def findpath(startdir,target):
os.curdir(startdir)
file=os.listdir(os.curdir)
for eachfile in file:
if os.path.isfile(eachfile):
if eachfile==target:
print(os.getcwd()+os.sep+target)
if os.path.isdir(eachfile):
findpath(eachfile,target)
os.curdir(os.pardir)
def chazhaolujing(startdir,target):
os.curdir(startdir)
file=os.listdir(os.curdir)
for eachfile in file:
if os.path.isfile(eachfile):
ext=os.path.splitext(eachfile)[1]
if ext in target:
return (os.getcwd()+os.sep+ext+os.linesep)
if os.path.isdir(eachfile):
chazhaolujing(eachfile,target)
os.chdir(os.pardir)
def zonalStats(inputf,raster):
""" Run zonal statistics """
try:
logging.info("Computing zonal statistics...")
output = os.path.join(os.path.dirname(inputf),'zonalstats.dbf')
logging.error('%s %s %s' % (inputf,raster,output))
os.curdir('/tmp')
arcpy.gp.ZonalStatisticsAsTable_sa(inputf,"NEAR_FID",raster, output, "DATA","ALL")
#arcpy.gp.ZonalStatisticsAsTable_sa('/tmp/tmp9RkU25/hotspot_areas.shp',"NEAR_FID",'/tmp/tmp9RkU25/scaled_20100607.010500.img','/tmp/tmp9RkU25/output.dbf',"DATA","ALL")
os.curdir(os.path.dirname(inputf))
except:
logging.error("Something happened during %s" % funcname())
logging.error(sys.exc_info())
def save_as_bitmap(self):
if self.selected_dir is None:
self.selected_dir = os.curdir()
save_filename = tkFileDialog.asksaveasfilename(initialdir=self.selected_dir, defaultextension='.bmp',
filetypes=[('Bitmap Image', '.bmp')])
print save_filename
self.modified_mask_image_label.pil_image.save(save_filename)
def Execute(self, temp_dir, main_form):
""" Run a simulation.
var
OldDir: String
AppTitle: String
"""
# Change the current directory to the application's temporary directory
old_dir = os.curdir()
os.chdir(temp_dir)
# Update the form's display
#Update
# Save the title Windows' uses for the application
app_title = main_form.getText()
# Run the simulation
self.RunSimulation()
# Restore the application's title
main_form.setText(app_title)
# Change back to the original directory
os.chdir(old_dir)
# Display the run's status on the ResultsPage of the form
self.DisplayRunStatus()
class Mapper:
#map out files{} -> classes{} & Imports{} -> functions{{inputs:[],returns:[]}
#moduleMap = files{{classes{functions{{inputs:[],returns:[]},"imports":[]}
moduleMap = {"files": {}}
RootJsfileList = []
RootDir = os.curdir() #or js library folder path
def __init__(self):
pass
def find_all_js_files(self, RootDir=RootDir):
for root, dirnames, filenames in os.walk(RootDir):
for filename in fnmatch.filter(filenames, '*.js'):
self.moduleMap["files"] += {str(filename): ""}
def find_imports_in_file(self):
imports = re.findall()
return imports
def find_all_classes_in_file(self):
pass
def find_all_functions_in_class(self):
pass
def get_inputs_from_function(self):
pass
def parseJSfile(self):
pass
def test_merge_utility(self, resource_group):
app_name = 'helloWorldApp'
yaml_files_path = "%s,%s,%s" % (_get_test_data_file('app.yaml'),
_get_test_data_file('service.yaml'),
_get_test_data_file('network.yaml'))
self.kwargs.update({
'resource_id':
'',
'resource_group':
resource_group,
'deployment_name':
self.create_random_name(prefix='cli', length=24),
'app_name':
app_name,
'input_yaml_files':
yaml_files_path
})
# Test create
self.cmd(
'az mesh deployment create -g {rg} --input-yaml-files {input_yaml_files} --name {deployment_name}'
)
# Test delete
self.cmd('az mesh app delete -g {rg} --name {app_name} --yes')
# Delete the generated ARM template
os.path.delete(os.path.combine(os.curdir(), 'merged-arm_rp.json'))
def __init__(self, web_url, username=None, password=None, logpath=None):
self.web_url = web_url
self.username = username
self.password = password
if logpath:
self.logpath = logpath
else:
self.logpath = os.curdir()
def trainWordEmbeddGensim():
if "model.bin" in os.curdir("."):
return
else:
model = Word2Vec(sentences, size=100, windows=5, min_count=25,\
workers=8)
model.save("model.bin")
return model
def get_config_dir():
"""Get configuration directory."""
confdir = os.environ.get("XDG_CONFIG_HOME")
if not confdir:
confdir = os.path.expanduser("~")
if confdir == "~":
confdir = os.curdir()
confdir = os.path.join(confdir, ".config")
return os.path.join(confdir, "rganalysis")
def checkVideoDurationSeconds():
# type: () -> None
for video in os.listdir(os.curdir):
if not video.endswith("mp4"):
continue
print(video)
os.system(
'ffprobe -i {} -show_entries format=duration -v quiet -of csv="p=0"'
.format(os.path.join(os.curdir(), video)))
def __init__(self, host, file_, do_piped_output=True):
self.dir = os.curdir()
self.cmd = "python"
self.is_piped = do_piped_output
thread = subprocess.Popen("", executable=self.cmd)
# TODO: savex please refactor code below
self.file_ = file_
self.host = host
# TODO: implement method get_configuration in utils
# or use existing config file which stores private key path and user
self._config = utils.get_configuration(__file__)
self.priv_key = self._config['priv_key_path']
self.user = self._config['user']
def clean(path: str) -> str:
"""
Cleans the specified path by expanding shorthand elements, redirecting to
the real path for symbolic links, and removing any relative components to
return a complete, absolute path to the specified location.
:param path:
The source path to be cleaned
"""
if not path or path == ".":
path = os.curdir()
if path.startswith("~"):
path = os.path.expanduser(path)
return os.path.realpath(os.path.abspath(path))
def test_merge_utility(self, resource_group):
app_name = 'helloWorldApp'
yaml_files_path = "%s,%s,%s" % (_get_test_data_file('app.yaml'), _get_test_data_file('service.yaml'), _get_test_data_file('network.yaml'))
self.kwargs.update({
'resource_id': '',
'resource_group': resource_group,
'deployment_name': self.create_random_name(prefix='cli', length=24),
'app_name': app_name,
'input_yaml_files': yaml_files_path
})
# Test create
self.cmd('az mesh deployment create -g {rg} --input-yaml-files {input_yaml_files} --name {deployment_name}')
# Test delete
self.cmd('az mesh app delete -g {rg} --name {app_name} --yes')
# Delete the generated ARM template
os.path.delete(os.path.combine(os.curdir(), 'merged-arm_rp.json'))
def render_GET(self,request):
index_name = 'index.html'
try:
# determine scheduler index.html
if hasattr(self.bh.scheduler,'index_html'):
index_name = self.bh.scheduler.index_html
# determine if application is a script file or frozen exe
if hasattr(sys, 'frozen'):
application_path = os.path.dirname(sys.executable)
elif __file__:
application_path = os.path.dirname(__file__)
index = os.path.join(application_path, index_name)
except:
index = os.path.join(os.curdir(), index_name)
file = open(index, 'r')
linestring = file.read()
file.close
request.write(linestring)
request.finish()
return server.NOT_DONE_YET
def convertmodisvihdf2envi(hdffile, outpath): # This converts a LEDAPS-generated HDF to ENVI format via GDAL
hdf=gdal.Open(hdffile)
basename=os.path.basename(hdffile)
dirname=os.path.dirname(os.path.abspath(hdffile))
outpath=os.path.abspath(outpath)
dtaglist=[]
taglist=[]
if len(dirname)==0:
dirname=os.curdir()
if len(outpath)==0:
outpath=dirname
print('Exporting '+basename+' to '+outpath)
i=basename.rfind('/')+1
j=basename.rfind('.')
dataset=basename[i:j]
sdsdict=hdf.GetSubDatasets()
NDVIdat=outpath+'/ndvi/'+dataset+'_NDVI.dat'
EVIdat=outpath+'/evi/'+dataset+'_EVI.dat'
VIQdat=outpath+'/viq/'+dataset+'_VIQ.dat'
PRdat=outpath+'/pixel_reliability/'+dataset+'_PR.dat'
proclist=[['gdalTranslate', '-of','ENVI',[x for x in sdsdict if 'NDVI' in x[0]][0][0],NDVIdat],
['gdalTranslate', '-of','ENVI',[x for x in sdsdict if 'EVI' in x[0]][0][0],EVIdat],
['gdalTranslate', '-of','ENVI',[x for x in sdsdict if 'VI Quality' in x[0]][0][0],VIQdat],
['gdalTranslate', '-of','ENVI',[x for x in sdsdict if 'pixel reliability' in x[0]][0][0],PRdat]]
b1name=proclist[0][3]
b1=gdal.Open(b1name)
rmlist=[]
x=0
for y in proclist:
bandname=y[3]
print('Processing ' +bandname)
i=bandname.rfind(':')+1
btag=bandname[i:]
p=Popen(y)
print(p.communicate())
# print('ENVI file created, updating header.')
makemodishdrfile(y[4])
hdf=None
b1=None
print('Processing complete.')
def new_sign_mark(self, name="", text=""):
"""
Find and create new sign mark
"""
old_dir = os.curdir()
os.chdir(self.directory)
sh.git("pull")
mark = self.last_sign_mark() + 1
new_dir = str(mark).zfill(3) + '-' + name
readme = os.path.join(new_dir, 'readme.md')
os.mkdir(new_dir)
with open(readme, "w") as file:
file.write('# Spis ' + mark + name)
file.write(text)
sh.git("add", readme)
sh.git("push")
os.chdir(old_dir)
def new_sign_mark(self, name="", text=""):
"""
Find and create new sign mark
"""
old_dir = os.curdir()
os.chdir(self.directory)
sh.git("pull")
mark = self.last_sign_mark() + 1
new_dir = str(mark).zfill(3) + '-' + name
readme = os.path.join(new_dir, 'readme.md')
os.mkdir(new_dir)
with open(readme, "w") as file:
file.write('# Spis ' + mark + name)
file.write(text)
sh.git("add", readme)
sh.git("push")
os.chdir(old_dir)
def doLS(self,ev=None):
error = ''
tdir = self.cwd.get() # 这个是啥用？
if not tdir:
tdir=os.curdir()
if not os.path.exists(tdir):
error = tdir+':no such file'
elif not os.path.isdir(tdir):
error = tdir+':not a directory'
if error:
self.cwd.set(error)
self.top.update()
sleep(2)
if not (hasattr(self,'last') and self.last):
# not(有last属性并且last有值的时候)反过来就是二者其中一个不满足就行了
self.last=os.curdir
self.cwd.set(self.last)
self.dirs.config(selectbackground='LightSkyBlue')
self.top.update()
return
self.cwd.set('FETCHING DIRECTORY CONTENTS...')
self.top.update()
dirlist = os.listdir(tdir)
dirlist.sort()
os.chdir(tdir)
self.dirl.config(text=os.getcwd())
self.dirs.delete(0,END)
self.dirs.insert(END,os.curdir)
self.dirs.insert(END,os.pardir)
for eachFile in dirlist:
self.dirs.insert(END,eachFile)
self.cwd.set(os.curdir)
self.dirs.config(selectbackground='LightSkyBlue')
def make_pf(source, target):
curfolder = os.curdir()
src_folder = source
tar_folder = target
if (not (src_folder.endswith("/"))):
src_folder += '/'
dic = {}
lst = os.listdir(src_folder)
for item in lst:
if (item != "Blank.jpg"):
im = Image.open(src_folder + item, "r")
xdim, ydim = im.size
try:
im = im.resize((int((xdim / ydim) * 150), 150))
item = item.replace(".jpg", "")
item = item.replace(".png", "")
dic[item] = textExtract(im)
except:
pass
try:
os.chdir("profiles")
except:
os.mkdir("profiles")
os.chdir("profiles")
try:
os.chdir(tar_folder)
except:
os.mkdir(tar_folder)
os.chdir(tar_folder)
for key in dic:
dic[key].save(key + ".png")
os.chdir(curfolder)
import os
if __name__=='__main__':
print('somecode %s'%os.curdir())
def link(self,
target_desc,
objects,
output_filename,
output_dir=None,
libraries=None,
library_dirs=None,
runtime_library_dirs=None,
export_symbols=None,
debug=0,
extra_preargs=None,
extra_postargs=None,
build_temp=None,
target_lang=None):
# First fixup.
(objects, output_dir) = self._fix_object_args(objects, output_dir)
(libraries, library_dirs, runtime_library_dirs) = \
self._fix_lib_args (libraries, library_dirs, runtime_library_dirs)
# First examine a couple of options for things that aren't implemented yet
if not target_desc in (self.SHARED_LIBRARY, self.SHARED_OBJECT):
raise DistutilsPlatformError, 'Can only make SHARED_LIBRARY or SHARED_OBJECT targets on the Mac'
if runtime_library_dirs:
raise DistutilsPlatformError, 'Runtime library dirs not implemented yet'
if extra_preargs or extra_postargs:
raise DistutilsPlatformError, 'Runtime library dirs not implemented yet'
if len(export_symbols) != 1:
raise DistutilsPlatformError, 'Need exactly one export symbol'
# Next there are various things for which we need absolute pathnames.
# This is because we (usually) create the project in a subdirectory of
# where we are now, and keeping the paths relative is too much work right
# now.
sources = map(self._filename_to_abs, self.__sources)
include_dirs = map(self._filename_to_abs, self.__include_dirs)
if objects:
objects = map(self._filename_to_abs, objects)
else:
objects = []
if build_temp:
build_temp = self._filename_to_abs(build_temp)
else:
build_temp = os.curdir()
if output_dir:
output_filename = os.path.join(output_dir, output_filename)
# The output filename needs special handling: splitting it into dir and
# filename part. Actually I'm not sure this is really needed, but it
# can't hurt.
output_filename = self._filename_to_abs(output_filename)
output_dir, output_filename = os.path.split(output_filename)
# Now we need the short names of a couple of things for putting them
# into the project.
if output_filename[-8:] == '.ppc.slb':
basename = output_filename[:-8]
elif output_filename[-11:] == '.carbon.slb':
basename = output_filename[:-11]
else:
basename = os.path.strip(output_filename)[0]
projectname = basename + '.mcp'
targetname = basename
xmlname = basename + '.xml'
exportname = basename + '.mcp.exp'
prefixname = 'mwerks_%s_config.h' % basename
# Create the directories we need
distutils.dir_util.mkpath(build_temp, dry_run=self.dry_run)
distutils.dir_util.mkpath(output_dir, dry_run=self.dry_run)
# And on to filling in the parameters for the project builder
settings = {}
settings['mac_exportname'] = exportname
settings['mac_outputdir'] = output_dir
settings['mac_dllname'] = output_filename
settings['mac_targetname'] = targetname
settings['sysprefix'] = sys.prefix
settings['mac_sysprefixtype'] = 'Absolute'
sourcefilenames = []
sourcefiledirs = []
for filename in sources + objects:
dirname, filename = os.path.split(filename)
sourcefilenames.append(filename)
if not dirname in sourcefiledirs:
sourcefiledirs.append(dirname)
settings['sources'] = sourcefilenames
settings['libraries'] = libraries
settings[
'extrasearchdirs'] = sourcefiledirs + include_dirs + library_dirs
if self.dry_run:
print 'CALLING LINKER IN', os.getcwd()
for key, value in settings.items():
print '%20.20s %s' % (key, value)
return
# Build the export file
exportfilename = os.path.join(build_temp, exportname)
log.debug("\tCreate export file %s", exportfilename)
fp = open(exportfilename, 'w')
fp.write('%s\n' % export_symbols[0])
fp.close()
# Generate the prefix file, if needed, and put it in the settings
if self.__macros:
prefixfilename = os.path.join(os.getcwd(),
os.path.join(build_temp, prefixname))
fp = open(prefixfilename, 'w')
fp.write('#include "mwerks_shcarbon_config.h"\n')
for name, value in self.__macros:
if value is None:
fp.write('#define %s\n' % name)
else:
fp.write('#define %s %s\n' % (name, value))
fp.close()
settings['prefixname'] = prefixname
# Build the XML file. We need the full pathname (only lateron, really)
# because we pass this pathname to CodeWarrior in an AppleEvent, and CW
# doesn't have a clue about our working directory.
xmlfilename = os.path.join(os.getcwd(),
os.path.join(build_temp, xmlname))
log.debug("\tCreate XML file %s", xmlfilename)
xmlbuilder = mkcwproject.cwxmlgen.ProjectBuilder(settings)
xmlbuilder.generate()
xmldata = settings['tmp_projectxmldata']
fp = open(xmlfilename, 'w')
fp.write(xmldata)
fp.close()
# Generate the project. Again a full pathname.
projectfilename = os.path.join(os.getcwd(),
os.path.join(build_temp, projectname))
log.debug('\tCreate project file %s', projectfilename)
mkcwproject.makeproject(xmlfilename, projectfilename)
# And build it
log.debug('\tBuild project')
mkcwproject.buildproject(projectfilename)
def parseExptConfig(configFile, librariesToSublibrariesDict):
parser = ConfigParser()
results = parser.read(configFile)
if len(results) == 0:
return None, 1, 'Experiment config file not found'
#output variables
paramDict = dict()
exitStatus = 0
warningString = ''
##check all sections
expectedSections = set([
'experiment_settings', 'library_settings', 'counts_files',
'filter_settings', 'sgrna_analysis', 'growth_values', 'gene_analysis'
])
parsedSections = set(parser.sections())
if len(expectedSections) != len(parsedSections) and len(
expectedSections) != len(
expectedSections.intersection(parsedSections)):
return paramDict, 1, 'Config file does not have all required sections or has extraneous sections!\nExpected:' + ','.join(
expectedSections) + '\nFound:' + ','.join(parsedSections)
##experiment settings
if parser.has_option('experiment_settings', 'output_folder'):
paramDict['output_folder'] = parser.get(
'experiment_settings',
'output_folder') #ways to check this is a valid path?
else:
warningString += 'No output folder specified, defaulting to current directory\n.'
paramDict['output_folder'] = os.curdir()
if parser.has_option('experiment_settings', 'experiment_name'):
paramDict['experiment_name'] = parser.get('experiment_settings',
'experiment_name')
else:
warningString += 'No experiment name specified, defaulting to \'placeholder_expt_name\'\n.'
