def get_html_association(self):
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools")
+ "/gdsctools/data/templates/")
template = env.get_template("boxplot_association.html")
jinja = {}
N = len(self.odof.negatives) + len(self.odof.positives)
jinja["title"] = "Individual Association"
if self.odof.drug_name:
drug_name = "%s (%s)" % (self.drug, self.odof.drug_name)
jinja["subtitle"] = "%s versus %s" % (drug_name, self.feature)
else:
jinja["subtitle"] = "%s versus %s" % (self.drug, self.feature)
jinja['factor'] = ["neg"] * len(self.odof.negatives) + ["pos"] * len(self.odof.positives)
jinja["data"] = self.odof.negatives.tolist() + self.odof.positives.tolist()
jinja["smps"] = [str(this) for this in self.odof.indices]
jinja["subject"] = [str(this) for this in self.odof.indices]
jinja['ylabel'] = '"logIC50"'
html = template.render(jinja)
return html
def get_html_association(self):
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools") + "/gdsctools/data/templates/")
template = env.get_template("boxplot_association.html")
jinja = {}
N = len(self.odof.negatives) + len(self.odof.positives)
jinja["title"] = "Individual Association"
if self.odof.drug_name:
drug_name = "%s (%s)" % (self.drug, self.odof.drug_name)
jinja["subtitle"] = "%s versus %s" % (drug_name, self.feature)
else:
jinja["subtitle"] = "%s versus %s" % (self.drug, self.feature)
jinja['factor'] = ["neg"] * len(self.odof.negatives) + ["pos"] * len(
self.odof.positives)
jinja["data"] = self.odof.negatives.tolist(
) + self.odof.positives.tolist()
jinja["smps"] = [str(this) for this in self.odof.indices]
jinja["subject"] = [str(this) for this in self.odof.indices]
jinja['ylabel'] = '"logIC50"'
html = template.render(jinja)
return html
def get_html_tissue(self):
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools") + "/gdsctools/data/templates/")
template = env.get_template("boxplot_tissue.html")
data = self._get_boxplot_data("tissue")
if data is None:
return ""
# Show from bottom to top
labels = data[1][::-1]
data = data[0][::-1]
jinja = {}
N = len(self.odof.negatives) + len(self.odof.positives)
jinja["title"] = "FEATURE/MS-instability interactions"
jinja["subtitle"] = "%s versus %s" % (self.drug, self.feature)
factor = []
for i, thisdata in enumerate(data):
factor.extend([labels[i]] * len(thisdata))
jinja['sign'] = [x.split()[1] for x in factor]
jinja['status'] = [x.split()[0] for x in factor]
jinja["data"] = list(pylab.flatten([list(this) for this in data]))
jinja['xlabel'] = '"logIC50"'
if len(labels) / 2 >= 10:
jinja["minTextSize"] = 10
html = template.render(jinja)
return html
def get_html_tissue(self):
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools")
+ "/gdsctools/data/templates/")
template = env.get_template("boxplot_tissue.html")
data = self._get_boxplot_data("tissue")
if data is None:
return ""
# Show from bottom to top
labels = data[1][::-1]
data = data[0][::-1]
jinja = {}
N = len(self.odof.negatives) + len(self.odof.positives)
jinja["title"] = "FEATURE/MS-instability interactions"
jinja["subtitle"] = "%s versus %s" % (self.drug, self.feature)
factor = []
for i, thisdata in enumerate(data):
factor.extend( [labels[i]] * len(thisdata))
jinja['sign'] = [x.split()[1] for x in factor]
jinja['status'] = [x.split()[0] for x in factor]
jinja["data"] = list(pylab.flatten([list(this) for this in data]))
jinja['xlabel'] = '"logIC50"'
if len(labels)/2 >= 10:
jinja["minTextSize"] = 10
html = template.render(jinja)
return html
def get_html(self):
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
"""try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
"""
# Jinja related
from easydev import get_package_location
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools") + "/gdsctools/data/templates/")
template = env.get_template("scatter.html")
# We need to cireate 20 different colors
from colormap import Colormap
c = Colormap()
cmap = c.cmap_linear("red", "blue", "yellow", N=20)
colors = self.data[self._colname_color]
colors = ["red" for x in self.data[self._colname_color]]
jinja = {}
jinja["colors"] = ["rgba(205,0,0,0.5)"]
jinja["Group"] = colors
jinja['xlabel'] = '"%s"' % self.xlabel
jinja['ylabel'] = '"%s"' % self.ylabel
selection = [self._colname_x, self._colname_y]
text = []
for index in zip(self.data.index):
text.append("<pre>%s</pre>" %
self.data.ix[index][selection].to_string())
jinja['vars'] = text
#self.data.markersize /= (self.data.markersize.max()/3.)
