def test_drugs():
r1 = DrugDecode(testing.drug_test_csv)
r1.drugIds
r2 = DrugDecode(testing.drug_test_tsv)
r2.drugIds
assert r1 == r2
# r1.get_info() this example fails because all webrelease are NAN
assert len(r1) == 11
dd = DrugDecode(gdsctools_data("test_drug_decode_comp.csv"))
assert dd.companies == ["ME"]
assert dd.is_public(5) == 'Y'
dd.check()
assert dd.get_info()['N_prop'] == 1
# test repr and print
print(dd)
dd
# test __add__
assert dd + dd == dd
assert len(dd.get_public_and_one_company("ME")) == 10
def test_drugs():
r1 = DrugDecode(testing.drug_test_csv)
r1.drugIds
r2 = DrugDecode(testing.drug_test_tsv)
r2.drugIds
assert r1 == r2
# r1.get_info() this example fails because all webrelease are NAN
assert len(r1) == 11
dd = DrugDecode(gdsctools_data("test_drug_decode_comp.csv"))
assert dd.companies == ["ME"]
assert dd.is_public(5) == 'Y'
dd.check()
assert dd.get_info()['N_prop'] == 1
# test repr and print
print(dd)
dd
# test __add__
assert dd + dd == dd
assert len(dd.get_public_and_one_company("ME")) == 10
def _create_summary_pages(self,
main_directory,
verbose=True,
company=None):
# Read all directories in tissue_packages
directories = glob.glob(main_directory + os.sep + '*')
summary = []
for directory in sorted(directories):
tcga = directory.split(os.sep)[-1]
if tcga not in self.tcga:
continue
if verbose:
print(directory, tcga)
# number of hits
path = directory + os.sep + 'OUTPUT' + os.sep
try:
hits = pd.read_csv(path + 'drugs_summary.csv', sep=',')
except:
summary.append([tcga] + [None] * 5)
continue
total_hits = hits.total.sum()
drug_involved = hits['Unnamed: 0'].unique()
results = ANOVAResults(path + 'results.csv')
if len(results) > 0:
drug_ids = results.df.DRUG_ID.unique()
else:
drug_ids = []
# where to find the DRUG DECODE file. Should
# have been copied
path = directory + os.sep + 'INPUT' + os.sep
drug_decode = DrugDecode(path + 'DRUG_DECODE.csv')
info = drug_decode.get_info()
webrelease = drug_decode.df.ix[drug_involved].WEBRELEASE
drug_inv_public = sum(webrelease == 'Y')
drug_inv_prop = sum(webrelease != 'Y')
summary.append([
tcga, total_hits, drug_inv_prop, info['N_prop'],
drug_inv_public, info['N_public']
])
df = pd.DataFrame(summary)
df.columns = [
'Analysis name', 'Number of hits',
'Number of involved proprietary compounds', 'out of',
'Number of involved public', 'out of'
]
try:
df.sort_values(by="Number of hits", ascending=False, inplace=True)
except:
df.sort("Number of hits", ascending=False, inplace=True)
output_dir = main_directory + os.sep + '..' + os.sep
output_file = output_dir + os.sep + 'index.html'
self.html_page = ReportMain(directory=main_directory,
filename='index.html',
template_filename='datapack_summary.html',
mode="summary")
# Let us use our HTMLTable to add the HTML references
self.html_table = HTMLTable(df)
self.html_table.add_href('Analysis name',
newtab=True,
url=None,
suffix='/index.html')
self.html_table.add_bgcolor('Number of hits')
self.html_page.jinja['data_table'] = self.html_table.to_html(
collapse_table=False)
if company:
self.html_page.jinja["collaborator"] = company
self.html_page.write()
return df
def _create_summary_pages(self, main_directory, verbose=True,
company=None):
# Read all directories in tissue_packages
directories = glob.glob(main_directory + os.sep + '*')
summary = []
for directory in sorted(directories):
tcga = directory.split(os.sep)[-1]
if tcga not in self.tcga:
continue
if verbose:
print(directory, tcga)
# number of hits
path = directory + os.sep + 'OUTPUT' + os.sep
try:
hits = pd.read_csv(path + 'drugs_summary.csv', sep=',')
except:
summary.append([tcga] + [None] * 5)
continue
total_hits = hits.total.sum()
drug_involved = hits['Unnamed: 0'].unique()
results = ANOVAResults(path + 'results.csv')
if len(results) > 0:
drug_ids = results.df.DRUG_ID.unique()
else:
drug_ids = []
# where to find the DRUG DECODE file. Should
# have been copied
path = directory + os.sep + 'INPUT' + os.sep
drug_decode = DrugDecode(path + 'DRUG_DECODE.csv')
info = drug_decode.get_info()
webrelease = drug_decode.df.ix[drug_involved].WEBRELEASE
drug_inv_public = sum(webrelease == 'Y')
drug_inv_prop = sum(webrelease != 'Y')
summary.append([tcga, total_hits,
drug_inv_prop, info['N_prop'],
drug_inv_public, info['N_public']])
df = pd.DataFrame(summary)
