3513662673

Build Type

github

Committed by GitHub

Commit Message

<a href="https://github.com/sequana/sequana/commit/<a class=hub.com/sequana/sequana/commit/<a class="double-link" href="https://git"><a class=hub.com/sequana/sequana/commit/<a class="double-link" href="https://git"><a class=hub.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10eec">e5f90e784<a href="https://github.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10eec">&quot;&gt;&amp;lt;a href=&amp;quot;https://github.com/sequana/sequana/commit/&lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/sequana/sequana/commit/&amp;lt;a class=&amp;quot;double-link&amp;quot; href=&amp;quot;https://git&quot;&gt;&amp;lt;a class=&lt;/a&gt;hub.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10eec&quot;&gt;e5f90e784&lt;/a&gt;&lt;a href=&quot;https://github.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10eec&quot;&gt;&amp;lt;a href=&amp;quot;https://github.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f1&lt;/a&gt;6bd10eec">&quot;&gt;Merge &lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/sequana/sequana/commit/&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/sequana/sequana/commit/<a class="double-link" href="https://github.com/sequana/sequana/commit/299660d2d71207614fc9204ba939f90c6e3f4d57">299660d2d</a><a href="https://github.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10eec">&amp;quot;&amp;gt;299660d2d&amp;lt;/a&amp;gt;&amp;quot;&amp;gt;299660d2d&amp;lt;/a&amp;gt;&amp;lt;a href=&amp;quot;https://github.com/sequana/sequana/commit/e5f90e78457ec3da590d38e6370367f16bd10&lt;/a&gt;eec&quot;&gt; into &lt;/a&gt;&lt;a class=&quot;double-link&quot; href=&quot;https://github.com/sequana/sequana/commit/<a class="double-link" href="https://github.com/sequana/sequana/commit/bcfa4acec">bcfa4acec">bcfa4acec</a>

Pull Request Pull Request #778: add snpeff build options

Run Details

12 of 12 new or added lines in 2 files covered. (100.0%)

11936 of 17079 relevant lines covered (69.89%)

2.1 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

62.0

/sequana/itol.py

#
#  This file is part of Sequana software
#
#  Copyright (c) 2016-2022 - Sequana Development Team
#
#  Distributed under the terms of the 3-clause BSD license.
#  The full license is in the LICENSE file, distributed with this software.
#
#  website: https://github.com/sequana/sequana
#  documentation: http://sequana.readthedocs.io
#
##############################################################################
import colorlog
from pathlib import Path

logger = colorlog.getLogger(__name__)


from itolapi import Itol
from itolapi.itol import ItolExport


__all__ = ["ITOL"]


class ITOL:
    """

    Tree with branch lengths::

       (A:0.1,(B:0.1,C:0.1)));

    Tree with bootstrap and branch lengths::

       (A:0.1,(B:0.1,C:0.1)90:0.1)98:0.3);

    ::

        from pylab import imshow, imread
        from easydev import TempFile
        from sequana import ITOL, sequana_data

        # You mut have an APIkey and project name defined on itol web site.
        itol = ITOL(sequana_data("test_itol_basic.tree.txt"), APIkey, projectName)
        itol.upload()
        # You can change the parameters in itol.params
        itol.params["display_mode"] = 1  # use linear layout instead of circular

        # finally export your image locally:
        with TempFile(suffix=".png") as fout:
            itol.export(fout.name)
            imshow(imread(fout.name))


    For details, please see https://itol.embl.de/help.cgi#annot Here are some
    parameters:

    * display_mode: 1,2 or 3 (1=rectangular, 2=circular, 3=unrooted)



    """

    def __init__(self, tree, APIkey=None, projectName=None):
        """.. rubric:: constructor"""
        
        self.itol = Itol()
        assert tree.endswith(".tree.txt"), "Your input tree must end in .tree.txt"

        try:
            self.itol.add_file(tree)
        except AttributeError:
            self.itol.add_file(Path(tree))
        self._datasets = 0
        self.status = None