self.data['markersize'] = 20
selection = [self._colname_x, self._colname_y, self._colname_size]
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[selection].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(self.data[selection]).values.tolist()
jinja[
'title'] = '"Regression coefficient vs Bayes factor for all drugs"'
jinja['minX'] = self.minX
jinja['minY'] = self.minY
jinja['maxX'] = self.maxX
jinja['maxY'] = self.maxY
self.html = template.render(jinja)
return self.html
def get_html(self):
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
"""try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
"""
# Jinja related
from easydev import get_package_location
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools")
+ "/gdsctools/data/templates/")
template = env.get_template("scatter.html")
# We need to cireate 20 different colors
from colormap import Colormap
c = Colormap()
cmap = c.cmap_linear("red", "blue", "yellow", N=20)
colors = self.data[self._colname_color]
colors = ["red" for x in self.data[self._colname_color]]
jinja = {}
jinja["colors"] = ["rgba(205,0,0,0.5)"]
jinja["Group"] = colors
jinja['xlabel'] = '"%s"' % self.xlabel
jinja['ylabel'] = '"%s"' % self.ylabel
text = []
for index in zip(self.data.index):
text.append("<pre>%s</pre>" % self.data.ix[index].to_string())
jinja['vars'] = text
#self.data.markersize /= (self.data.markersize.max()/3.)
self.data['markersize'] = 20
selection = [self._colname_x, self._colname_y, self._colname_size]
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[selection].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(self.data[selection]).values.tolist()
jinja['title'] = '"Regression coefficient/ttest/bayes factor for all drugs"'
jinja['minX'] = 0
jinja['minY'] = 0
jinja['maxX'] = 1
jinja['maxY'] = self.data[self._colname_y].max() * 1.1
self.html = template.render(jinja)
return self.html
def fa_data(filename=None, where=None):
"""retrieve data set path from fragment_analyser/data dir"""
import os
import easydev
import glob
fa_path = easydev.get_package_location('fragment_analyser')
sharedir = os.sep.join([fa_path , "fragment_analyser", 'data'])
filename = sharedir + os.sep + filename
if os.path.exists(filename) is False:
raise Exception('unknown file %s' % filename)
return filename
def gdsctools_data(filename, where=None):
"""Simple utilities to retrieve data sets from gdsctools/share directory"""
gdsctools_path = easydev.get_package_location('gdsctools')
share = os.sep.join([gdsctools_path, "gdsctools", 'data'])
# in the code one may use / or \
if where:
filename = os.sep.join([share, where, filename])
else:
filename = os.sep.join([share, filename])
if os.path.exists(filename) is False:
raise Exception('unknown file %s' % filename)
return filename
def gdsctools_data(filename, where=None):
"""Simple utilities to retrieve data sets from gdsctools/share directory"""
gdsctools_path = easydev.get_package_location('gdsctools')
share = os.sep.join([gdsctools_path, "gdsctools", 'data'])
# in the code one may use / or \
if where:
filename = os.sep.join([share, where, filename])
else:
filename = os.sep.join([share, filename])
if os.path.exists(filename) is False:
raise Exception('unknown file %s' % filename)
return filename
def _init_report(self):
"""create the report directory and return the directory name"""
self.sections = []
self.section_names = []
# if the directory already exists, print a warning
try:
if os.path.isdir(self.directory) is False:
if self.verbose:
print("Created directory {}".format(self.directory))
os.mkdir(self.directory)
# list of directories created in the constructor
for this in self._to_create:
try:
os.mkdir(self.directory + os.sep + this)
except:
pass # already created ?
except Exception:
pass
finally:
# Once the main directory is created, copy files required
temp_path = easydev.get_package_location("reports")
temp_path += os.sep + "reports" + os.sep + "resources"
# Copy the CSS from reports/resources/css
filenames = glob.glob(os.sep.join([temp_path, "css", "*.css"]))
# If there are CSS in the directory with JINJA templates, use them
# as well
filenames += glob.glob(os.sep.join([self.searchpath, '*.css']))
# In addition, the user may also provide his own CSS as a list
filenames += self.extra_css_list
for filename in filenames:
target = os.sep.join([self.directory, 'css'])
if os.path.isfile(target) is False:
shutil.copy(filename, target)
# We copy all javascript from reports resources
for filename in [
'sorttable.js', 'highlight.pack.js', "jquery-1.12.3.min.js"
]:
target = os.sep.join([self.directory, 'js', filename])
if os.path.isfile(target) is False:
filename = os.sep.join([temp_path, "javascript", filename])
shutil.copy(filename, target)
for filename in self.extra_js_list:
basename = os.path.basename(filename)
target = os.sep.join([self.directory, 'js', basename])
if os.path.isfile(target) is False:
shutil.copy(filename, target)
def _init_report(self):
"""create the report directory and return the directory name"""
self.sections = []
self.section_names = []
# if the directory already exists, print a warning
try:
if os.path.isdir(self.directory) is False:
if self.verbose:
print("Created directory {}".format(self.directory))
os.mkdir(self.directory)
# list of directories created in the constructor
for this in self._to_create:
try:
os.mkdir(self.directory + os.sep + this)
except:
pass # already created ?
except Exception:
pass
finally:
# Once the main directory is created, copy files required
temp_path = easydev.get_package_location("reports")
temp_path += os.sep + "reports" + os.sep + "resources"
# Copy the CSS from reports/resources/css
filenames = glob.glob(os.sep.join([temp_path, "css", "*.css"]))
# If there are CSS in the directory with JINJA templates, use them
# as well
filenames += glob.glob(os.sep.join([self.searchpath, '*.css']))
# In addition, the user may also provide his own CSS as a list
filenames += self.extra_css_list
for filename in filenames:
target = os.sep.join([self.directory, 'css' ])
if os.path.isfile(target) is False:
shutil.copy(filename, target)
# We copy all javascript from reports resources
for filename in ['sorttable.js', 'highlight.pack.js', "jquery-1.12.3.min.js"]:
target = os.sep.join([self.directory, 'js', filename ])
if os.path.isfile(target) is False:
filename = os.sep.join([temp_path, "javascript", filename])
shutil.copy(filename, target)
for filename in self.extra_js_list:
basename = os.path.basename(filename)
target = os.sep.join([self.directory, 'js', basename ])
if os.path.isfile(target) is False:
shutil.copy(filename, target)
def biokit_data(filename, where=None):
"""Simple utilities to retrieve data sets from biokit/data directory"""
import os
import easydev
biokit_path = easydev.get_package_location('biokit')
share = os.sep.join([biokit_path , "biokit", 'data'])
# in the code one may use / or \
if where:
filename = os.sep.join([share, where, filename])
else:
filename = os.sep.join([share, filename])
if os.path.exists(filename) is False:
raise Exception('unknown file %s' % filename)
return filename
def bioconvert_data(filename, where=None):
"""Simple utilities to retrieve data sets from bioconvert/data directory"""
import os
import easydev
bioconvert_path = easydev.get_package_location('bioconvert')
share = os.sep.join([bioconvert_path, "bioconvert", 'data'])
# in the code one may use / or \
if where:
filename = os.sep.join([share, where, filename])
else:
filename = os.sep.join([share, filename])
if os.path.exists(filename) is False:
raise Exception('unknown file %s' % filename)
return filename
def write_report(self,
template_name="simple",
template_path=None,
filename="report.html",
prettify=True):
"""
Writes the html report.