df.columns = ['Analysis name', 'Number of hits',
'Number of involved proprietary compounds', 'out of',
'Number of involved public', 'out of']
try:
df.sort_values(by="Number of hits", ascending=False, inplace=True)
except:
df.sort("Number of hits", ascending=False, inplace=True)
output_dir = main_directory + os.sep + '..' + os.sep
output_file = output_dir + os.sep + 'index.html'
self.html_page = ReportMain(directory=main_directory,
filename='index.html',
template_filename='datapack_summary.html',
mode="summary")
# Let us use our HTMLTable to add the HTML references
self.html_table = HTMLTable(df)
self.html_table.add_href('Analysis name', newtab=True, url=None,
suffix='/index.html')
self.html_table.add_bgcolor('Number of hits')
self.html_page.jinja['data_table'] = self.html_table.to_html(
collapse_table=False)
if company:
self.html_page.jinja["collaborator"] = company
self.html_page.write()
return df
def create_summary_pages(self, main_directory="tissue_packages"):
# Read in ALL all directories
# create directories and copy relevant files
directories = glob.glob(main_directory + os.sep + '*')
directories = [x for x in directories if os.path.isdir(x)]
summary = []
for directory in sorted(directories):
tcga = directory.split(os.sep)[1]
if tcga in ['css', 'images', 'INPUT', 'OUTPUT', 'code', 'js' ]:
continue
# number of hits
path = directory + os.sep + 'OUTPUT' + os.sep
try:
hits = pd.read_csv(path + 'drugs_summary.csv', sep=',')
except:
summary.append([tcga] + [None] * 5)
continue
total_hits = hits.total.sum()
drug_involved = get_drug_id(hits['Unnamed: 0'].unique())
results = ANOVAResults(path + 'results.csv')
if len(results) > 0:
drug_ids = get_drug_id(results.df.DRUG_ID.unique())
else:
drug_ids = []
path = directory + os.sep + 'INPUT' + os.sep
drug_decode = DrugDecode(path + 'DRUG_DECODE.csv')
info = drug_decode.get_info()
webrelease = drug_decode.df.ix[drug_involved].WEBRELEASE
drug_inv_public = sum(webrelease == 'Y')
drug_inv_prop = sum(webrelease != 'Y')
summary.append([tcga, total_hits,
drug_inv_prop, info['N_prop'],
drug_inv_public, info['N_public']])
df = pd.DataFrame(summary)
df.columns = ['Analysis name', 'Number of hits',
'Number of involved proprietary compounds', 'out of',
'Number of involved public', 'out of']
# FIXME include css and images of logo
# FIXME save in the proper directory
output_dir = main_directory + os.sep
output_file = output_dir + os.sep + 'index.html'
self.html_page = ReportMAIN(directory=main_directory,
filename='index.html',
template_filename='datapack_summary.html')
# Let us use our HTMLTable to add the HTML references
self.html_table = HTMLTable(df)
self.html_table.add_href('Analysis name', newtab=True, url=None,
suffix='/index.html')
#html_table.add_bgcolor('Number of hits')
self.html_page.jinja['data_table'] = self.html_table.to_html()
self.html_page.jinja['collaborator'] = main_directory
#self.html_page.jinja['analysis_domain'] = 'v18'
self.html_page.write()
return df
def create_summary_pages(self, main_directory='ALL'):
# Read in ALL all directories
# create directories and copy relevant files
self.mkdir(main_directory + os.sep + 'images')
self.mkdir(main_directory + os.sep + 'css')
self.mkdir(main_directory + os.sep + 'js')
from gdsctools import gdsctools_data
for filename in ['gdsc.css', 'github-gist.css']:
target = os.sep.join([main_directory, 'css', filename ])
if os.path.isfile(target) is False:
filename = gdsctools_data(filename)
shutil.copy(filename, target)
for filename in ['highlight.pack.js']:
target = os.sep.join([main_directory, 'js', filename ])
if os.path.isfile(target) is False:
filename = gdsctools_data(filename)
shutil.copy(filename, target)
for filename in ['EBI_logo.png', 'sanger-logo.png']:
target = os.sep.join([main_directory, 'images', filename ])
if os.path.isfile(target) is False:
dire = 'data' + os.sep + 'images'
filename = gdsctools_data("images" + os.sep +filename)
shutil.copy(filename, target)
directories = glob.glob('ALL' + os.sep + '*')
directories = [x for x in directories if os.path.isdir(x)]
summary = []
for directory in sorted(directories):
tcga = directory.split(os.sep)[1]
if tcga in ['css', 'images']:
continue
# number of hits
path = directory + os.sep + 'OUTPUT' + os.sep
try:
hits = pd.read_csv(path + 'drugs_summary.csv', sep=',')
except:
summary.append([tcga] + [None] * 5)
continue
total_hits = hits.total.sum()
drug_involved = get_drug_id(hits['Unnamed: 0'].unique())
results = ANOVAResults(path + 'results.csv')
if len(results)>0:
drug_ids = get_drug_id(results.df.DRUG_ID.unique())
else:
drug_ids = []
path = directory + os.sep + 'INPUT' + os.sep
drug_decode = DrugDecode(path + 'DRUG_DECODE.csv')
info = drug_decode.get_info()
webrelease = drug_decode.df.ix[drug_involved].WEBRELEASE
drug_inv_public = sum(webrelease == 'Y')
drug_inv_prop = sum(webrelease != 'Y')
summary.append([tcga, total_hits,
drug_inv_prop, info['N_prop'],
drug_inv_public, info['N_public']])
df = pd.DataFrame(summary)
df.columns = ['Analysis name', 'Number of hits',
'Number of involved proprietary compounds', 'out of',
'Number of involved public', 'out of']
# FIXME include css and images of logo
# FIXME save in the proper directory
output_dir = main_directory + os.sep + '..' + os.sep
output_file = output_dir + os.sep + 'index.html'
self.html_page = ReportMAIN(directory='ALL', filename='index.html',
template_filename='datapack_summary.html' )
# Let us use our HTMLTable to add the HTML references
from gdsctools.report import HTMLTable
self.html_table = HTMLTable(df)
self.html_table.add_href('Analysis name', newtab=True, url=None,
suffix='/index.html')
#html_table.add_bgcolor('Number of hits')
self.html_page.jinja['data_table'] = self.html_table.to_html()
self.html_page.write()
return df
def create_summary_pages(self, main_directory='ALL'):
# Read in ALL all directories
# create directories and copy relevant files
self.mkdir(main_directory + os.sep + 'images')
self.mkdir(main_directory + os.sep + 'css')
self.mkdir(main_directory + os.sep + 'js')
from gdsctools import gdsctools_data
for filename in ['gdsc.css', 'github-gist.css']:
target = os.sep.join([main_directory, 'css', filename])
if os.path.isfile(target) is False:
filename = gdsctools_data(filename)
shutil.copy(filename, target)
for filename in ['highlight.pack.js']:
target = os.sep.join([main_directory, 'js', filename])
if os.path.isfile(target) is False:
filename = gdsctools_data(filename)
shutil.copy(filename, target)
for filename in ['EBI_logo.png', 'sanger-logo.png']:
target = os.sep.join([main_directory, 'images', filename])
if os.path.isfile(target) is False:
dire = 'data' + os.sep + 'images'
filename = gdsctools_data("images" + os.sep + filename)
shutil.copy(filename, target)
directories = glob.glob('ALL' + os.sep + '*')
directories = [x for x in directories if os.path.isdir(x)]
summary = []
for directory in sorted(directories):
tcga = directory.split(os.sep)[1]
if tcga in ['css', 'images']:
continue
# number of hits
path = directory + os.sep + 'OUTPUT' + os.sep
try:
hits = pd.read_csv(path + 'drugs_summary.csv', sep=',')
except:
summary.append([tcga] + [None] * 5)
continue
total_hits = hits.total.sum()
drug_involved = get_drug_id(hits['Unnamed: 0'].unique())
results = ANOVAResults(path + 'results.csv')
if len(results) > 0:
drug_ids = get_drug_id(results.df.DRUG_ID.unique())
else:
drug_ids = []
path = directory + os.sep + 'INPUT' + os.sep
drug_decode = DrugDecode(path + 'DRUG_DECODE.csv')
info = drug_decode.get_info()
webrelease = drug_decode.df.ix[drug_involved].WEBRELEASE
drug_inv_public = sum(webrelease == 'Y')
drug_inv_prop = sum(webrelease != 'Y')
summary.append([
tcga, total_hits, drug_inv_prop, info['N_prop'],
drug_inv_public, info['N_public']
])
df = pd.DataFrame(summary)
df.columns = [
'Analysis name', 'Number of hits',
'Number of involved proprietary compounds', 'out of',
'Number of involved public', 'out of'
]
# FIXME include css and images of logo
# FIXME save in the proper directory
output_dir = main_directory + os.sep + '..' + os.sep
output_file = output_dir + os.sep + 'index.html'
self.html_page = ReportMAIN(directory='ALL',
filename='index.html',
template_filename='datapack_summary.html')
# Let us use our HTMLTable to add the HTML references
from gdsctools.report import HTMLTable
self.html_table = HTMLTable(df)
self.html_table.add_href('Analysis name',
newtab=True,
url=None,
suffix='/index.html')
#html_table.add_bgcolor('Number of hits')
self.html_page.jinja['data_table'] = self.html_table.to_html()
self.html_page.write()
return df