        # datasets_visible should not be used if there is no datasets.
        #
        self.params = {
            "display_mode": 2,  # rotation
            "ignore_branch_length": 1,
            "line_width": 5,
            # "datasets_visible": "0,1",
            "bootstrap_display": 1,
            "bootstrap_type": 2,
            "bootstrap_label_size": 32,
        }

        if APIkey:
            self.params["APIkey"] = APIkey
            self.params["projectName"] = projectName

    def add_file(self, filename):
        try: # itol 4.0.1
            self.itol.add_file(filename)
        except AttributeError: #itol 4.1.0
            self.itol.add_file(Path(filename))
        N = len(self.itol.files) - 1  # remove the input tree file
        self.params["datasets_visible"] = ",".join([str(x) for x in range(0, N)])

    def upload(self):
        self.itol.params = self.params
        self.status = self.itol.upload()
        if not self.status:
            logger.error("Something is wrong with your input tree")
            logger.error(self.itol.comm.upload_output)
            raise ItolExport

    def export(self, filename="test.png", extra_params={}, tree_id=None, circular=True):
        """Export or retrieve an existing tree to get back the resulting image

        :param str filename: the filename where to store the image
        :param extra_params: parameters use to tune the trre are stored in
            :attr:`params` but you may provide extra parameters here ot alter
            some. If you this paramterm, the main attribute  :attr:`params` is unchanged.
        :param tree_id: if you have a known tree identifier, you can retrieve it using the
           **tree_id** parameter. Otherwise, if you have just uploaded a
           tree with :meth:`upload`, the
           identifier is automatically populated and that is the tree you will
           export.


        """

        if self.status is None and tree_id is None:
            logger.error("Upload the tree first with upload() method")

        export = self.itol.get_itol_export()
        export.params.update(**self.params)
        export.params.update(**extra_params)

        # replace tree id by user tree id if any. Otherwise, the user must have
        # used the upload() method first.
        if tree_id:
            export.params["tree"] = tree_id

        # display mode set to 1 means circular, 2 means linear.
        export.params["display_mode"] = 2 if circular else 1

        # Set the output format to png/svg/epd/pdf
        extension = filename.split(".")[-1]
        if extension in {"png", "svg", "pdf", "eps"}:
            logger.info(f"Exporting in {extension} format")
            export.params["format"] = extension
        else:
            raise ValueError("filename must end in pdf, png, svg or eps")

        export.export(filename)