Args:
template_name: name of the template to use (only used if template_path is None)
template_path: path of the custom template to use
filename: output file to write
prettify: bool to prettify the output html
Available templates are:
* simple
"""
# If no custom path, use one of the predefined templates
if template_path is None:
relative_uri = f"html_reports/templates/{template_name}.html"
template_uri = os.sep.join(
[easydev.get_package_location("html_reports")] +
relative_uri.split("/"))
# Else, use user template
else:
template_uri = template_path
# Load jinja2 template
template = read_template(template_uri)
# Render jinja2 template
output = template.render(
body="\n".join(self.body),
scripts=self.scripts,
raw_scripts=self.raw_scripts,
styles=self.styles,
**self.args,
)
# Prettify html file
if prettify:
output = BeautifulSoup(output, "html.parser").prettify()
# Write html file
with open(filename, "w") as file:
file.write(output)
def __init__(self,
filename='index.html',
directory='report',
overwrite=True,
verbose=True,
template_filename='index.html',
mode=None,
init_report=True):
""".. rubric:: Constructor
:param filename: default to **index.html**
:param directory: defaults to **report**
:param overwrite: default to True
:param verbose: default to True
:param dependencies: add the dependencies table at the end of the
document if True.
:param str mode: if none, report have a structure that contains the
following directories: OUTPUT, INPUT, js, css, images, code.
Otherwise, if mode is set to 'summary', only the following
directories are created: js, css, images
"""
gdsctools_path = easydev.get_package_location('gdsctools')
extra_css_path = sepjoin([gdsctools_path, "gdsctools", "data", "css"])
extra_js_path = sepjoin(
[gdsctools_path, "gdsctools", "data", "javascript"])
extra_css_list = glob.glob(extra_css_path + os.sep + "*css")
extra_js_list = glob.glob(extra_js_path + os.sep + "*js")
searchpath = sepjoin(
[gdsctools_path, "gdsctools", "data", "templates"])
super(ReportMain, self).__init__(searchpath,
filename=filename,
template_filename=template_filename,
directory=directory,
extra_css_list=extra_css_list,
extra_js_list=extra_js_list,
init_report=init_report)
self.jinja['dependencies'] = self.get_table_dependencies(
"gdsctools").to_html()
self.jinja['analysis'] = 'anova'
from gdsctools import version
self.jinja['version'] = version
self.jinja['title'] = 'ANOVA analysis summary'
self.jinja["analysis_domain"] = "PANCAN"
self.jinja['resource_path'] = "."
self._directory = directory
self._filename = filename
if mode is None:
self._to_create = [
'OUTPUT', 'INPUT', 'images', 'css', 'js', 'code',
'associations'
]
elif mode == 'summary':
self._to_create = [
'images',
'css',
'js',
]
if init_report:
self._init_report()
def _render_data(self, name="all associations"):
self.data['log10pvalue'] = -log10(self.data['pvalue'])
self.data['color'] = self.data['color'].apply(
lambda x: x.replace("black", "not_significant"))
self.data['color'] = self.data['color'].apply(
lambda x: x.replace("green", "sensitive"))
self.data['color'] = self.data['color'].apply(
lambda x: x.replace("red", "resistant"))
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
colors = []
if "not_significant" in self.data.color.values:
colors.append("rgba(0,0,0,0.5)") # black
if "resistant" in self.data.color.values:
colors.append("rgba(205,0,0,0.5)") # red
if "sensitive" in self.data.color.values:
colors.append("rgba(0,205,0,0.5)") # green
env = Environment()
from easydev import get_package_location
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools") + "/gdsctools/data/templates/")
template = env.get_template("volcano.html")
jinja = {}
jinja["colors"] = colors
jinja["Group"] = list(self.data['color'].values)
jinja['xlabel'] = "Signed Effect Size"
jinja['ylabel'] = "-log10(pvalue)"
text = []
for x, y, z in zip(self.data['Drug'].values,
self.data['Feature'].values,
self.data['FDR'].values):
text.append(
"<b>Drug:</b>%s <br><b>Feature:</b>%s <br><b>FDR:</b>%s" %
(x, y, z))
jinja['vars'] = text
"""
# does not work in the JS somehow some points do not appear
# disabled for now
markersize = self.data['markersize']
markersize -= markersize.min()
markersize /= markersize.max()
markersize = (3*markersize).round()
#markersize[markersize == 0] = 1
FC = list(markersize.astype(int).astype(str))
jinja['FC'] = FC
"""
self.data.markersize /= (self.data.markersize.max() / 3.)
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[[
"signed_effect", "log10pvalue", "markersize"
]].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(
self.data[["signed_effect", "log10pvalue",
"markersize"]]).values.tolist()
jinja['title'] = '"%s"' % name
fdrs = self.get_fdr_ypos()
fdrs = [0 if np.isnan(x) else x for x in fdrs]
jinja['additional_fdrs'] = ""
for i, this in enumerate(fdrs):
line = '\n{"color": "red", "width": 1, "type": "dashed", "y": %s}'
if i == len(fdrs) - 1:
pass
else:
line += ","
jinja['additional_fdrs'] += line % this
m = abs(self.data.signed_effect.min())
M = abs(self.data.signed_effect.max())
jinja['minX'] = -max([m, M]) * 1.1
jinja['maxX'] = max([m, M]) * 1.1
jinja['maxY'] = self.data["log10pvalue"].max() * 1.2
if max(fdrs) > jinja['maxY']:
jinja['maxY'] = max(fdrs) * 1.2
self.html = template.render(jinja)
return self.html
import easydev
import os
import tempfile
import subprocess
import sys
sequana_path = easydev.get_package_location('sequana_fastqc')
sharedir = os.sep.join([sequana_path , "sequana_pipelines", 'fastqc', 'data'])
#
def test_standalone_subprocess():
directory = tempfile.TemporaryDirectory()
cmd = "sequana_pipelines_fastqc --input-directory {} "
cmd += "--working-directory {} --run-mode local --force"
cmd = cmd.format(sharedir, directory.name)
subprocess.call(cmd.split())
def test_standalone_script():
directory = tempfile.TemporaryDirectory()
import sequana_pipelines.fastqc.main as m
sys.argv = ["test", "--input-directory", sharedir, "--working-directory",
directory.name, "--run-mode", "local", "--force"]
m.main()
def test_full():
with tempfile.TemporaryDirectory() as directory:
def sequana_data(filename=None, where=None):
"""Return full path of a sequana resource data file.
:param str filename: a valid filename to be found
:param str where: one of the registered data directory (see below)
:return: the path of file. See also here below in the case where
filename is set to "*".
.. code-block:: python
from sequana import sequana_data
filename = sequana_data("test.bam")
Type the function name with "*" parameter to get a list of
available files. Withe where argument set, the function returns a
list of files. Without the where argument, a dictionary is returned where
keys correspond to the registered directories::
filenames = sequana_data("*", where="images")
Registered directories are:
- data
- testing
- data/adapters
- images
.. note:: this does not handle wildcards. The * means retrieve all files.
"""
sequana_path = easydev.get_package_location('sequana')
sharedir = os.sep.join([sequana_path, "sequana", 'resources'])
directories = ['data', 'testing', 'data/adapters', 'images', 'scripts']
if filename == "*":
found = collections.defaultdict(list)
if where is not None:
directories = [where]
for thisdir in directories:
for filename in glob.glob(sharedir + "/%s/*" % thisdir):
filename = os.path.split(filename)[1]
to_ignore = ["__init__.py", "__pycache__"]
if filename.endswith('.pyc') or filename in to_ignore:
pass
else:
found[thisdir].append(os.path.split(filename)[1])
if where is not None:
return found[where]
return found
if filename is None:
for thisdir in directories:
print('From %s directory:' % thisdir)
for filename in glob.glob(sharedir + "/%s/*" % thisdir):
filename = os.path.split(filename)[1]
to_ignore = ["__init__.py", "__pycache__"]
if filename.endswith('.pyc') or filename in to_ignore:
pass
else:
print(' - sequana("%s", "%s")' %
(os.path.split(filename)[1], thisdir))
raise ValueError("Choose a valid file from the list above")
# in the code one may use / or \
if where:
filename = os.sep.join([sharedir, where, filename])
else:
def _get_valid_file(filename, directory):
filename = os.sep.join([sharedir, directory, filename])
if os.path.exists(filename) is False:
return False
else:
return filename
# try to introspect the different directories
# return filename if found otherwise raise error
for thisdir in directories:
if _get_valid_file(filename, thisdir):
return _get_valid_file(filename, thisdir)
raise Exception(
"unknown file %s. Type sequana_data() to get a list of valid names"
% filename)
return filename
import easydev
import os
import tempfile
import subprocess
import sys
sequana_path = easydev.get_package_location('sequana_coverage')
sharedir = os.sep.join([sequana_path, "sequana_pipelines/coverage/data"])
annotation = sharedir + os.sep + "JB409847.gbk"
reference = sharedir + os.sep + "JB409847.fa"
def test_standalone_subprocess():
directory = tempfile.TemporaryDirectory()
cmd = "sequana_pipelines_coverage --input-directory {} "
cmd += "--working-directory {} --force --annotation {} "
cmd += " --reference {} -o "
cmd = cmd.format(sharedir, directory.name, annotation, reference)
subprocess.call(cmd.split())
def test_standalone_script():
directory = tempfile.TemporaryDirectory()
import sequana_pipelines.coverage.main as m
sys.argv = ["test", "--input-directory", sharedir, "--force"]
m.main()
def test_wrong_reference():
directory = tempfile.TemporaryDirectory()
import sequana_pipelines.coverage.main as m
def __init__(self,
searchpath=None,
filename='index.html',
directory='report',
overwrite=True,
verbose=True,
template_filename='index.html',
extra_css_list=[],
extra_js_list=[],
init_report=True):
""".. rubric:: Constructor
:param searchpath: where to find the jina templates.
If not provided, uses the generic template
:param filename: output filename (default to **index.html**)
:param directory: defaults to **report**
:param overwrite: default to True
:param verbose: default to True
:param template_filename: entry point of the jinja code
:param extra_css_list: where to find the extra css
:param extra_js_list: where to find the extra css
:param bool init_report: init the report that is create
the directories to store css and JS.
"""
self.verbose = verbose
self._directory = directory
self._filename = filename
self.extra_css_list = extra_css_list
self.extra_js_list = extra_js_list
# This contains the sections and their names
# Not used yet but could be in jinja templating
self.sections = []
self.section_names = []
#: flag to add dependencies
self.add_dependencies = False
# For jinja2 inheritance, we need to use the environment
# to indicate where are the parents' templates
if searchpath is None:
thispath = easydev.get_package_location('reports')
thispath += os.sep + "reports"
thispath += os.sep + "resources"
self.searchpath = os.sep.join([thispath, 'templates', "generic"])
else:
# path to the template provided by the user
self.searchpath = searchpath
# The JINJA environment
# TODO check that the path exists
self.env = Environment()
self.env.loader = FileSystemLoader(self.searchpath)
# input template file
self.template = self.env.get_template(template_filename)
# This dictionary will be used to populate the JINJA template
self.jinja = {
'time_now': self.get_time_now(),
"title": "Title to be defined",
'dependencies': self.get_table_dependencies().to_html(),
"report_version": _get_report_version()
}
# Directories to create
self._to_create = [
'images',
'css',
'js',
]
# Create directories and stored css/js/images
if init_report:
self._init_report()
import glob
import easydev
from datetime import datetime
time_now = datetime.now().strftime("%m-%d-%Y %H:%M:%S")
# Get sequana informations
version = pkg_resources.get_distribution('sequana').version
script_path = os.path.dirname(os.path.realpath(__file__))
# Default options
output_dir = os.path.realpath(os.getcwd())
def get_entry_name(entry_point):
return str(entry_point).split('=')[0].strip()
# Modules available
module_dict = {get_entry_name(entry_point): entry_point for entry_point
in pkg_resources.iter_entry_points('sequana.module')}
# Find css/js file necessary for the report
sequana_path = easydev.get_package_location('sequana')
css_path = os.sep.join([sequana_path, "sequana", "resources", "css"])
js_path = os.sep.join([sequana_path, "sequana", "resources", "js"])
css_list = glob.glob(css_path + os.sep + "*css")
js_list = glob.glob(js_path + os.sep + "*js")
# Sections list for summary.html
summary_sections = list()
import easydev
import os
import tempfile
import subprocess
import sys
sequana_path = easydev.get_package_location('sequana_revcomp')
sharedir = os.sep.join([sequana_path, "sequana_pipelines", 'revcomp', 'data'])
#
def test_standalone_subprocess():
directory = tempfile.TemporaryDirectory()
cmd = "sequana_pipelines_revcomp --input-directory {} "
cmd += "--working-directory {} --force"
cmd = cmd.format(sharedir, directory.name)
subprocess.call(cmd.split())
def test_standalone_script():
directory = tempfile.TemporaryDirectory()
import sequana_pipelines.revcomp.main as m
sys.argv = [
"test", "--input-directory", sharedir, "--working-directory",
directory.name, "--force"
]
m.main()
def test_full():
def _render_data(self, name="all associations"):
self.data['log10pvalue'] = -log10(self.data['pvalue'])
self.data['color'] = self.data['color'].apply(lambda x:
x.replace("black", "not_significant"))
self.data['color'] = self.data['color'].apply(lambda x:
x.replace("green", "sensitive"))
self.data['color'] = self.data['color'].apply(lambda x:
x.replace("red", "resistant"))
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
colors = []
if "not_significant" in self.data.color.values:
colors.append("rgba(0,0,0,0.5)") # black
if "resistant" in self.data.color.values:
colors.append("rgba(205,0,0,0.5)") # red
if "sensitive" in self.data.color.values:
colors.append("rgba(0,205,0,0.5)") # green
env = Environment()
from easydev import get_package_location
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools")
+ "/gdsctools/data/templates/")
template = env.get_template("volcano.html")
jinja = {}
jinja["colors"] = colors
jinja["Group"] = list(self.data['color'].values)
jinja['xlabel'] = "Signed Effect Size"
jinja['ylabel'] = "-log10(pvalue)"
text = []
for x,y,z in zip(self.data['Drug'].values,
self.data['Feature'].values,
self.data['FDR'].values):
text.append("<b>Drug:</b>%s <br><b>Feature:</b>%s <br><b>FDR:</b>%s" % (x,y,z))
jinja['vars'] = text
"""
# does not work in the JS somehow some points do not appear
# disabled for now
markersize = self.data['markersize']
markersize -= markersize.min()
markersize /= markersize.max()
markersize = (3*markersize).round()
#markersize[markersize == 0] = 1
FC = list(markersize.astype(int).astype(str))
jinja['FC'] = FC
"""
self.data.markersize /= (self.data.markersize.max()/3.)
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[["signed_effect", "log10pvalue",
"markersize"]].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(self.data[["signed_effect", "log10pvalue",
"markersize"]]).values.tolist()
jinja['title'] = '"%s"' % name
fdrs = self.get_fdr_ypos()
fdrs = [0 if np.isnan(x) else x for x in fdrs]
jinja['additional_fdrs'] = ""
for i,this in enumerate(fdrs):
line = '\n{"color": "red", "width": 1, "type": "dashed", "y": %s}'
if i == len(fdrs)-1:
pass
else:
line += ","
jinja['additional_fdrs'] += line % this
m = abs(self.data.signed_effect.min())
M = abs(self.data.signed_effect.max())
jinja['minX'] = -max([m, M]) * 1.1
jinja['maxX'] = max([m, M]) * 1.1
jinja['maxY'] = self.data["log10pvalue"].max() * 1.2
if max(fdrs) > jinja['maxY']:
jinja['maxY'] = max(fdrs) * 1.2
self.html = template.render(jinja)
return self.html
def __init__(self,
searchpath=None,
filename='index.html',
directory='report',
overwrite=True,
verbose=True,
template_filename='index.html',
extra_css_list=[],
extra_js_list=[],
init_report=True):
""".. rubric:: Constructor
:param searchpath: where to find the jina templates.