paramDict['experiment_name'] = 'placeholder_expt_name'
##library settings
libraryDict = librariesToSublibrariesDict
if parser.has_option('library_settings', 'library'):
parsedLibrary = parser.get('library_settings', 'library')
if parsedLibrary.lower() in libraryDict:
paramDict['library'] = parsedLibrary.lower()
else:
warningString += 'Library name \"%s\" not recognized\n' % parsedLibrary
exitStatus += 1
else:
warningString += 'No library specified\n'
exitStatus += 1
parsedLibrary = ''
if 'library' in paramDict:
if parser.has_option('library_settings', 'sublibraries'):
parsedSubList = parser.get('library_settings',
'sublibraries').strip().split('\n')
paramDict['sublibraries'] = []
for sub in parsedSubList:
sub = sub.lower()
if sub in libraryDict[paramDict['library']]:
paramDict['sublibraries'].append(sub)
else:
warningString += 'Sublibrary %s not recognized\n' % sub
else:
paramDict['sublibraries'] = libraryDict[paramDict['library']]
##counts files
if parser.has_option('counts_files', 'counts_file_string'):
countsFileString = parser.get('counts_files',
'counts_file_string').strip()
paramDict['counts_file_list'] = []
for stringLine in countsFileString.split('\n'):
stringLine = stringLine.strip()
if len(stringLine.split(':')) != 2 or len(
stringLine.split('|')) != 2:
warningString += 'counts file entry could not be parsed: ' + stringLine + '\n'
exitStatus += 1
else:
parsedPath = stringLine.split(':')[0]
if os.path.isfile(parsedPath) == False:
warningString += 'Counts file not found: ' + parsedPath + '\n'
exitStatus += 1
condition, replicate = stringLine.split(':')[1].split('|')
paramDict['counts_file_list'].append(
(condition, replicate, parsedPath))
else:
warningString += 'No counts files entered\n'
exitStatus += 1
##filter settings
filterOptions = ['either', 'both']
if parser.has_option('filter_settings', 'filter_type') and parser.get(
'filter_settings', 'filter_type').lower() in filterOptions:
paramDict['filter_type'] = parser.get('filter_settings',
'filter_type').lower()
else:
warningString += 'Filter type not set or not recognized, defaulting to \'either\'\n'
paramDict['filter_type'] = 'either'
if parser.has_option('filter_settings', 'minimum_reads'):
try:
paramDict['minimum_reads'] = parser.getint('filter_settings',
'minimum_reads')
except ValueError:
warningString += 'Minimum read value not an integer, defaulting to 0\n' #recommended value is 50 but seems arbitrary to default to that
paramDict['minimum_reads'] = 0
else:
warningString += 'Minimum read value not found, defaulting to 0\n' #recommended value is 50 but seems arbitrary to default to that
paramDict['minimum_reads'] = 0
##sgRNA Analysis
if parser.has_option('sgrna_analysis', 'condition_string'):
conditionString = parser.get('sgrna_analysis',
'condition_string').strip()
paramDict['condition_tuples'] = []
if 'counts_file_list' in paramDict:
expectedConditions = set(
list(zip(*paramDict['counts_file_list']))[0])
else:
expectedConditions = []
enteredConditions = set()
for conditionStringLine in conditionString.split('\n'):
conditionStringLine = conditionStringLine.strip()
if len(conditionStringLine.split(':')) != 3:
warningString += 'Phenotype condition line not understood: ' + conditionStringLine + '\n'
exitStatus += 1
else:
phenotype, condition1, condition2 = conditionStringLine.split(
':')
if condition1 not in expectedConditions or condition2 not in expectedConditions:
warningString += 'One of the conditions entered does not correspond to a counts file: ' + conditionStringLine + '\n'
exitStatus += 1
else:
paramDict['condition_tuples'].append(
(phenotype, condition1, condition2))
enteredConditions.add(condition1)
enteredConditions.add(condition2)
if len(paramDict['condition_tuples']) == 0:
warningString += 'No phenotype score/condition pairs found\n'
exitStatus += 1
unusedConditions = list(expectedConditions - enteredConditions)
if len(unusedConditions) > 0:
warningString += 'Some conditions assigned to counts files will not be incorporated in sgRNA analysis:\n' \
+ ','.join(unusedConditions) + '\n'
else:
warningString += 'No phenotype score/condition pairs entered\n'
exitStatus += 1
pseudocountOptions = ['zeros only', 'all values', 'filter out']
if parser.has_option(
'sgrna_analysis', 'pseudocount_behavior') and parser.get(
'sgrna_analysis',
'pseudocount_behavior').lower() in pseudocountOptions:
paramDict['pseudocount_behavior'] = parser.get(
'sgrna_analysis', 'pseudocount_behavior').lower()
else:
warningString += 'Pseudocount behavior not set or not recognized, defaulting to \'zeros only\'\n'
paramDict['pseudocount_behavior'] = 'zeros only'
if parser.has_option('sgrna_analysis', 'pseudocount'):
try:
paramDict['pseudocount'] = parser.getfloat('sgrna_analysis',
'pseudocount')
except ValueError:
warningString += 'Pseudocount value not an number, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
else:
warningString += 'Pseudocount value not found, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
##Growth Values
if parser.has_option('growth_values', 'growth_value_string') and len(
parser.get('growth_values', 'growth_value_string').strip()) != 0:
growthValueString = parser.get('growth_values',
'growth_value_string').strip()
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(
list(zip(*paramDict['condition_tuples']))[0])
expectedReplicates = set(
list(zip(*paramDict['counts_file_list']))[1])
expectedTupleList = []
for comp in expectedComparisons:
for rep in expectedReplicates:
expectedTupleList.append((comp, rep))
else:
expectedTupleList = []
enteredTupleList = []
growthValueTuples = []
for growthValueLine in growthValueString.split('\n'):
growthValueLine = growthValueLine.strip()
linesplit = growthValueLine.split(':')
if len(linesplit) != 3:
warningString += 'Growth value line not understood: ' + growthValueLine + '\n'
exitStatus += 1
continue
comparison = linesplit[0]
replicate = linesplit[1]
try:
growthVal = float(linesplit[2])
except ValueError:
warningString += 'Growth value not a number: ' + growthValueLine + '\n'
exitStatus += 1
continue
curTup = (comparison, replicate)
if curTup in expectedTupleList:
if curTup not in enteredTupleList:
enteredTupleList.append(curTup)
growthValueTuples.append(
(comparison, replicate, growthVal))
else:
warningString += ':'.join(
curTup) + ' has multiple growth values entered\n'
exitStatus += 1
else:
warningString += ':'.join(
curTup
) + ' was not expected given the specified counts file assignments and sgRNA phenotypes\n'
exitStatus += 1
#because we enforced no duplicates or unexpected values these should match up unless there were values not entered
#require all growth values to be explictly entered if some were
if len(enteredTupleList) != len(expectedTupleList):
warningString += 'Growth values were not entered for all expected comparisons/replicates. Expected: ' + \
','.join([':'.join(tup) for tup in expectedTupleList]) + '\nEntered: ' + \
','.join([':'.join(tup) for tup in enteredTupleList]) + '\n'
exitStatus += 1
else:
paramDict['growth_value_tuples'] = growthValueTuples
else:
warningString += 'No growth values--all phenotypes will be reported as log2enrichments\n'
paramDict['growth_value_tuples'] = []
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(
list(zip(*paramDict['condition_tuples']))[0])
expectedReplicates = set(
list(zip(*paramDict['counts_file_list']))[1])
for comp in expectedComparisons:
for rep in expectedReplicates:
paramDict['growth_value_tuples'].append((comp, rep, 1))
##Gene Analysis
if parser.has_option('gene_analysis', 'collapse_to_transcripts'):
try:
paramDict['collapse_to_transcripts'] = parser.getboolean(
'gene_analysis', 'collapse_to_transcripts')
except ValueError:
warningString += 'Collapse to transcripts entry not a recognized boolean value\n'
exitStatus += 1
else:
paramDict['collapse_to_transcripts'] = True
warningString += 'Collapse to transcripts defaulting to True\n'
#pseudogene parameters
if parser.has_option('gene_analysis', 'generate_pseudogene_dist'):
paramDict['generate_pseudogene_dist'] = parser.get(
'gene_analysis', 'generate_pseudogene_dist').lower()
if paramDict['generate_pseudogene_dist'] not in [
'auto', 'manual', 'off'
]:
warningString += 'Generate pseudogene dist entry not a recognized option\n'
exitStatus += 1
else:
paramDict['generate_pseudogene_dist'] = False
warningString += 'Generate pseudogene dist defaulting to False\n'
if 'generate_pseudogene_dist' in paramDict and paramDict[
'generate_pseudogene_dist'] == 'manual':
if parser.has_option('gene_analysis', 'pseudogene_size'):
try:
paramDict['pseudogene_size'] = parser.getint(
'gene_analysis', 'pseudogene_size')
except ValueError:
warningString += 'Pseudogene size entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
exitStatus += 1
if parser.has_option('gene_analysis', 'num_pseudogenes'):
try:
paramDict['num_pseudogenes'] = parser.getint(
'gene_analysis', 'num_pseudogenes')
except ValueError:
warningString += 'Pseudogene number entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
#list possible analyses in param dict as dictionary with keys = analysis and values = analysis-specific params
paramDict['analyses'] = dict()
#analyze by average of best n
if parser.has_option('gene_analysis', 'calculate_ave'):
try:
if parser.getboolean('gene_analysis', 'calculate_ave') == True:
paramDict['analyses']['calculate_ave'] = []
except ValueError:
warningString += 'Calculate ave entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_ave' in paramDict['analyses']:
if parser.has_option('gene_analysis', 'best_n'):
try:
paramDict['analyses']['calculate_ave'].append(
parser.getint('gene_analysis', 'best_n'))
except ValueError:
warningString += 'Best_n entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No best_n value provided for average analysis function\n'
exitStatus += 1
else:
warningString += 'Best n average analysis not specified, defaulting to False\n'
#analyze by Mann-Whitney
if parser.has_option('gene_analysis', 'calculate_mw'):
try:
if parser.getboolean('gene_analysis', 'calculate_mw') == True:
paramDict['analyses']['calculate_mw'] = []
except ValueError:
warningString += 'Calculate Mann-Whitney entry not a recognized boolean value\n'
exitStatus += 1
#analyze by K-S, skipping for now
#analyze by nth best sgRNA
if parser.has_option('gene_analysis', 'calculate_nth'):
try:
if parser.getboolean('gene_analysis', 'calculate_nth') == True:
paramDict['analyses']['calculate_nth'] = []
except ValueError:
warningString += 'Calculate best Nth sgRNA entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_nth' in paramDict['analyses']:
if parser.has_option('gene_analysis', 'nth'):
try:
paramDict['analyses']['calculate_nth'].append(
parser.getint('gene_analysis', 'nth'))
except ValueError:
warningString += 'Nth best sgRNA entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No Nth best value provided for that analysis function\n'
exitStatus += 1
else:
warningString += 'Nth best sgRNA analysis not specified, defaulting to False\n'
if len(paramDict['analyses']) == 0:
warningString += 'No analyses selected to compute gene scores\n' #should this raise exitStatus?