        self.last_export = export

1	#
2	# This file is part of Sequana software
3	#
4	# Copyright (c) 2016-2022 - Sequana Development Team
5	#
6	# Distributed under the terms of the 3-clause BSD license.
7	# The full license is in the LICENSE file, distributed with this software.
8	#
9	# website: https://github.com/sequana/sequana
10	# documentation: http://sequana.readthedocs.io
11	#
12	##############################################################################
13	import colorlog	3✔
14	from pathlib import Path	3✔
15
16	logger = colorlog.getLogger(__name__)	3✔
17
18
19	from itolapi import Itol	3✔
20	from itolapi.itol import ItolExport	3✔
21
22
23	__all__ = ["ITOL"]	3✔
24
25
26	class ITOL:	3✔
27	"""
28
29	Tree with branch lengths::
30
31	(A:0.1,(B:0.1,C:0.1)));
32
33	Tree with bootstrap and branch lengths::
34
35	(A:0.1,(B:0.1,C:0.1)90:0.1)98:0.3);
36
37	::
38
39	from pylab import imshow, imread
40	from easydev import TempFile
41	from sequana import ITOL, sequana_data
42
43	# You mut have an APIkey and project name defined on itol web site.
44	itol = ITOL(sequana_data("test_itol_basic.tree.txt"), APIkey, projectName)
45	itol.upload()
46	# You can change the parameters in itol.params
47	itol.params["display_mode"] = 1 # use linear layout instead of circular
48
49	# finally export your image locally:
50	with TempFile(suffix=".png") as fout:
51	itol.export(fout.name)
52	imshow(imread(fout.name))
53
54
55	For details, please see https://itol.embl.de/help.cgi#annot Here are some
56	parameters:
57
58	* display_mode: 1,2 or 3 (1=rectangular, 2=circular, 3=unrooted)
59
60
61
62	"""
63
64	def __init__(self, tree, APIkey=None, projectName=None):	3✔
65	""".. rubric:: constructor"""
66
67	self.itol = Itol()	3✔
68	assert tree.endswith(".tree.txt"), "Your input tree must end in .tree.txt"	3✔
69
70	try:	3✔
71	self.itol.add_file(tree)	3✔
72	except AttributeError:	3✔
73	self.itol.add_file(Path(tree))	3✔
74	self._datasets = 0	3✔
75	self.status = None	3✔
76
77	# datasets_visible should not be used if there is no datasets.
78	#
79	self.params = {	3✔
80	"display_mode": 2, # rotation
81	"ignore_branch_length": 1,
82	"line_width": 5,
83	# "datasets_visible": "0,1",
84	"bootstrap_display": 1,
85	"bootstrap_type": 2,
86	"bootstrap_label_size": 32,
87	}
88
89	if APIkey:	3✔
90	self.params["APIkey"] = APIkey	×
91	self.params["projectName"] = projectName	×
92
93	def add_file(self, filename):	3✔
94	try: # itol 4.0.1	×
95	self.itol.add_file(filename)	×
96	except AttributeError: #itol 4.1.0	×
97	self.itol.add_file(Path(filename))	×
98	N = len(self.itol.files) - 1 # remove the input tree file	×
99	self.params["datasets_visible"] = ",".join([str(x) for x in range(0, N)])	×
100
101	def upload(self):	3✔
102	self.itol.params = self.params	×
103	self.status = self.itol.upload()	×
104	if not self.status:	×
105	logger.error("Something is wrong with your input tree")	×
106	logger.error(self.itol.comm.upload_output)	×
107	raise ItolExport	×
108
109	def export(self, filename="test.png", extra_params={}, tree_id=None, circular=True):	3✔
110	"""Export or retrieve an existing tree to get back the resulting image
111
112	:param str filename: the filename where to store the image
113	:param extra_params: parameters use to tune the trre are stored in
114	:attr:`params` but you may provide extra parameters here ot alter
115	some. If you this paramterm, the main attribute :attr:`params` is unchanged.
116	:param tree_id: if you have a known tree identifier, you can retrieve it using the
117	tree_id parameter. Otherwise, if you have just uploaded a
118	tree with :meth:`upload`, the
119	identifier is automatically populated and that is the tree you will
120	export.
121
122
123	"""
124
125	if self.status is None and tree_id is None:	3✔
126	logger.error("Upload the tree first with upload() method")	3✔
127
128	export = self.itol.get_itol_export()	3✔
129	export.params.update(**self.params)	3✔
130	export.params.update(**extra_params)	3✔
131
132	# replace tree id by user tree id if any. Otherwise, the user must have
133	# used the upload() method first.
134	if tree_id:	3✔
135	export.params["tree"] = tree_id	×
136
137	# display mode set to 1 means circular, 2 means linear.
138	export.params["display_mode"] = 2 if circular else 1	3✔
139
140	# Set the output format to png/svg/epd/pdf
141	extension = filename.split(".")[-1]	3✔
142	if extension in {"png", "svg", "pdf", "eps"}:	3✔
143	logger.info(f"Exporting in {extension} format")	×
144	export.params["format"] = extension	×
145	else:
146	raise ValueError("filename must end in pdf, png, svg or eps")	3✔
147
148	export.export(filename)	×
149
150	self.last_export = export	×

sequana / sequana / 3513662673

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous