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allianceauth/allianceauth | allianceauth/timerboard/views.py | AddUpdateMixin.get_form_kwargs | def get_form_kwargs(self):
"""
Inject the request user into the kwargs passed to the form
"""
kwargs = super(AddUpdateMixin, self).get_form_kwargs()
kwargs.update({'user': self.request.user})
return kwargs | python | def get_form_kwargs(self):
"""
Inject the request user into the kwargs passed to the form
"""
kwargs = super(AddUpdateMixin, self).get_form_kwargs()
kwargs.update({'user': self.request.user})
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allianceauth/allianceauth | allianceauth/services/abstract.py | ServicesCRUDMixin.get_object | def get_object(self, queryset=None):
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Returns the object the view is displaying.
"""
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queryset = self.get_queryset()
try:
return queryset.get(user__pk=self.request.user.pk)
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allianceauth/allianceauth | allianceauth/groupmanagement/managers.py | GroupManager.can_manage_groups | def can_manage_groups(cls, user):
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Check if the user can manage groups. Either has the
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"""
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allianceauth/allianceauth | allianceauth/groupmanagement/managers.py | GroupManager.can_manage_group | def can_manage_group(cls, user, group):
"""
Check user has permission to manage the given group
:param user: User object to test permission of
:param group: Group object the user is attempting to manage
:return: True if the user can manage the group
"""
if user.is... | python | def can_manage_group(cls, user, group):
"""
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allianceauth/allianceauth | allianceauth/groupmanagement/models.py | create_auth_group | def create_auth_group(sender, instance, created, **kwargs):
"""
Creates the AuthGroup model when a group is created
"""
if created:
AuthGroup.objects.create(group=instance) | python | def create_auth_group(sender, instance, created, **kwargs):
"""
Creates the AuthGroup model when a group is created
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto.construct_command | def construct_command(self, command, keys=None, opts=None):
"""
Constructs a TS3 formatted command string
Keys can have a single nested list to construct a nested parameter
@param command: Command list
@type command: string
@param keys: Key/Value pairs
@type keys:... | python | def construct_command(self, command, keys=None, opts=None):
"""
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@type command: string
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto.parse_command | def parse_command(self, commandstr):
"""
Parses a TS3 command string into command/keys/opts tuple
@param commandstr: Command string
@type commandstr: string
"""
if len(commandstr.split('|')) > 1:
vals = []
for cmd in commandstr.split('|'):
... | python | def parse_command(self, commandstr):
"""
Parses a TS3 command string into command/keys/opts tuple
@param commandstr: Command string
@type commandstr: string
"""
if len(commandstr.split('|')) > 1:
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto._escape_str | def _escape_str(value):
"""
Escape a value into a TS3 compatible string
@param value: Value
@type value: string/int
"""
if isinstance(value, int):
return "%d" % value
value = value.replace("\\", r'\\')
for i, j in ts3_escape.items():
... | python | def _escape_str(value):
"""
Escape a value into a TS3 compatible string
@param value: Value
@type value: string/int
"""
if isinstance(value, int):
return "%d" % value
value = value.replace("\\", r'\\')
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Proto._unescape_str | def _unescape_str(value):
"""
Unescape a TS3 compatible string into a normal string
@param value: Value
@type value: string/int
"""
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value = value.replace(r"\\", "\\")
for i, j in ts3_escape.items(... | python | def _unescape_str(value):
"""
Unescape a TS3 compatible string into a normal string
@param value: Value
@type value: string/int
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Server.login | def login(self, username, password):
"""
Login to the TS3 Server
@param username: Username
@type username: str
@param password: Password
@type password: str
"""
d = self.send_command('login', keys={'client_login_name': username, 'client_login_password': pa... | python | def login(self, username, password):
"""
Login to the TS3 Server
@param username: Username
@type username: str
@param password: Password
@type password: str
"""
d = self.send_command('login', keys={'client_login_name': username, 'client_login_password': pa... | [
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allianceauth/allianceauth | allianceauth/services/modules/teamspeak3/util/ts3.py | TS3Server.use | def use(self, id):
"""
Use a particular Virtual Server instance
@param id: Virtual Server ID
@type id: int
"""
if self._connected and id > 0:
self.send_command('use', keys={'sid': id}) | python | def use(self, id):
"""
Use a particular Virtual Server instance
@param id: Virtual Server ID
@type id: int
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allianceauth/allianceauth | allianceauth/services/modules/example/auth_hooks.py | ExampleService.render_services_ctrl | def render_services_ctrl(self, request):
"""
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You can override the default template and create a
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:param request:
:return:
"""
urls = self.Urls()
urls.auth_activate = 'auth_e... | python | def render_services_ctrl(self, request):
"""
Example for rendering the service control panel row
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allianceauth/allianceauth | allianceauth/eveonline/models.py | EveCharacter.alliance | def alliance(self) -> Union[EveAllianceInfo, None]:
"""
Pseudo foreign key from alliance_id to EveAllianceInfo
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:return: EveAllianceInfo or None
"""
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Pseudo foreign key from alliance_id to EveAllianceInfo
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | pre_save_config | def pre_save_config(sender, instance, *args, **kwargs):
"""
Checks if enable was toggled on group config and
deletes groups if necessary.