return paramDict, exitStatus, warningString
def teste():
print("teste")
print(os.curdir())
def path(self):
return self.config.path or os.curdir()
help='Site name for preset data directory (%default)')
parser.add_option('-D',
'--datdir',
default=None,
help='Sentinel-1 data directory (%default)')
(opts, args) = parser.parse_args()
if opts.datdir is None:
if opts.site is not None:
if opts.site.lower() == 'cihea':
opts.datdir = os.path.join(DATDIR, 'Cihea', 'sigma0_speckle')
elif opts.site.lower() == 'bojongsoang':
opts.datdir = os.path.join(DATDIR, 'Bojongsoang', 'sigma0_speckle')
else:
raise ValueError('Error, unknown site >>> ' + opts.site)
else:
opts.datdir = os.curdir()
angs = []
for f in sorted(os.listdir(opts.datdir)):
m = re.search('(' + '\d' * 8 + ')_resample.tif', f)
if not m:
continue
fnam = os.path.join(opts.datdir, f)
dstr = m.group(1)
#print(dstr)
command = 'gdalinfo'
command += ' ' + fnam
out = check_output(command, shell=True)
iangle = None
direction = None
for line in out.decode().splitlines():
os.getegid()
os.geteuid()
os.getpid()
os.getppid()
os.getenv()
os.getenvb()
os.abort()
os.chmod()
os.chown()
os.close()
os.cpu_count()
os.kill()
os.open()
os.getgid()
os.chdir("dirname") # 改变当前脚本工作目录；相当于shell下cd
os.curdir() # 返回当前目录: ('.')
os.pardir() # 获取当前目录的父目录字符串名：('..')
os.mkdir('dirname') # 生成单级目录；相当于shell中mkdir dirname
os.makedirs('dirname1/dirname2') # 可生成多层递归目录
os.rmdir('dirname') # 删除单级空目录，若目录不为空则无法删除，报错；相当于shell中rmdir dirname
os.removedirs('dirname1') # 若目录为空，则删除，并递归到上一级目录，如若也为空，则删除，依此类推
os.listdir('dirname') # 列出指定目录下的所有文件和子目录，包括隐藏文件，并以列表方式打印
os.remove('1.txt') # 删除一个文件
os.rename("oldname","newname") # 重命名文件/目录/移动目录/，只能同设备（在同一块磁盘，不同设备看下面shutil模块）。
os._exit(n) # 直接推出，不抛异常，不执行相关清理工作。常用在子进程中
os.stat('path/filename') # 获取文件/目录信息
# l = os.stat('path/filename')
# print(list(l))
# print(list(l)[2])
os.sep() # 输出操作系统特定的路径分隔符，win下为"\\",Linux下为"/"
os.linesep() # 输出当前平台使用的行分隔符，win下为"\t\n",Linux下为"\n"
def parseExptConfig(configFile, librariesToSublibrariesDict):
parser = SafeConfigParser()
results = parser.read(configFile)
if len(results) == 0:
return None, 1, "Experiment config file not found"
# output variables
paramDict = dict()
exitStatus = 0
warningString = ""
##check all sections
expectedSections = set(
[
"experiment_settings",
"library_settings",
"counts_files",
"filter_settings",
"sgrna_analysis",
"growth_values",
"gene_analysis",
]
)
parsedSections = set(parser.sections())
if len(expectedSections) != len(parsedSections) and len(expectedSections) != len(
expectedSections.intersection(parsedSections)
):
return (
paramDict,
1,
"Config file does not have all required sections or has extraneous sections!\nExpected:"
+ ",".join(expectedSections)
+ "\nFound:"
+ ",".join(parsedSections),
)
##experiment settings
if parser.has_option("experiment_settings", "output_folder"):
paramDict["output_folder"] = parser.get(
"experiment_settings", "output_folder"
) # ways to check this is a valid path?
else:
warningString += "No output folder specified, defaulting to current directory\n."
paramDict["output_folder"] = os.curdir()
if parser.has_option("experiment_settings", "experiment_name"):
paramDict["experiment_name"] = parser.get("experiment_settings", "experiment_name")
else:
warningString += "No experiment name specified, defaulting to 'placeholder_expt_name'\n."
paramDict["experiment_name"] = "placeholder_expt_name"
##library settings
libraryDict = librariesToSublibrariesDict
if parser.has_option("library_settings", "library"):
parsedLibrary = parser.get("library_settings", "library")
if parsedLibrary.lower() in libraryDict:
paramDict["library"] = parsedLibrary.lower()
else:
warningString += 'Library name "%s" not recognized\n' % parsedLibrary
exitStatus += 1
else:
warningString += "No library specified\n"
exitStatus += 1
parsedLibrary = ""
if "library" in paramDict:
if parser.has_option("library_settings", "sublibraries"):
parsedSubList = parser.get("library_settings", "sublibraries").strip().split("\n")
paramDict["sublibraries"] = []
for sub in parsedSubList:
sub = sub.lower()
if sub in libraryDict[paramDict["library"]]:
paramDict["sublibraries"].append(sub)
else:
warningString += "Sublibrary %s not recognized\n" % sub
else:
paramDict["sublibraries"] = libraryDict[paramDict["library"]]
##counts files
if parser.has_option("counts_files", "counts_file_string"):
countsFileString = parser.get("counts_files", "counts_file_string").strip()
paramDict["counts_file_list"] = []
for stringLine in countsFileString.split("\n"):
stringLine = stringLine.strip()
if len(stringLine.split(":")) != 2 or len(stringLine.split("|")) != 2:
warningString += "counts file entry could not be parsed: " + stringLine + "\n"
exitStatus += 1
else:
parsedPath = stringLine.split(":")[0]
if os.path.isfile(parsedPath) == False:
warningString += "Counts file not found: " + parsedPath + "\n"
exitStatus += 1
condition, replicate = stringLine.split(":")[1].split("|")
paramDict["counts_file_list"].append((condition, replicate, parsedPath))
else:
warningString += "No counts files entered\n"
exitStatus += 1
##filter settings
filterOptions = ["either", "both"]
if (
parser.has_option("filter_settings", "filter_type")
and parser.get("filter_settings", "filter_type").lower() in filterOptions
):
paramDict["filter_type"] = parser.get("filter_settings", "filter_type").lower()
else:
warningString += "Filter type not set or not recognized, defaulting to 'either'\n"
paramDict["filter_type"] = "either"
if parser.has_option("filter_settings", "minimum_reads"):
try:
paramDict["minimum_reads"] = parser.getint("filter_settings", "minimum_reads")
except ValueError:
warningString += (
"Minimum read value not an integer, defaulting to 0\n"
) # recommended value is 50 but seems arbitrary to default to that
paramDict["minimum_reads"] = 0
else:
warningString += (
"Minimum read value not found, defaulting to 0\n"
) # recommended value is 50 but seems arbitrary to default to that
paramDict["minimum_reads"] = 0
##sgRNA Analysis
if parser.has_option("sgrna_analysis", "condition_string"):
conditionString = parser.get("sgrna_analysis", "condition_string").strip()
paramDict["condition_tuples"] = []
if "counts_file_list" in paramDict:
expectedConditions = set(zip(*paramDict["counts_file_list"])[0])
else:
expectedConditions = []
enteredConditions = set()
for conditionStringLine in conditionString.split("\n"):
conditionStringLine = conditionStringLine.strip()
if len(conditionStringLine.split(":")) != 3:
warningString += "Phenotype condition line not understood: " + conditionStringLine + "\n"
exitStatus += 1
else:
phenotype, condition1, condition2 = conditionStringLine.split(":")
if condition1 not in expectedConditions or condition2 not in expectedConditions:
warningString += (
"One of the conditions entered does not correspond to a counts file: "
+ conditionStringLine
+ "\n"
)
exitStatus += 1
else:
paramDict["condition_tuples"].append((phenotype, condition1, condition2))
enteredConditions.add(condition1)
enteredConditions.add(condition2)
if len(paramDict["condition_tuples"]) == 0:
warningString += "No phenotype score/condition pairs found\n"
exitStatus += 1
unusedConditions = list(expectedConditions - enteredConditions)
if len(unusedConditions) > 0:
warningString += (
"Some conditions assigned to counts files will not be incorporated in sgRNA analysis:\n"
+ ",".join(unusedConditions)
+ "\n"
)
else:
warningString += "No phenotype score/condition pairs entered\n"
exitStatus += 1
pseudocountOptions = ["zeros only", "all values", "filter out"]
if (
parser.has_option("sgrna_analysis", "pseudocount_behavior")
and parser.get("sgrna_analysis", "pseudocount_behavior").lower() in pseudocountOptions
):
paramDict["pseudocount_behavior"] = parser.get("sgrna_analysis", "pseudocount_behavior").lower()
else:
warningString += "Pseudocount behavior not set or not recognized, defaulting to 'zeros only'\n"
paramDict["pseudocount_behavior"] = "zeros only"
if parser.has_option("sgrna_analysis", "pseudocount"):
try:
paramDict["pseudocount"] = parser.getfloat("sgrna_analysis", "pseudocount")
except ValueError:
warningString += "Pseudocount value not an number, defaulting to 0.1\n"
paramDict["pseudocount"] = 0.1
else:
warningString += "Pseudocount value not found, defaulting to 0.1\n"
paramDict["pseudocount"] = 0.1
##Growth Values
if (
parser.has_option("growth_values", "growth_value_string")
and len(parser.get("growth_values", "growth_value_string").strip()) != 0
):
growthValueString = parser.get("growth_values", "growth_value_string").strip()
if "condition_tuples" in paramDict and "counts_file_list" in paramDict:
expectedComparisons = set(zip(*paramDict["condition_tuples"])[0])
expectedReplicates = set(zip(*paramDict["counts_file_list"])[1])
expectedTupleList = []
for comp in expectedComparisons:
for rep in expectedReplicates:
expectedTupleList.append((comp, rep))
else:
expectedTupleList = []
enteredTupleList = []
growthValueTuples = []
for growthValueLine in growthValueString.split("\n"):
growthValueLine = growthValueLine.strip()
linesplit = growthValueLine.split(":")
if len(linesplit) != 3:
warningString += "Growth value line not understood: " + growthValueLine + "\n"
exitStatus += 1
continue
comparison = linesplit[0]
replicate = linesplit[1]
try:
growthVal = float(linesplit[2])
except ValueError:
warningString += "Growth value not a number: " + growthValueLine + "\n"
exitStatus += 1
continue
curTup = (comparison, replicate)
if curTup in expectedTupleList:
if curTup not in enteredTupleList:
enteredTupleList.append(curTup)
growthValueTuples.append((comparison, replicate, growthVal))
else:
warningString += ":".join(curTup) + " has multiple growth values entered\n"
exitStatus += 1
else:
warningString += (
":".join(curTup)
+ " was not expected given the specified counts file assignments and sgRNA phenotypes\n"
)
exitStatus += 1
# because we enforced no duplicates or unexpected values these should match up unless there were values not entered
# require all growth values to be explictly entered if some were
if len(enteredTupleList) != len(expectedTupleList):
warningString += (
"Growth values were not entered for all expected comparisons/replicates. Expected: "
+ ",".join([":".join(tup) for tup in expectedTupleList])
+ "\nEntered: "
+ ",".join([":".join(tup) for tup in enteredTupleList])
+ "\n"
)
exitStatus += 1
else:
paramDict["growth_value_tuples"] = growthValueTuples
else:
warningString += "No growth values--all phenotypes will be reported as log2enrichments\n"
paramDict["growth_value_tuples"] = []
if "condition_tuples" in paramDict and "counts_file_list" in paramDict:
expectedComparisons = set(zip(*paramDict["condition_tuples"])[0])
expectedReplicates = set(zip(*paramDict["counts_file_list"])[1])
for comp in expectedComparisons:
for rep in expectedReplicates:
paramDict["growth_value_tuples"].append((comp, rep, 1))
##Gene Analysis
if parser.has_option("gene_analysis", "collapse_to_transcripts"):
try:
paramDict["collapse_to_transcripts"] = parser.getboolean("gene_analysis", "collapse_to_transcripts")
except ValueError:
warningString += "Collapse to transcripts entry not a recognized boolean value\n"
exitStatus += 1
else:
paramDict["collapse_to_transcripts"] = True
warningString += "Collapse to transcripts defaulting to True\n"
# pseudogene parameters
if parser.has_option("gene_analysis", "generate_pseudogene_dist"):
paramDict["generate_pseudogene_dist"] = parser.get("gene_analysis", "generate_pseudogene_dist").lower()
if paramDict["generate_pseudogene_dist"] not in ["auto", "manual", "off"]:
warningString += "Generate pseudogene dist entry not a recognized option\n"
exitStatus += 1
else:
paramDict["generate_pseudogene_dist"] = False
warningString += "Generate pseudogene dist defaulting to False\n"
if "generate_pseudogene_dist" in paramDict and paramDict["generate_pseudogene_dist"] == "manual":
if parser.has_option("gene_analysis", "pseudogene_size"):
try:
paramDict["pseudogene_size"] = parser.getint("gene_analysis", "pseudogene_size")
except ValueError:
warningString += "Pseudogene size entry not a recognized integer value\n"
exitStatus += 1
else:
warningString += "No pseudogene size provided\n"
exitStatus += 1
if parser.has_option("gene_analysis", "num_pseudogenes"):
try:
paramDict["num_pseudogenes"] = parser.getint("gene_analysis", "num_pseudogenes")
except ValueError:
warningString += "Pseudogene number entry not a recognized integer value\n"
exitStatus += 1
else:
warningString += "No pseudogene size provided\n"
# list possible analyses in param dict as dictionary with keys = analysis and values = analysis-specific params
paramDict["analyses"] = dict()
# analyze by average of best n
if parser.has_option("gene_analysis", "calculate_ave"):
try:
if parser.getboolean("gene_analysis", "calculate_ave") == True:
paramDict["analyses"]["calculate_ave"] = []
except ValueError:
warningString += "Calculate ave entry not a recognized boolean value\n"
exitStatus += 1
if "calculate_ave" in paramDict["analyses"]:
if parser.has_option("gene_analysis", "best_n"):
try:
paramDict["analyses"]["calculate_ave"].append(parser.getint("gene_analysis", "best_n"))
except ValueError:
warningString += "Best_n entry not a recognized integer value\n"
exitStatus += 1
else:
warningString += "No best_n value provided for average analysis function\n"
exitStatus += 1
else:
warningString += "Best n average analysis not specified, defaulting to False\n"
# analyze by Mann-Whitney
if parser.has_option("gene_analysis", "calculate_mw"):
try:
if parser.getboolean("gene_analysis", "calculate_mw") == True:
paramDict["analyses"]["calculate_mw"] = []
except ValueError:
warningString += "Calculate Mann-Whitney entry not a recognized boolean value\n"
exitStatus += 1
# analyze by K-S, skipping for now
# analyze by nth best sgRNA
if parser.has_option("gene_analysis", "calculate_nth"):
try:
if parser.getboolean("gene_analysis", "calculate_nth") == True:
paramDict["analyses"]["calculate_nth"] = []
except ValueError:
warningString += "Calculate best Nth sgRNA entry not a recognized boolean value\n"
exitStatus += 1
if "calculate_nth" in paramDict["analyses"]:
if parser.has_option("gene_analysis", "nth"):
try:
paramDict["analyses"]["calculate_nth"].append(parser.getint("gene_analysis", "nth"))
except ValueError:
warningString += "Nth best sgRNA entry not a recognized integer value\n"
exitStatus += 1
else:
warningString += "No Nth best value provided for that analysis function\n"
exitStatus += 1
else:
warningString += "Nth best sgRNA analysis not specified, defaulting to False\n"
if len(paramDict["analyses"]) == 0:
warningString += "No analyses selected to compute gene scores\n" # should this raise exitStatus?
return paramDict, exitStatus, warningString
soup=BeautifulSoup(temp)
frames=soup.find_all(attrs={'class':'list-item'})
for item in frames:
sec_frame=item.find(attrs={'class':'detail'})
title=sec_frame.h3.a['title']
href=sec_frame.h3.a['href']
try:judge_href=sec_frame.find(attrs={'class':'score-dot'})['href']
except:judge_href='-'
store_title=sec_frame.find(attrs={'class':'store'})['title']
store_href=sec_frame.find(attrs={'class':'store'})['href']
try:is_top_rate_seller=sec_frame.find(attrs={'class':'top-rated-seller'}).contents[0]
except:is_top_rate_seller='NO'
thr_frame=item.find(attrs={'class':'info infoprice'})
price=thr_frame.span.span.contents[0]
price_unit=thr_frame.span.find_all('span')[-1].text
try:del_price=thr_frame.find(attrs={'class':'original-price'}).contents[0]
except:del_price='-'
try:shipping_service=thr_frame.strong.contents[0]
except:shipping_service='-'
try:
product_rate=thr_frame.find(itemprop="ratingValue").contents[0]
feedback=thr_frame.find(attrs={'class':'rate-num'}).contents[0]
except:product_rate='-';feedback='-'
orders=thr_frame.find(title="Total Orders").contents[0]
result=[title,href,judge_href,store_title,is_top_rate_seller,store_href,price,price_unit,
del_price,shipping_service,product_rate,feedback,orders]
print('='*80)
for item in result:
print(item)
os.curdir(file_name)
def path(self):
return self.config.path or os.curdir()
def curdir(self):
f = self.environment['__file__']
if f is None:
return os.curdir()
else:
return os.path.dirname(f)
"""distutils.mwerkscompiler
def main():
print("__file__", __file__)
print("os.curdir()", os.curdir())
print
def __init__(self, parent=None):
super(FrontEnd, self).__init__(parent)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
# Header image.. Need to get a Quality image
self.hlabel = QLabel()
self.hpixmap = QPixmap(os.curdir() + 'images\header.png')
self.hlabel.setPixmap(self.hpixmap)
#self.hlabel.setMaximumWidth(400)
# Password Stuff
self._password = qt.QLabel('Please Provide a Password')
self._passwordEdit = qt.QLineEdit()
self._passwordEdit.setMaximumWidth(500)
self._passwordEdit.setText("Password")
self._passwordEdit.setEchoMode(qt.QLineEdit.Password)
self._passwordEdit.setMaximumWidth(400)
# Get the folder path
self._path = qt.QLabel("Please Provide a Path")
self._path.setMaximumWidth(500)
self._pathEdit = qt.QLineEdit()
self._pathEdit.setText("/home or C:\\")
self._pathEdit.setMaximumWidth(400)
# Encrypt Button
self._encryptButton = qt.QPushButton("Encrypt")
self._encryptButton.clicked.connect(self.encryptFolder)
#self._encryptButton.setStyleSheet("background-color: #79ff4d")
self._encryptButton.setMaximumWidth(400)
# Decrypt Button
self._decryptButton = qt.QPushButton("Decrypt")
self._decryptButton.clicked.connect(self.decryptFolder)
#self._decryptButton.setStyleSheet("background-color: #ff4d4d")
self._decryptButton.setMaximumWidth(400)
# Footer Need to get a Quality image
self.flabel = QLabel()
self.fpixmap = QPixmap(os.curdir + '/images/footer.png')
self.flabel.setPixmap(self.fpixmap)
# Add widgets to the grid
self.widget = QWidget()
self.grid = qt.QGridLayout(self.widget)
self.grid.setSpacing(10)
self.grid.maximumSize()
self.grid.addWidget(self.hlabel, 0, 0)
self.grid.addWidget(self._password, 1, 0)
self.grid.addWidget(self._passwordEdit, 2, 0)
self.grid.addWidget(self._path, 3, 0)
self.grid.addWidget(self._pathEdit, 4, 0)
self.grid.addWidget(self._encryptButton, 5, 0)
self.grid.addWidget(self._decryptButton, 6, 0)
self.grid.addWidget(self.flabel, 7, 0)
self.setLayout(self.grid)
self.setGeometry(350, 300, 350, 300)
self.setWindowTitle("Enkryptor- Keeps your files safe")
self.show()
def to_abs_model_file_path(model_file_path):
if model_file_path is None:
model_file_path = os.curdir()
elif not os.path.isabs(model_file_path):
model_file_path = os.path.join(os.curdir(), model_file_path)
return model_file_path
import numpy as np
from sklearn import metrics
import time
import os
import glob
import re
# In[14]:
#read in the answers
answers = pd.read_csv('test_actuals.csv',
index_col=0,
header=None,
names=['Genres'])
path = os.curdir()
extension = 'csv'
os.chdir(path)
files = glob.glob('*.{}'.format(extension))
print(files)
# In[35]:
#create dictionary to store results
results = {}
# In[ ]:
# loop over the list read the file, and score the answers
# In[36]:
def get_idx_mock():
""
p=os.curdir()
return list_files_ext(p,'png')
def getDrive(path=None):
if not path: path = os.curdir()
match = drivePattern.search(path)
if not match:
return ''
return match.group('drive')
def main():
node_regs = ["CFixedIntervalsNRD", "CICPCriteriaNRD"]
edge_regs = ["CICPCriteriaERD", "CLoopCloserERD"]
optimizers = ["CLevMarqGSO"]
datasets_dir = os.environ['dataset'] or os.curdir()
datasets_dir += os.sep
dataset_files = ["action_observations_map_short", "observation_only_short"]
datasets = [datasets_dir + os.sep + d + os.sep for d in dataset_files]
config_file = "".join([
"{home}".format(home=os.environ["HOME"]), os.sep,
"sharedWros/codes/various/mrpt/share/mrpt/config_files/",
"graphslam-engine/odometry_2DRangeScans.ini"
])
visuals = [True, False]
combs = [[i, j, k, l, m] for i in node_regs for j in edge_regs
for k in optimizers for l in datasets for m in visuals]
total_combs = len(combs)
# find the graphslam-engine executable
bash_mrpt_var = "MRPT_DIR"
if bash_mrpt_var in os.environ:
mrpt_path = os.environ[bash_mrpt_var]
app_path = "".join(
[mrpt_path, os.sep, "bin", os.sep, "graphslam-engine"])
elif subprocess.call(["which", "graphslam-engine"
]): # search for it in the user path
app_path = "graphslam-engine" # already in path
else: # can't be found - inform user
raise MRPTExecutableNotFoundError("graphslam-engine")
errors_num = 0
# take all the possible combinations and execute graphSLAM
for comb_i, curr_comb in enumerate(combs):
#
# Announce operation
#
intro_msg = "# {}/{}".format(comb_i + 1, total_combs)
tPrint(intro_msg)
node = curr_comb[0]
edge = curr_comb[1]
opt = curr_comb[2]
dataset = curr_comb[3]
disable_visuals = curr_comb[4] is False
current_run_input = ""
current_run_input += "\tNode Registration Decider: {}\n".format(node)
current_run_input += "\tEdge Registration Decider: {}\n".format(edge)
current_run_input += "\tGraphSLAM Optimizer : {}\n".format(opt)
current_run_input += "\tDataset : {}\n".format(
dataset)
current_run_input += "\t.ini Configuration File : {}\n".format(
config_file)
current_run_input += "\tDisable visuals : {}\n".format(
disable_visuals)
print(current_run_input)
#
# Execute it
#
redirect_null = True
command_parts = [app_path]
command_parts.extend(["--node-reg", node])
command_parts.extend(["--edge-reg", edge])
command_parts.extend(["--optimizer", opt])
command_parts.extend(["--ini-file", config_file])
command_parts.extend(["--rawlog", dataset + "basic.rawlog"])
command_parts.extend(
["--ground-truth", dataset + "basic.rawlog.GT.txt"])
if disable_visuals:
command_parts.extend(["--disable-visuals"])
if redirect_null:
with open(os.devnull, 'w') as fp:
result = subprocess.Popen(command_parts, stdout=fp).wait()
else:
result = subprocess.Popen(command_parts).wait()
#
# Announce results
#
output_dir_name_init = "graphslam_results"
dir_exists = os.path.isdir(output_dir_name_init)
if result == 0:
sPrint(intro_msg)
if dir_exists:
print("Removing the graphslam_results directory")
shutil.rmtree(output_dir_name_init)
else:
errors_num += 1
code = "Error code: {r}".format(r=result)
# is there a graphslam_results directory generated?
if dir_exists:
# If directory was created, rename it and add a new file in it
# with the statistics of the current run
# date string
date_string = "Automatically generated file - {}".format(
time.strftime("%c"))
date_string.replace(":", "_")
date_string.replace(" ", "_")
# new file
with open(output_dir_name_init + os.sep + "test_info",
"w") as f:
f.writelines([
i + os.linesep
for i in [date_string, "=" * 60, current_run_input]
])
# moving results file
output_dir_name_moved = "{d}_graphslam_results_test_{i}_of_{t}".format(
d=date_string, i=comb_i + 1, t=total_combs)
os.rename(output_dir_name_init, output_dir_name_moved)
logdir = "For more info on this see directory \"{d}\"".format(
d=output_dir_name_moved)
else:
logdir = "Results directory was not generated."
ePrint("\t\n".join([intro_msg, code, logdir]))
# total report
iPrint("Summary:")
if errors_num == 0:
print("No execution errors were reported... {col}OK".format(
col=Fore.RED))
else:
print("Failed executions: {}/{}... {col}ERROR".format(errors_num,
total_combs,
col=Fore.RED))
#_*_coding:utf-8_*_ # Ver el directorio actual import os print os.getcwd() print os.curdir()
import sys
print sys.argv
command = sys.argv[1]
path =sys.argv[2]
import time
for i in range(10):
sys.stdout.write('#')
time.sleep(0.1)
sys.stdout.flush()#正常的会将10个#放到缓存中，然后十个之后一块显示出
#但是用了flush()后就是有一个返回一个，就想就像进度条一样了
#4:os模块
os.getcwd()#获取当前工作目录
os.chdir("test1")#改变当前脚本的工作目录，相当于shell下的cd
os.curdir()#返回当前目录（.）
os.pardir()#获取当前目录的父目录字符串
os.makedirs("dirname/dirname1")#可生成多层的递归目录
os.removedirs("dirname1:")#若目录为空则删除，并递归到上一层
os.mkdir()#生成单级目录
os.rmdir()#删除单机空目录
os.listdir()#列出指定目录下的所有文件和子目录,并以列表的形式打印
#若目录为空，则删除，并递归到上一层目录;如果要删除dirname2，要写成dirname1/dirnam2，然后返回到dirname1，如果dirname1为空，则dirname1也将被删除
os.removedirs('dirname1/dirname2')
os.rename('name1','name2')
os.stat('day_01_str.py')#获取文件目录信息
os.sep#输出os特定的路径分隔符，win下为\\,linux下为/
os.linesep#输出当前平台使用的终止符，win下为\t\r\n,linux下为\n
os.pathsep#输出分割文件路径的
os.system("bash command")#运行shell命令，直接显示
os.environ()#获取系统环境变量
def main():
# Look for a ProPresenter installation to use default values from.
if pro6_install:
default_size = (pro6_install.output_width, pro6_install.output_height)
scaling = {v: k
for k, v in SCALE_MODES.items()
}.get(pro6_install.foreground_scaling)
library = pro6_install.get_library()
else:
default_size = (1280, 720)
scaling = "fit"
library = None
parser = ArgumentParser(
description=
"Loads a directory or list of images into a ProPresenter document.")
parser.add_argument("files",
type=str,
nargs='+',
help="Path(s) of files or directories to import.")
parser.add_argument("--title", type=str, help="The title of the document.")
parser.add_argument("--category",
type=str,
default="Presentation",
help="The type of document being created.")
parser.add_argument("--width",
type=int,
default=default_size[0],
help="The width of the created document.")
parser.add_argument("--height",
type=int,
default=default_size[1],
help="The height of the created document.")
parser.add_argument("--interval",
type=int,
help="Seconds between each slide on the timeline.")
parser.add_argument("--loop",
action="store_true",
help="If the timeline should loop.")
parser.add_argument("--scaling",
type=str.lower,
choices=list(SCALE_MODES.keys()),
default=scaling,
help="How the image should be scaled to the document.")
parser.add_argument(
"--outdir",
type=str,
help="The directory where the document should be saved.")
args = parser.parse_args()
# Validate some arguments
if args.width <= 0:
print("Invalid image width: %i - must be a positive integer." %
args.width)
if args.height <= 0:
print("Invalid image height: %i - must be a positive integer." %
args.height)
# Create a new document with the given settings.
print("Creating '%s' document with resolution %i x %i..." %
(args.category, args.width, args.height))
doc = PresentationDocument(args.category, args.height, args.width)
# Import files to the document.
for item in args.files:
import_file(doc, item)
print("DONE! Imported %i files to document." % len(doc.slides()))
# Setup the optional timeline.
if args.interval:
print("Setting timeline interval to %i seconds (loop: %s)." %
(args.interval, args.loop))
doc.create_slideshow(args.interval, args.loop)
# Determine a title for the document if none specified.
title = args.title
if not title:
if len(args.files) == 1:
title = path.basename(path.splitext(args.files[0])[0])
else:
title = "Imported files"
# Save the document to disk (prefers: --outdir, active library, current directory)
doc.path = path.join(args.outdir or library or curdir(), title + ".pro6")
doc.write()
if library and not args.outdir:
print("Document saved to library: %s" % title)
else:
print("Document saved: %s" % doc.path)
os.chdir(path)
out_path = r'E:\just language\reports\data\out'
is_exist = os.path.exists(out_path)
if not is_exist:
os.makedirs(out_path)
# 是否存在文件
os.path.isfile(filename)
# 列出目录和文件
os.listdir(path)
# 返回当前目录
os.curdir()
# 是不是一个目录
os.path.isdir(path)
# 文件夹大小
os.path.getsize(path)
# 分隔目录
os.path.split(path)
# 绝对路径
os.path.abspath(path)
# 分离文件名和拓展名
os.path.splitext()
def find_dat_files(directory=None):
if directory is None:
directory = os.curdir()
data_list = sorted(glob.glob(os.path.join(directory, '*.dat')))
return data_list
are messages and output files makes a call/return model less useful.
Suggested enhancement: could be extended to allow multiple sets
of command-line arguments and/or inputs per test script, to run a
script multiple times (glob for multiple ".in*" files in Inputs?).
Might also seem simpler to store all test files in same directory
with different extensions, but this could grow large over time.
Could also save both stderr and stdout to Errors on failures, but
I prefer to have expected/actual output in Outputs on regressions.
################################################################################
"""
import sys, os, glob,time
from subprocess import Popen,PIPE
#configure args
testdir = sys.argv[1] if len(sys.argv) > 1 else os.curdir()
forcegen = len(sys.argv) > 2
print('Start tester: ',time.asctime())
print('in ',os.path.abspath(testdir))
def verbose(*args):
print('-'*80)
for arg in args:
print(arg)
def quiet(*args): pass
trace = quiet
#glob scripts to be tested
testpatt = os.path.join(testdir,'Scripts','*.py')
testfiles = glob.glob(testpatt)
import sqlite3
import os
import os.path
import sys
from twisted.internet.task import LoopingCall
try:
# determine if application is a script file or frozen exe
if hasattr(sys, 'frozen'):
DB_DIR = os.path.dirname(sys.executable)
else:
DB_DIR = os.path.dirname(os.path.abspath(__file__))
except:
DB_DIR = os.curdir()
VERSION_FN = os.path.join(DB_DIR, 'db-version')
DB_FN = os.path.join(DB_DIR, 'stats.db')
class Database():
def __init__(self,bitHopper):
self.curs = None
self.bitHopper = bitHopper
self.pool = bitHopper.pool
self.check_database()
self.shares = {}
self.rejects = {}
self.payout = {}
self.user = {}
import os, time, pickle
import collabFiltering, preprocess
start_time = time.time()
"""
Parameters
----------
"""
m = 5 # number of items to recommend
n = 100 # number of more similar neighbours to visit
dist = "cosine" # distance to use: "cosine", "jaccard" or "basic"
normalizing = False # "True" to use the normalizing datas, "False" otherwise
U = 6 # recommend movies to U
path = os.curdir()
"""
Generate the "Movies" file
--------------------------
"""
listfiles = os.listdir(os.curdir)
if "Movies" not in listfiles:
preprocess.CreateMovies()
fMovies = open("Movies","rb")
pM = pickle.Unpickler(fMovies)
Movies = pM.load()
fMovies.close()
os.chdir(path+"/training_set")
def link (self,
target_desc,
objects,
output_filename,
output_dir=None,
libraries=None,
library_dirs=None,
runtime_library_dirs=None,
export_symbols=None,
debug=0,
extra_preargs=None,
extra_postargs=None,
build_temp=None,
target_lang=None):
# First fixup.
(objects, output_dir) = self._fix_object_args (objects, output_dir)
(libraries, library_dirs, runtime_library_dirs) = \
self._fix_lib_args (libraries, library_dirs, runtime_library_dirs)
# First examine a couple of options for things that aren't implemented yet
if not target_desc in (self.SHARED_LIBRARY, self.SHARED_OBJECT):
raise DistutilsPlatformError, 'Can only make SHARED_LIBRARY or SHARED_OBJECT targets on the Mac'
if runtime_library_dirs:
raise DistutilsPlatformError, 'Runtime library dirs not implemented yet'
if extra_preargs or extra_postargs:
raise DistutilsPlatformError, 'Runtime library dirs not implemented yet'
if len(export_symbols) != 1:
raise DistutilsPlatformError, 'Need exactly one export symbol'
# Next there are various things for which we need absolute pathnames.
# This is because we (usually) create the project in a subdirectory of
# where we are now, and keeping the paths relative is too much work right
# now.
sources = map(self._filename_to_abs, self.__sources)
include_dirs = map(self._filename_to_abs, self.__include_dirs)
if objects:
objects = map(self._filename_to_abs, objects)
else:
objects = []
if build_temp:
build_temp = self._filename_to_abs(build_temp)
else:
build_temp = os.curdir()
if output_dir:
output_filename = os.path.join(output_dir, output_filename)
# The output filename needs special handling: splitting it into dir and
# filename part. Actually I'm not sure this is really needed, but it
# can't hurt.
output_filename = self._filename_to_abs(output_filename)
output_dir, output_filename = os.path.split(output_filename)
# Now we need the short names of a couple of things for putting them
# into the project.
if output_filename[-8:] == '.ppc.slb':
basename = output_filename[:-8]
elif output_filename[-11:] == '.carbon.slb':
basename = output_filename[:-11]
else:
basename = os.path.strip(output_filename)[0]
projectname = basename + '.mcp'
targetname = basename
xmlname = basename + '.xml'
exportname = basename + '.mcp.exp'
prefixname = 'mwerks_%s_config.h'%basename
# Create the directories we need
distutils.dir_util.mkpath(build_temp, dry_run=self.dry_run)
distutils.dir_util.mkpath(output_dir, dry_run=self.dry_run)
# And on to filling in the parameters for the project builder
settings = {}
settings['mac_exportname'] = exportname
settings['mac_outputdir'] = output_dir
settings['mac_dllname'] = output_filename
settings['mac_targetname'] = targetname
settings['sysprefix'] = sys.prefix
settings['mac_sysprefixtype'] = 'Absolute'
sourcefilenames = []
sourcefiledirs = []
for filename in sources + objects:
dirname, filename = os.path.split(filename)
sourcefilenames.append(filename)
if not dirname in sourcefiledirs:
sourcefiledirs.append(dirname)
settings['sources'] = sourcefilenames
settings['libraries'] = libraries
settings['extrasearchdirs'] = sourcefiledirs + include_dirs + library_dirs
if self.dry_run:
print 'CALLING LINKER IN', os.getcwd()
for key, value in settings.items():
print '%20.20s %s'%(key, value)
return
# Build the export file
exportfilename = os.path.join(build_temp, exportname)
log.debug("\tCreate export file %s", exportfilename)
fp = open(exportfilename, 'w')
fp.write('%s\n'%export_symbols[0])
fp.close()
# Generate the prefix file, if needed, and put it in the settings
if self.__macros:
prefixfilename = os.path.join(os.getcwd(), os.path.join(build_temp, prefixname))
fp = open(prefixfilename, 'w')
fp.write('#include "mwerks_shcarbon_config.h"\n')
for name, value in self.__macros:
if value is None:
fp.write('#define %s\n'%name)
else:
fp.write('#define %s %s\n'%(name, value))
fp.close()
settings['prefixname'] = prefixname
# Build the XML file. We need the full pathname (only lateron, really)
# because we pass this pathname to CodeWarrior in an AppleEvent, and CW
# doesn't have a clue about our working directory.
xmlfilename = os.path.join(os.getcwd(), os.path.join(build_temp, xmlname))
log.debug("\tCreate XML file %s", xmlfilename)
xmlbuilder = mkcwproject.cwxmlgen.ProjectBuilder(settings)
xmlbuilder.generate()
xmldata = settings['tmp_projectxmldata']
fp = open(xmlfilename, 'w')
fp.write(xmldata)
fp.close()
# Generate the project. Again a full pathname.
projectfilename = os.path.join(os.getcwd(), os.path.join(build_temp, projectname))
log.debug('\tCreate project file %s', projectfilename)
mkcwproject.makeproject(xmlfilename, projectfilename)
# And build it
log.debug('\tBuild project')
mkcwproject.buildproject(projectfilename)
def parseExptConfig(configFile, librariesToSublibrariesDict):
parser = SafeConfigParser()
parser.read(configFile)
#output variables
paramDict = dict()
exitStatus = 0
warningString = ''
##check all sections
expectedSections = set(['experiment_settings',
'library_settings',
'counts_files',
'filter_settings',
'sgrna_analysis',
'growth_values',
'gene_analysis'])
parsedSections = set(parser.sections())
if len(expectedSections) != len(parsedSections) and len(expectedSections) != len(expectedSections.intersection(parsedSections)):
return paramDict, 1, 'Config file does not have all required sections or has extraneous sections!\nExpected:' + ','.join(expectedSections)
##experiment settings
if parser.has_option('experiment_settings','output_folder'):
paramDict['output_folder'] = parser.get('experiment_settings','output_folder') #ways to check this is a valid path?
else:
warningString += 'No output folder specified, defaulting to current directory\n.'
paramDict['output_folder'] = os.curdir()
if parser.has_option('experiment_settings','experiment_name'):
paramDict['experiment_name'] = parser.get('experiment_settings','experiment_name')
else:
warningString += 'No experiment name specified, defaulting to \'placeholder_expt_name\'\n.'
paramDict['experiment_name'] = 'placeholder_expt_name'
##library settings
libraryDict = librariesToSublibrariesDict
if parser.has_option('library_settings','library'):
parsedLibrary = parser.get('library_settings','library')
if parsedLibrary.lower() in libraryDict:
paramDict['library'] = parsedLibrary.lower()
else:
warningString += 'Library name not recognized\n'
exitStatus += 1
else:
warningString += 'No library specified\n'
exitStatus += 1
parsedLibrary = ''
if 'library' in paramDict:
if parser.has_option('library_settings','sublibraries'):
parsedSubList = parser.get('library_settings','sublibraries').strip().split('\n')
paramDict['sublibraries'] = []
for sub in parsedSubList:
sub = sub.lower()
if sub in libraryDict[paramDict['library']]:
paramDict['sublibraries'].append(sub)
else:
warningString += 'Sublibrary %s not recognized\n' % sub
else:
paramDict['sublibraries'] = libraryDict[paramDict['library']]
##counts files
if parser.has_option('counts_files','counts_file_string'):
countsFileString = parser.get('counts_files','counts_file_string').strip()
paramDict['counts_file_list'] = []
for stringLine in countsFileString.split('\n'):
stringLine = stringLine.strip()
if len(stringLine.split(':')) != 2 or len(stringLine.split('|')) != 2:
warningString += 'counts file entry could not be parsed: ' + stringLine + '\n'
exitStatus += 1
else:
parsedPath = stringLine.split(':')[0]
if os.path.isfile(parsedPath) == False:
warningString += 'Counts file not found: ' + parsedPath + '\n'
exitStatus += 1
condition, replicate = stringLine.split(':')[1].split('|')
paramDict['counts_file_list'].append((condition, replicate,parsedPath))
else:
warningString += 'No counts files entered\n'
exitStatus += 1
##filter settings
filterOptions = ['either','both']
if parser.has_option('filter_settings','filter_type') and parser.get('filter_settings','filter_type').lower() in filterOptions:
paramDict['filter_type'] = parser.get('filter_settings','filter_type').lower()
else:
warningString += 'Filter type not set or not recognized, defaulting to \'either\'\n'
paramDict['filter_type'] = 'either'
if parser.has_option('filter_settings','minimum_reads'):
try:
paramDict['minimum_reads'] = parser.getint('filter_settings','minimum_reads')
except ValueError:
warningString += 'Minimum read value not an integer, defaulting to 0\n' #recommended value is 50 but seems arbitrary to default to that
paramDict['minimum_reads'] = 0
else:
warningString += 'Minimum read value not found, defaulting to 0\n' #recommended value is 50 but seems arbitrary to default to that
paramDict['minimum_reads'] = 0
##sgRNA Analysis
if parser.has_option('sgrna_analysis','condition_string'):
conditionString = parser.get('sgrna_analysis','condition_string').strip()
paramDict['condition_tuples'] = []
if 'counts_file_list' in paramDict:
expectedConditions = set(zip(*paramDict['counts_file_list'])[0])
else:
expectedConditions = []
enteredConditions = set()
for conditionStringLine in conditionString.split('\n'):
conditionStringLine = conditionStringLine.strip()
if len(conditionStringLine.split(':')) != 3:
warningString += 'Phenotype condition line not understood: ' + conditionStringLine + '\n'
exitStatus += 1
else:
phenotype, condition1, condition2 = conditionStringLine.split(':')
if condition1 not in expectedConditions or condition2 not in expectedConditions:
warningString += 'One of the conditions entered does not correspond to a counts file: ' + conditionStringLine + '\n'
exitStatus += 1
else:
paramDict['condition_tuples'].append((phenotype,condition1,condition2))
enteredConditions.add(condition1)
enteredConditions.add(condition2)
if len(paramDict['condition_tuples']) == 0:
warningString += 'No phenotype score/condition pairs found\n'
exitStatus += 1
unusedConditions = list(expectedConditions - enteredConditions)
if len(unusedConditions) > 0:
warningString += 'Some conditions assigned to counts files will not be incorporated in sgRNA analysis:\n' \
+ ','.join(unusedConditions) + '\n'
else:
warningString += 'No phenotype score/condition pairs entered\n'
exitStatus += 1
pseudocountOptions = ['zeros only','all values','filter out']
if parser.has_option('sgrna_analysis','pseudocount_behavior') and parser.get('sgrna_analysis','pseudocount_behavior').lower() in pseudocountOptions:
paramDict['pseudocount_behavior'] = parser.get('sgrna_analysis','pseudocount_behavior').lower()
else:
warningString += 'Pseudocount behavior not set or not recognized, defaulting to \'zeros only\'\n'
paramDict['pseudocount_behavior'] = 'zeros only'
if parser.has_option('sgrna_analysis','pseudocount'):
try:
paramDict['pseudocount'] = parser.getfloat('sgrna_analysis','pseudocount')
except ValueError:
warningString += 'Pseudocount value not an number, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
else:
warningString += 'Pseudocount value not found, defaulting to 0.1\n'
paramDict['pseudocount'] = 0.1
##Growth Values
if parser.has_option('growth_values','growth_value_string') and len(parser.get('growth_values','growth_value_string').strip()) != 0:
growthValueString = parser.get('growth_values','growth_value_string').strip()
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(zip(*paramDict['condition_tuples'])[0])
expectedReplicates = set(zip(*paramDict['counts_file_list'])[1])
expectedTupleList = []
for comp in expectedComparisons:
for rep in expectedReplicates:
expectedTupleList.append((comp,rep))
else:
expectedTupleList = []
enteredTupleList = []
growthValueTuples = []
for growthValueLine in growthValueString.split('\n'):
growthValueLine = growthValueLine.strip()
linesplit = growthValueLine.split(':')
if len(linesplit) != 3:
warningString += 'Growth value line not understood: ' + growthValueLine + '\n'
exitStatus += 1
continue
comparison = linesplit[0]
replicate = linesplit[1]
try:
growthVal = float(linesplit[2])
except ValueError:
warningString += 'Growth value not a number: ' + growthValueLine + '\n'
exitStatus += 1
continue
curTup = (comparison,replicate)
if curTup in expectedTupleList:
if curTup not in enteredTupleList:
enteredTupleList.append(curTup)
growthValueTuples.append((comparison,replicate,growthVal))
else:
warningString += ':'.join(curTup) + ' has multiple growth values entered\n'
exitStatus += 1
else:
warningString += ':'.join(curTup) + ' was not expected given the specified counts file assignments and sgRNA phenotypes\n'
exitStatus += 1
#because we enforced no duplicates or unexpected values these should match up unless there were values not entered
#require all growth values to be explictly entered if some were
if len(enteredTupleList) != len(expectedTupleList):
warningString += 'Growth values were not entered for all expected comparisons/replicates. Expected: ' + \
','.join([':'.join(tup) for tup in expectedTupleList]) + '\nEntered: ' + \
','.join([':'.join(tup) for tup in enteredTupleList]) + '\n'
exitStatus += 1
else:
paramDict['growth_value_tuples'] = growthValueTuples
else:
warningString += 'No growth values--all phenotypes will be reported as log2enrichments\n'
paramDict['growth_value_tuples'] = []
if 'condition_tuples' in paramDict and 'counts_file_list' in paramDict:
expectedComparisons = set(zip(*paramDict['condition_tuples'])[0])
expectedReplicates = set(zip(*paramDict['counts_file_list'])[1])
for comp in expectedComparisons:
for rep in expectedReplicates:
paramDict['growth_value_tuples'].append((comp,rep,1))
##Gene Analysis
if parser.has_option('gene_analysis','collapse_to_transcripts'):
try:
paramDict['collapse_to_transcripts'] = parser.getboolean('gene_analysis','collapse_to_transcripts')
except ValueError:
warningString += 'Collapse to transcripts entry not a recognized boolean value\n'
exitStatus += 1
else:
paramDict['collapse_to_transcripts'] = True
warningString += 'Collapse to transcripts defaulting to True\n'
#pseudogene parameters
if parser.has_option('gene_analysis','generate_pseudogene_dist'):
try:
paramDict['generate_pseudogene_dist'] = parser.getboolean('gene_analysis','generate_pseudogene_dist')
except ValueError:
warningString += 'Generate pseudogene dist entry not a recognized boolean value\n'
exitStatus += 1
else:
paramDict['generate_pseudogene_dist'] = False
warningString += 'Generate pseudogene dist defaulting to False\n'
if 'generate_pseudogene_dist' in paramDict and paramDict['generate_pseudogene_dist'] == True:
if parser.has_option('gene_analysis','pseudogene_size'):
try:
paramDict['pseudogene_size'] = parser.getint('gene_analysis','pseudogene_size')
except ValueError:
warningString += 'Pseudogene size entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
exitStatus += 1
if parser.has_option('gene_analysis','num_pseudogenes'):
try:
paramDict['num_pseudogenes'] = parser.getint('gene_analysis','num_pseudogenes')
except ValueError:
warningString += 'Pseudogene number entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No pseudogene size provided\n'
#list possible analyses in param dict as dictionary with keys = analysis and values = analysis-specific params
paramDict['analyses'] = dict()
#analyze by average of best n
if parser.has_option('gene_analysis','calculate_ave'):
try:
if parser.getboolean('gene_analysis','calculate_ave') == True:
paramDict['analyses']['calculate_ave'] = []
except ValueError:
warningString += 'Calculate ave entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_ave' in paramDict['analyses']:
if parser.has_option('gene_analysis','best_n'):
try:
paramDict['analyses']['calculate_ave'].append(parser.getint('gene_analysis','best_n'))
except ValueError:
warningString += 'Best_n entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No best_n value provided for average analysis function\n'
exitStatus += 1
else:
warningString += 'Best n average analysis not specified, defaulting to False\n'
#analyze by Mann-Whitney
if parser.has_option('gene_analysis','calculate_mw'):
try:
if parser.getboolean('gene_analysis','calculate_mw') == True:
paramDict['analyses']['calculate_mw'] = []
except ValueError:
warningString += 'Calculate Mann-Whitney entry not a recognized boolean value\n'
exitStatus += 1
#analyze by K-S, skipping for now
#analyze by nth best sgRNA
if parser.has_option('gene_analysis','calculate_nth'):
try:
if parser.getboolean('gene_analysis','calculate_nth') == True:
paramDict['analyses']['calculate_nth'] = []
except ValueError:
warningString += 'Calculate best Nth sgRNA entry not a recognized boolean value\n'
exitStatus += 1
if 'calculate_nth' in paramDict['analyses']:
if parser.has_option('gene_analysis','nth'):
try:
paramDict['analyses']['calculate_nth'].append(parser.getint('gene_analysis','nth'))
except ValueError:
warningString += 'Nth best sgRNA entry not a recognized integer value\n'
exitStatus += 1
else:
warningString += 'No Nth best value provided for that analysis function\n'
exitStatus += 1
else:
warningString += 'Nth best sgRNA analysis not specified, defaulting to False\n'
if len(paramDict['analyses']) == 0:
warningString += 'No analyses selected to compute gene scores\n' #should this raise exitStatus?
return paramDict, exitStatus, warningString