If not provided, uses the generic template
:param filename: output filename (default to **index.html**)
:param directory: defaults to **report**
:param overwrite: default to True
:param verbose: default to True
:param template_filename: entry point of the jinja code
:param extra_css_list: where to find the extra css
:param extra_js_list: where to find the extra css
:param bool init_report: init the report that is create
the directories to store css and JS.
"""
self.verbose = verbose
self._directory = directory
self._filename = filename
self.extra_css_list = extra_css_list
self.extra_js_list = extra_js_list
# This contains the sections and their names
# Not used yet but could be in jinja templating
self.sections = []
self.section_names = []
#: flag to add dependencies
self.add_dependencies = False
# For jinja2 inheritance, we need to use the environment
# to indicate where are the parents' templates
if searchpath is None:
thispath = easydev.get_package_location('reports')
thispath += os.sep + "reports"
thispath += os.sep + "resources"
self.searchpath = os.sep.join([thispath, 'templates', "generic"])
else:
# path to the template provided by the user
self.searchpath = searchpath
# The JINJA environment
# TODO check that the path exists
self.env = Environment()
self.env.loader = FileSystemLoader(self.searchpath)
# input template file
self.template = self.env.get_template(template_filename)
# This dictionary will be used to populate the JINJA template
self.jinja = {
'time_now': self.get_time_now(),
"title": "Title to be defined",
'dependencies': self.get_table_dependencies().to_html(),
"report_version": _get_report_version()
}
# Directories to create
self._to_create = ['images', 'css', 'js',]
# Create directories and stored css/js/images
if init_report:
self._init_report()
def __init__(
self,
filename="index.html",
directory="report",
overwrite=True,
verbose=True,
template_filename="index.html",
mode=None,
init_report=True,
):
""".. rubric:: Constructor
:param filename: default to **index.html**
:param directory: defaults to **report**
:param overwrite: default to True
:param verbose: default to True
:param dependencies: add the dependencies table at the end of the
document if True.
:param str mode: if none, report have a structure that contains the
following directories: OUTPUT, INPUT, js, css, images, code.
Otherwise, if mode is set to 'summary', only the following
directories are created: js, css, images
"""
gdsctools_path = easydev.get_package_location("gdsctools")
extra_css_path = sepjoin([gdsctools_path, "gdsctools", "data", "css"])
extra_js_path = sepjoin([gdsctools_path, "gdsctools", "data", "javascript"])
extra_css_list = glob.glob(extra_css_path + os.sep + "*css")
extra_js_list = glob.glob(extra_js_path + os.sep + "*js")
searchpath = sepjoin([gdsctools_path, "gdsctools", "data", "templates"])
super(ReportMain, self).__init__(
searchpath,
filename=filename,
template_filename=template_filename,
directory=directory,
extra_css_list=extra_css_list,
extra_js_list=extra_js_list,
init_report=init_report,
)
self.jinja["dependencies"] = self.get_table_dependencies("gdsctools").to_html()
self.jinja["analysis"] = "anova"
from gdsctools import version
self.jinja["version"] = version
self.jinja["title"] = "ANOVA analysis summary"
self.jinja["analysis_domain"] = "PANCAN"
self.jinja["resource_path"] = "."
self._directory = directory
self._filename = filename
if mode is None:
self._to_create = ["OUTPUT", "INPUT", "images", "css", "js", "code", "associations"]
elif mode == "summary":
self._to_create = ["images", "css", "js"]
if init_report:
self._init_report()