"""
logger.debug("Received pre_save from {}".format(instance))
if not instance.pk:
# new model being created
return
try:
old_insta... | python | def pre_save_config(sender, instance, *args, **kwargs):
"""
Checks if enable was toggled on group config and
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logger.debug("Received pre_save from {}".format(instance))
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | check_groups_on_profile_update | def check_groups_on_profile_update(sender, instance, created, *args, **kwargs):
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Trigger check when main character or state changes.
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/signals.py | autogroups_states_changed | def autogroups_states_changed(sender, instance, action, reverse, model, pk_set, *args, **kwargs):
"""
Trigger group membership update when a state is added or removed from
an autogroup config.
"""
if action.startswith('post_'):
for pk in pk_set:
try:
state = State... | python | def autogroups_states_changed(sender, instance, action, reverse, model, pk_set, *args, **kwargs):
"""
Trigger group membership update when a state is added or removed from
an autogroup config.
"""
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allianceauth/allianceauth | allianceauth/authentication/admin.py | make_service_hooks_update_groups_action | def make_service_hooks_update_groups_action(service):
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:param service: services.hooks.ServicesHook
:return: fn to update services groups for the selected users
"""
def update_service_groups(modeladmin, request, queryset):
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:return: fn to update services groups for the selected users
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allianceauth/allianceauth | allianceauth/thirdparty/navhelper/templatetags/navactive.py | renavactive | def renavactive(request, pattern):
"""
{% renavactive request "^/a_regex" %}
"""
if re.search(pattern, request.path):
return getattr(settings, "NAVHELPER_ACTIVE_CLASS", "active")
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"""
{% renavactive request "^/a_regex" %}
"""
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allianceauth/allianceauth | allianceauth/thirdparty/navhelper/templatetags/navactive.py | navactive | def navactive(request, urls):
"""
{% navactive request "view_name another_view_name" %}
"""
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"""
{% navactive request "view_name another_view_name" %}
"""
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resolved = resolve(request.path)
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allianceauth/allianceauth | allianceauth/eveonline/autogroups/models.py | AutogroupsConfigManager.update_groups_for_state | def update_groups_for_state(self, state: State):
"""
Update all the Group memberships for the users
who have State
:param state: State to update for
:return:
"""
users = get_users_for_state(state)
for config in self.filter(states=state):
logger... | python | def update_groups_for_state(self, state: State):
"""
Update all the Group memberships for the users
who have State
:param state: State to update for
:return:
"""
users = get_users_for_state(state)
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:param user: User to update for
:param state: State to update user for
:return:
"""
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:return: name with spaces replaced with the configured character(s) or unchanged if configured
"""
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... | python | def _replace_spaces(self, name: str) -> str:
"""
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allianceauth/allianceauth | allianceauth/services/modules/discord/manager.py | api_backoff | def api_backoff(func):
"""
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Decorator, Handles HTTP 429 "Too Many Requests" messages from the Discord API
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allianceauth/allianceauth | allianceauth/srp/views.py | random_string | def random_string(string_length=10):
"""Returns a random string of length string_length."""
random = str(uuid.uuid4()) # Convert UUID format to a Python string.
random = random.upper() # Make all characters uppercase.
random = random.replace("-", "") # Remove the UUID '-'.
return random[0:string_... | python | def random_string(string_length=10):
"""Returns a random string of length string_length."""
random = str(uuid.uuid4()) # Convert UUID format to a Python string.
random = random.upper() # Make all characters uppercase.
random = random.replace("-", "") # Remove the UUID '-'.
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tariqdaouda/pyGeno | pyGeno/Genome.py | getGenomeList | def getGenomeList() :
"""Return the names of all imported genomes"""
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f = rfilt.RabaQuery(Genome_Raba)
names = []
for g in f.iterRun() :
names.append(g.name)
return names | python | def getGenomeList() :
"""Return the names of all imported genomes"""
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names = []
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tariqdaouda/pyGeno | pyGeno/Transcript.py | Transcript.iterCodons | def iterCodons(self) :
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yield self.getCodon(i) | python | def iterCodons(self) :
"""iterates through the codons"""
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | removeDuplicates | def removeDuplicates(inFileName, outFileName) :
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legend = f.readline()
data = ''
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h[l] = 0
data +=... | python | def removeDuplicates(inFileName, outFileName) :
"""removes duplicated lines from a 'inFileName' CSV file, the results are witten in 'outFileName'"""
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | catCSVs | def catCSVs(folder, ouputFileName, removeDups = False) :
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res = ''
legend = []
csvs = []
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cs... | python | def joinCSVs(csvFilePaths, column, ouputFileName, separator = ',') :
"""csvFilePaths should be an iterable. Joins all CSVs according to the values in the column 'column'. Write the results in a new file 'ouputFileName' """
res = ''
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.addField | def addField(self, field) :
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.parse | def parse(self, filePath, skipLines=0, separator = ',', stringSeparator = '"', lineSeparator = '\n') :
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.commitLine | def commitLine(self, line) :
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.closeStreamToFile | def closeStreamToFile(self) :
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if self.streamBuffer is None :
raise ValueError("Commit lines is only for when you are streaming to a file")
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.newLine | def newLine(self) :
"""Appends an empty line at the end of the CSV and returns it"""
l = CSVEntry(self)
if self.keepInMemory :
self.lines.append(l)
return l | python | def newLine(self) :
"""Appends an empty line at the end of the CSV and returns it"""
l = CSVEntry(self)
if self.keepInMemory :
self.lines.append(l)
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.insertLine | def insertLine(self, i) :
"""Inserts an empty line at position i and returns it"""
self.data.insert(i, CSVEntry(self))
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tariqdaouda/pyGeno | pyGeno/tools/parsers/CSVTools.py | CSVFile.save | def save(self, filePath) :
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f = open(filePath, 'w')
f.write(self.toStr())
f.flush()
f.close() | python | def save(self, filePath) :
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tariqdaouda/pyGeno | pyGeno/pyGenoObjectBases.py | pyGenoRabaObjectWrapper.count | def count(self, objectType, *args, **coolArgs) :
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tariqdaouda/pyGeno | pyGeno/pyGenoObjectBases.py | pyGenoRabaObjectWrapper.get | def get(self, objectType, *args, **coolArgs) :
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Usage examples:
* myGenome.get("Gene", name = 'TPST2')
* myGene.get(Protein, id = 'ENSID...')
* myGenome.get(Transcript, {'start >' : x, 'end <' : y})"""
ret =... | python | def get(self, objectType, *args, **coolArgs) :
"""Raba Magic inside. This is th function that you use for
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Usage examples:
* myGenome.get("Gene", name = 'TPST2')
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | importSNPs | def importSNPs(packageFile) :
"""The big wrapper, this function should detect the SNP type by the package manifest and then launch the corresponding function.
Here's an example of a SNP manifest file for Casava SNPs::
[package_infos]
description = Casava SNPs for testing purposes
maintainer = Tariq Daouda
ma... | python | def importSNPs(packageFile) :
"""The big wrapper, this function should detect the SNP type by the package manifest and then launch the corresponding function.
Here's an example of a SNP manifest file for Casava SNPs::
[package_infos]
description = Casava SNPs for testing purposes
maintainer = Tariq Daouda
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | deleteSNPs | def deleteSNPs(setName) :
"""deletes a set of polymorphisms"""
con = conf.db
try :
SMaster = SNPMaster(setName = setName)
con.beginTransaction()
SNPType = SMaster.SNPType
con.delete(SNPType, 'setName = ?', (setName,))
SMaster.delete()
con.endTransaction()
except KeyError :
raise KeyError("Can't delete... | python | def deleteSNPs(setName) :
"""deletes a set of polymorphisms"""
con = conf.db
try :
SMaster = SNPMaster(setName = setName)
con.beginTransaction()
SNPType = SMaster.SNPType
con.delete(SNPType, 'setName = ?', (setName,))
SMaster.delete()
con.endTransaction()
except KeyError :
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | _importSNPs_AgnosticSNP | def _importSNPs_AgnosticSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno wil interpret all positions as 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = CSVFile()
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"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno wil interpret all positions as 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
snpData = CSVFile()
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snpData = SNPsTxtFile(snpsFile)
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"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
printf('importing SNP set %s for species %s...' % (setName, species))
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tariqdaouda/pyGeno | pyGeno/importation/SNPs.py | _importSNPs_dbSNPSNP | def _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) :
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snpData = VCFFile(snpsFile, gziped = True, stream = True)
dbSNPSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
conf.db.be... | python | def _importSNPs_dbSNPSNP(setName, species, genomeSource, snpsFile) :
"This function will also create an index on start->chromosomeNumber->setName. Warning : pyGeno positions are 0 based"
snpData = VCFFile(snpsFile, gziped = True, stream = True)
dbSNPSNP.dropIndex(('start', 'chromosomeNumber', 'setName'))
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tariqdaouda/pyGeno | pyGeno/SNP.py | getSNPSetsList | def getSNPSetsList() :
"""Return the names of all imported snp sets"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(SNPMaster)
names = []
for g in f.iterRun() :
names.append(g.setName)
return names | python | def getSNPSetsList() :
"""Return the names of all imported snp sets"""
import rabaDB.filters as rfilt
f = rfilt.RabaQuery(SNPMaster)
names = []
for g in f.iterRun() :
names.append(g.setName)
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for e in s[:-1] :
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sys.stdout.flush() | python | def printf(*s) :
'print + sys.stdout.flush()'
for e in s[:-1] :
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tariqdaouda/pyGeno | pyGeno/tools/Stats.py | kullback_leibler | def kullback_leibler(p, q) :
"""Discrete Kullback-Leibler divergence D(P||Q)"""
p = np.asarray(p, dtype=np.float)
q = np.asarray(q, dtype=np.float)
if p.shape != q.shape :
raise ValueError("p and q must be of the same dimensions")
return np.sum(np.where(p > 0, np.log(p / q) * p, 0)) | python | def kullback_leibler(p, q) :
"""Discrete Kullback-Leibler divergence D(P||Q)"""
p = np.asarray(p, dtype=np.float)
q = np.asarray(q, dtype=np.float)
if p.shape != q.shape :
raise ValueError("p and q must be of the same dimensions")
return np.sum(np.where(p > 0, np.log(p / q) * p, 0)) | [
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f.close() | python | def parseFile(self, fil) :
"""Opens a file and parses it"""
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self.data.append(('>'+header, data))
else :
self.data.append((header, data)) | python | def add(self, header, data) :
"""appends a new entry to the file"""
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self.data.append(('>'+header, data))
else :
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offset = 0
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offset += f+len(needle)
h = h[f+len(needle):]
f = h.find(needle)
return res | python | def findAll(haystack, needle) :
"""returns a list of all occurances of needle in haystack"""
h = haystack
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offset = 0
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"""returns a list of complementary sequence without inversing it"""
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"""returns a list of complementary sequence without inversing it"""
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | translateDNA_6Frames | def translateDNA_6Frames(sequence) :
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"""returns 6 translation of sequence. One for each reading frame"""
trans = (
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translateDNA(sequence, 'f3'),
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | translateDNA | def translateDNA(sequence, frame = 'f1', translTable_id='default') :
"""Translates DNA code, frame : fwd1, fwd2, fwd3, rev1, rev2, rev3"""
protein = ""
if frame == 'f1' :
dna = sequence
elif frame == 'f2':
dna = sequence[1:]
elif frame == 'f3' :
dna = sequence[2:]
elif frame == 'r1' :
dna = reverseCompl... | python | def translateDNA(sequence, frame = 'f1', translTable_id='default') :
"""Translates DNA code, frame : fwd1, fwd2, fwd3, rev1, rev2, rev3"""
protein = ""
if frame == 'f1' :
dna = sequence
elif frame == 'f2':
dna = sequence[1:]
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dna = sequence[2:]
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | getSequenceCombinaisons | def getSequenceCombinaisons(polymorphipolymorphicDnaSeqSeq, pos = 0) :
"""Takes a dna sequence with polymorphismes and returns all the possible sequences that it can yield"""
if type(polymorphipolymorphicDnaSeqSeq) is not types.ListType :
seq = list(polymorphipolymorphicDnaSeqSeq)
else :
seq = polymorphipolymor... | python | def getSequenceCombinaisons(polymorphipolymorphicDnaSeqSeq, pos = 0) :
"""Takes a dna sequence with polymorphismes and returns all the possible sequences that it can yield"""
if type(polymorphipolymorphicDnaSeqSeq) is not types.ListType :
seq = list(polymorphipolymorphicDnaSeqSeq)
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seq = polymorphipolymor... | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | encodePolymorphicNucleotide | def encodePolymorphicNucleotide(polySeq) :
"""returns a single character encoding all nucletides of polySeq
in a single character. PolySeq must have one of the following forms:
['A', 'T', 'G'], 'ATG', 'A/T/G'"""
if type(polySeq) is types.StringType :
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sseq = list(polySeq)
else :... | python | def encodePolymorphicNucleotide(polySeq) :
"""returns a single character encoding all nucletides of polySeq
in a single character. PolySeq must have one of the following forms:
['A', 'T', 'G'], 'ATG', 'A/T/G'"""
if type(polySeq) is types.StringType :
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sseq = list(polySeq)
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | decodePolymorphicNucleotide | def decodePolymorphicNucleotide(nuc) :
"""the opposite of encodePolymorphicNucleotide, from 'R' to ['A', 'G']"""
if nuc in polymorphicNucleotides :
return polymorphicNucleotides[nuc]
if nuc in nucleotides :
return nuc
raise ValueError('nuc: %s, is not a valid nucleotide' % nuc) | python | def decodePolymorphicNucleotide(nuc) :
"""the opposite of encodePolymorphicNucleotide, from 'R' to ['A', 'G']"""
if nuc in polymorphicNucleotides :
return polymorphicNucleotides[nuc]
if nuc in nucleotides :
return nuc
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | getNucleotideCodon | def getNucleotideCodon(sequence, x1) :
"""Returns the entire codon of the nucleotide at pos x1 in sequence,
and the position of that nocleotide in the codon in a tuple"""
if x1 < 0 or x1 >= len(sequence) :
return None
p = x1%3
if p == 0 :
return (sequence[x1: x1+3], 0)
elif p ==1 :
return (sequence[x1-1:... | python | def getNucleotideCodon(sequence, x1) :
"""Returns the entire codon of the nucleotide at pos x1 in sequence,
and the position of that nocleotide in the codon in a tuple"""
if x1 < 0 or x1 >= len(sequence) :
return None
p = x1%3
if p == 0 :
return (sequence[x1: x1+3], 0)
elif p ==1 :
return (sequence[x1-1:... | [
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | showDifferences | def showDifferences(seq1, seq2) :
"""Returns a string highligthing differences between seq1 and seq2:
* Matches by '-'
* Differences : 'A|T'
* Exceeded length : '#'
"""
ret = []
for i in range(max(len(seq1), len(seq2))) :
if i >= len(seq1) :
c1 = '#'
else :
c1 = seq1[i]
if i >= len(seq2) :
... | python | def showDifferences(seq1, seq2) :
"""Returns a string highligthing differences between seq1 and seq2:
* Matches by '-'
* Differences : 'A|T'
* Exceeded length : '#'
"""
ret = []
for i in range(max(len(seq1), len(seq2))) :
if i >= len(seq1) :
c1 = '#'
else :
c1 = seq1[i]
if i >= len(seq2) :
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tariqdaouda/pyGeno | pyGeno/tools/UsefulFunctions.py | highlightSubsequence | def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') :
"""returns a sequence where the subsequence in [x1, x2[ is placed
in bewteen 'start' and 'stop'"""
seq = list(sequence)
print x1, x2-1, len(seq)
seq[x1] = start + seq[x1]
seq[x2-1] = seq[x2-1] + stop
return ''.join(seq) | python | def highlightSubsequence(sequence, x1, x2, start=' [', stop = '] ') :
"""returns a sequence where the subsequence in [x1, x2[ is placed
in bewteen 'start' and 'stop'"""
seq = list(sequence)
print x1, x2-1, len(seq)
seq[x1] = start + seq[x1]
seq[x2-1] = seq[x2-1] + stop
return ''.join(seq) | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | backUpDB | def backUpDB() :
"""backup the current database version. automatically called by importGenome(). Returns the filename of the backup"""
st = time.ctime().replace(' ', '_')
fn = conf.pyGeno_RABA_DBFILE.replace('.db', '_%s-bck.db' % st)
shutil.copy2(conf.pyGeno_RABA_DBFILE, fn)
return fn | python | def backUpDB() :
"""backup the current database version. automatically called by importGenome(). Returns the filename of the backup"""
st = time.ctime().replace(' ', '_')
fn = conf.pyGeno_RABA_DBFILE.replace('.db', '_%s-bck.db' % st)
shutil.copy2(conf.pyGeno_RABA_DBFILE, fn)
return fn | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | deleteGenome | def deleteGenome(species, name) :
"""Removes a genome from the database"""
printf('deleting genome (%s, %s)...' % (species, name))
conf.db.beginTransaction()
objs = []
allGood = True
try :
genome = Genome_Raba(name = name, species = species.lower())
objs.append(genome)
... | python | def deleteGenome(species, name) :
"""Removes a genome from the database"""
printf('deleting genome (%s, %s)...' % (species, name))
conf.db.beginTransaction()
objs = []
allGood = True
try :
genome = Genome_Raba(name = name, species = species.lower())
objs.append(genome)
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | importGenome | def importGenome(packageFile, batchSize = 50, verbose = 0) :
"""Import a pyGeno genome package. A genome packages is folder or a tar.gz ball that contains at it's root:
* gziped fasta files for all chromosomes, or URLs from where them must be downloaded
* gziped GTF gene_set file from Ensembl, or an U... | python | def importGenome(packageFile, batchSize = 50, verbose = 0) :
"""Import a pyGeno genome package. A genome packages is folder or a tar.gz ball that contains at it's root:
* gziped fasta files for all chromosomes, or URLs from where them must be downloaded
* gziped GTF gene_set file from Ensembl, or an U... | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | _importGenomeObjects | def _importGenomeObjects(gtfFilePath, chroSet, genome, batchSize, verbose = 0) :
"""verbose must be an int [0, 4] for various levels of verbosity"""
class Store(object) :
def __init__(self, conf) :
self.conf = conf
self.chromosomes = {}
self.gen... | python | def _importGenomeObjects(gtfFilePath, chroSet, genome, batchSize, verbose = 0) :
"""verbose must be an int [0, 4] for various levels of verbosity"""
class Store(object) :
def __init__(self, conf) :
self.conf = conf
self.chromosomes = {}
self.gen... | [
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tariqdaouda/pyGeno | pyGeno/importation/Genomes.py | _importSequence | def _importSequence(chromosome, fastaFile, targetDir) :
"Serializes fastas into .dat files"
f = gzip.open(fastaFile)
header = f.readline()
strRes = f.read().upper().replace('\n', '').replace('\r', '')
f.close()
fn = '%s/chromosome%s.dat' % (targetDir, chromosome.number)
f = open(fn, 'w')
... | python | def _importSequence(chromosome, fastaFile, targetDir) :
