10)
+ :param strand: defines gene orientation. "-" entails left-oriented arrows
+ while "+" strand right-oriented arrows.
+ :param colors: array containing values to color stripes
+
+ """
+
+ def __init__(self, width, height, strand, colors):
+ Face.__init__(self)
+ self.width = width
+ self.height = height
+ self.strand = strand
+ self.colors = colors
+
+ def _width(self):
+ return self.width
+
+ def _height(self):
+ return self.height
+
+ def update_items(self):
+ return
+
+ def update_pixmap(self):
+ # Create pixmap
+ self.pixmap = QPixmap(self.width, self.height)
+ self.pixmap.fill(QColor("white"))
+ p = QPainter(self.pixmap)
+
+ # Create pen
+ solidPen = QPen(QBrush(QColor("black")), 0)
+ solidPen.setStyle(Qt.SolidLine)
+ p.setPen(solidPen)
+
+ # Define bands width and arrow height taking padding into account
+ rect_w = (self.width - 10) / len(self.colors)
+ rect_h = self.height - 10
+
+ # Draw each of the color bands and the arrow pointer depending on the
+ # strand (+,right/-,left)
+ for i, color in enumerate(self.colors):
+ if self.strand == "+":
+ p.fillRect(3 + i*rect_w, 5, math.ceil(rect_w), rect_h, QColor(color))
+ if i == (len(self.colors) - 1):
+ path = QPainterPath()
+ path.moveTo(3+(i+1)*rect_w, 5)
+ path.lineTo(7+(i+1)*rect_w, 5+rect_h / 2)
+ path.lineTo(3+(i+1)*rect_w, 5+rect_h)
+ p.fillPath(path, QColor(color))
+ elif self.strand == "-":
+ p.fillRect(7 + i*rect_w, 5, math.ceil(rect_w), rect_h, QColor(color))
+ if i == 0:
+ path = QPainterPath()
+ path.moveTo(7, 5)
+ path.lineTo(3, 5+rect_h / 2)
+ path.lineTo(7, 5+rect_h)
+ p.fillPath(path, QColor(color))
=====================================
ete3/treeview/main.py
=====================================
@@ -407,7 +407,7 @@ class TreeStyle(object):
for ly in layout:
# Validates layout function
- if (type(ly) == types.FunctionType or type(ly) == types.MethodType or ly is None):
+ if callable(ly) is True or ly is None:
self._layout_handler.append(ly)
else:
from . import layouts
@@ -682,7 +682,7 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
if ext == "SVG":
svg = QSvgGenerator()
targetRect = QRectF(0, 0, w, h)
- svg.setSize(QSize(w, h))
+ svg.setSize(QSize(int(w), int(h)))
svg.setViewBox(targetRect)
svg.setTitle("Generated with ETE http://etetoolkit.org")
svg.setDescription("Generated with ETE http://etetoolkit.org")
@@ -703,7 +703,9 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
compatible_code = str(ba)
print('from memory')
else:
- compatible_code = open(imgName).read()
+ with open(imgName) as f:
+ compatible_code = f.read()
+
# Fix a very annoying problem with Radial gradients in
# inkscape and browsers...
compatible_code = compatible_code.replace("xml:id=", "id=")
@@ -718,8 +720,8 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
elif imgName == '%%return':
return x_scale, y_scale, compatible_code
else:
- open(imgName, "w").write(compatible_code)
-
+ with open(imgName, "w") as f:
+ f.write(compatible_code)
elif ext == "PDF" or ext == "PS":
if ext == "PS":
@@ -749,10 +751,10 @@ def save(scene, imgName, w=None, h=None, dpi=90,\
scene.render(pp, targetRect, scene.sceneRect(), ratio_mode)
else:
targetRect = QRectF(0, 0, w, h)
- ii= QImage(w, h, QImage.Format_ARGB32)
+ ii= QImage(int(w), int(h), QImage.Format_ARGB32)
ii.fill(QColor(Qt.white).rgb())
- ii.setDotsPerMeterX(dpi / 0.0254) # Convert inches to meters
- ii.setDotsPerMeterY(dpi / 0.0254)
+ ii.setDotsPerMeterX(int(dpi / 0.0254)) # Convert inches to meters
+ ii.setDotsPerMeterY(int(dpi / 0.0254))
pp = QPainter(ii)
pp.setRenderHint(QPainter.Antialiasing)
pp.setRenderHint(QPainter.TextAntialiasing)
=====================================
ete3/treeview/qt.py
=====================================
@@ -1,6 +1,6 @@
try:
from PyQt4 import QtGui, QtCore
- from PyQt4.QtCore import (Qt, QPointF, QRect, QRectF, QBuffer, QByteArray,
+ from PyQt4.QtCore import (Qt, QPointF, QRect, QLineF, QRectF, QBuffer, QByteArray,
QThread, QIODevice, QMetaObject, QModelIndex, QObject, QRegExp, QSize,
QSizeF,QVariant )
from PyQt4.QtGui import (QAction, QApplication, QBrush, QCheckBox, QColor,
@@ -25,7 +25,13 @@ try:
except ImportError:
from PyQt5 import QtGui, QtCore
- from PyQt5.QtCore import (Qt, QPointF, QRect, QRectF, QBuffer, QByteArray,
+
+ # Fixes incompatibilities due to new overflow checking when converting integers introduced in qt 5.12
+ # https://www.riverbankcomputing.com/static/Docs/PyQt5/incompatibilities.html#pyqt-v5-12
+ import sip
+ sip.enableoverflowchecking(False)
+
+ from PyQt5.QtCore import (Qt, QPointF, QLineF, QRect, QRectF, QBuffer, QByteArray,
QThread, QIODevice, QMetaObject, QModelIndex, QObject, QRegExp, QSize,
QSizeF, QVariant) #QString
from PyQt5.QtSvg import QGraphicsSvgItem, QSvgGenerator
=====================================
ete3/treeview/qt4_face_render.py
=====================================
@@ -248,7 +248,7 @@ class _FaceGroupItem(QGraphicsRectItem): # I was about to name this FaceBookItem
elif f.vt_align == 1:
# Vertically centered
y_offset = (max_h - h) / 2
- elif f.hz_align == 2:
+ elif f.vt_align == 2:
# Vertically at bottom
y_offset = (max_h - h)
=====================================
ete3/treeview/qt4_gui.py
=====================================
@@ -72,17 +72,12 @@ class _SelectorItem(QGraphicsRectItem):
def paint(self, p, option, widget):
p.setPen(self.Color)
p.setBrush(QBrush(Qt.NoBrush))
- p.drawRect(self.rect().x(),self.rect().y(),self.rect().width(),self.rect().height())
+ p.drawRect(QRectF(self.rect().x(),self.rect().y(),self.rect().width(),self.rect().height()))
return
# Draw info text
font = QFont("Arial",13)
text = "%d selected." % len(self.get_selected_nodes())
textR = QFontMetrics(font).boundingRect(text)
- if self.rect().width() > textR.width() and \
- self.rect().height() > textR.height()/2 and 0: # OJO !!!!
- p.setPen(QPen(self.Color))
- p.setFont(QFont("Arial",13))
- p.drawText(self.rect().bottomLeft().x(),self.rect().bottomLeft().y(),text)
def get_selected_nodes(self):
selPath = QPainterPath()
@@ -169,7 +164,7 @@ class _GUI(QMainWindow):
# Shows the whole tree by default
#self.view.fitInView(self.scene.sceneRect(), Qt.KeepAspectRatio)
splitter.setCollapsible(1, True)
- splitter.setSizes([self.scene.sceneRect().width(), 10])
+ splitter.setSizes([int(self.scene.sceneRect().width()), 10])
self.view.fitInView(0, 0, self.scene.sceneRect().width(), 200, Qt.KeepAspectRatio)
=====================================
ete3/version.py
=====================================
@@ -1,2 +1,2 @@
#autogenerated during release process. Do not modify
-__version__='3.1.2'
+__version__='3.1.3'
=====================================
setup.py
=====================================
@@ -18,42 +18,12 @@ except ImportError:
from urllib.request import urlopen
from urllib.error import HTTPError
-HERE = os.path.abspath(os.path.split(os.path.realpath(__file__))[0])
-
-if "--donottrackinstall" in sys.argv:
- TRACKINSTALL = None
- sys.argv.remove("--donottrackinstall")
-else:
- # Avoids importing self module
- orig_path = list(sys.path)
- _wd = os.getcwd()
- try:
- sys.path.remove(_wd)
- except ValueError:
- pass
- try:
- sys.path.remove("")
- except ValueError:
- pass
-
- # Is this and upgrade or a new install?
- try:
- import ete3
- except ImportError:
- TRACKINSTALL = "ete-new-installation"
- else:
- TRACKINSTALL = "ete-upgrade"
-
- sys.path = orig_path
-
-
try:
from setuptools import setup, find_packages
except ImportError:
ez_setup.use_setuptools()
from setuptools import setup, find_packages
-
PYTHON_DEPENDENCIES = [
["numpy", "Numpy is required for the ArrayTable and ClusterTree classes.", 0],
["PyQt", "PyQt4/5 is required for tree visualization and image rendering.", 0],
@@ -78,40 +48,14 @@ CLASSIFIERS= [
"Topic :: Software Development :: Libraries :: Python Modules",
]
-def can_import(mname):
- 'Test if a module can be imported '
- if mname == "PyQt":
- try:
- __import__("PyQt4.QtCore")
- __import__("PyQt4.QtGui")
- except ImportError:
- try:
- __import__("PyQt5.QtCore")
- __import__("PyQt5.QtGui")
- except ImportError:
- return False
- else:
- return True
- else:
- return True
- else:
- try:
- __import__(mname)
- except ImportError:
- return False
- else:
- return True
+
+HERE = os.path.abspath(os.path.split(os.path.realpath(__file__))[0])
try:
ETE_VERSION = open(os.path.join(HERE, "VERSION")).readline().strip()
except IOError:
ETE_VERSION = 'unknown'
-print("\nInstalling ETE (%s) \n" %ETE_VERSION)
-print()
-
-
-
MOD_NAME = "ete3"
LONG_DESCRIPTION="""
@@ -133,8 +77,8 @@ please cite:
Visit http://etetoolkit.org for more info.
"""
-try:
- _s = setup(
+
+_s = setup(
include_package_data = True,
name = MOD_NAME,
@@ -167,31 +111,10 @@ try:
provides = [MOD_NAME],
keywords = "tree, tree reconstruction, tree visualization, tree comparison, phylogeny, phylogenetics, phylogenomics",
url = "http://etetoolkit.org",
+ project_urls = {
+ "Documentation": "http://etetoolkit.org/docs/latest/tutorial/index.html",
+ "Source": "https://github.com/etetoolkit/ete",
+ },
download_url = "http://etetoolkit.org/static/releases/ete3/",
- )
-
-except:
- print("\033[91m - Errors found! - \033[0m")
- raise
-
-else:
-
- print("\033[92m - Done! - \033[0m")
- missing = False
- for mname, msg, ex in PYTHON_DEPENDENCIES:
- if not can_import(mname):
- print(" Warning:\033[93m Optional library [%s] could not be found \033[0m" %mname)
- print(" ",msg)
- missing=True
-
- notwanted = set(["-h", "--help", "-n", "--dry-run"])
- seen = set(_s.script_args)
- wanted = set(["install", "bdist", "bdist_egg"])
- if TRACKINSTALL is not None and (wanted & seen) and not (notwanted & seen):
- try:
- welcome = quote("New alien in earth! (%s %s)" %(TRACKINSTALL, time.ctime()))
- urlopen("http://etetoolkit.org/static/et_phone_home.php?ID=%s&VERSION=%s&MSG=%s"
- %(TRACKINSTALL, ETE_VERSION, welcome))
- except Exception:
- pass
+)
View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/compare/1ccb7a3fe282c6a5b8d538cc54d8cd6d9f574929...fe52ec8644b7dec36539cf763370fea3f9be8ed3
--
View it on GitLab: https://salsa.debian.org/med-team/python-ete3/-/compare/1ccb7a3fe282c6a5b8d538cc54d8cd6d9f574929...fe52ec8644b7dec36539cf763370fea3f9be8ed3
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20231115/7951962d/attachment-0001.htm>
More information about the debian-med-commit
mailing list