"Serializes fastas into .dat files"
f = gzip.open(fastaFile)
header = f.readline()
strRes = f.read().upper().replace('\n', '').replace('\r', '')
f.close()
fn = '%s/chromosome%s.dat' % (targetDir, chromosome.number)
f = open(fn, 'w')
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tariqdaouda/pyGeno | pyGeno/configuration.py | createDefaultConfigFile | def createDefaultConfigFile() :
"""Creates a default configuration file"""
s = "[pyGeno_config]\nsettings_dir=%s\nremote_location=%s" % (pyGeno_SETTINGS_DIR, pyGeno_REMOTE_LOCATION)
f = open('%s/config.ini' % pyGeno_SETTINGS_DIR, 'w')
f.write(s)
f.close() | python | def createDefaultConfigFile() :
"""Creates a default configuration file"""
s = "[pyGeno_config]\nsettings_dir=%s\nremote_location=%s" % (pyGeno_SETTINGS_DIR, pyGeno_REMOTE_LOCATION)
f = open('%s/config.ini' % pyGeno_SETTINGS_DIR, 'w')
f.write(s)
f.close() | [
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tariqdaouda/pyGeno | pyGeno/configuration.py | getSettingsPath | def getSettingsPath() :
"""Returns the path where the settings are stored"""
parser = SafeConfigParser()
try :
parser.read(os.path.normpath(pyGeno_SETTINGS_DIR+'/config.ini'))
return parser.get('pyGeno_config', 'settings_dir')
except :
createDefaultConfigFile()
return getSettingsPath() | python | def getSettingsPath() :
"""Returns the path where the settings are stored"""
parser = SafeConfigParser()
try :
parser.read(os.path.normpath(pyGeno_SETTINGS_DIR+'/config.ini'))
return parser.get('pyGeno_config', 'settings_dir')
except :
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return getSettingsPath() | [
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tariqdaouda/pyGeno | pyGeno/configuration.py | pyGeno_init | def pyGeno_init() :
"""This function is automatically called at launch"""
global db, dbConf
global pyGeno_SETTINGS_PATH
global pyGeno_RABA_DBFILE
global pyGeno_DATA_PATH
if not checkPythonVersion() :
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"""This function is automatically called at launch"""
global db, dbConf
global pyGeno_SETTINGS_PATH
global pyGeno_RABA_DBFILE
global pyGeno_DATA_PATH
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tariqdaouda/pyGeno | pyGeno/Exon.py | Exon.pluck | def pluck(self) :
"""Returns a plucked object. Plucks the exon off the tree, set the value of self.transcript into str(self.transcript). This effectively disconnects the object and
makes it much more lighter in case you'd like to pickle it"""
e = copy.copy(self)
e.transcript = str(self.transcript)
return e | python | def pluck(self) :
"""Returns a plucked object. Plucks the exon off the tree, set the value of self.transcript into str(self.transcript). This effectively disconnects the object and
makes it much more lighter in case you'd like to pickle it"""
e = copy.copy(self)
e.transcript = str(self.transcript)
return e | [
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tariqdaouda/pyGeno | pyGeno/Exon.py | Exon.previousExon | def previousExon(self) :
"""Returns the previous exon of the transcript, or None if there is none"""
if self.number == 0 :
return None
try :
return self.transcript.exons[self.number-1]
except IndexError :
return None | python | def previousExon(self) :
"""Returns the previous exon of the transcript, or None if there is none"""
if self.number == 0 :
return None
try :
return self.transcript.exons[self.number-1]
except IndexError :
return None | [
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastqTools.py | FastqFile.parseStr | def parseStr(self, st) :
"""Parses a string"""
self.data = st.replace('\r', '\n')
self.data = self.data.replace('\n\n', '\n')
self.data = self.data.split('\n') | python | def parseStr(self, st) :
"""Parses a string"""
self.data = st.replace('\r', '\n')
self.data = self.data.replace('\n\n', '\n')
self.data = self.data.split('\n') | [
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tariqdaouda/pyGeno | pyGeno/tools/parsers/FastqTools.py | FastqFile.get | def get(self, li) :
"""returns the ith entry"""
i = li*4
self.__splitEntry(i)
return self.data[i] | python | def get(self, li) :
"""returns the ith entry"""
i = li*4
self.__splitEntry(i)
return self.data[i] | [
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"""Lists all the datawraps availabe from a remote a remote location."""
loc = location + "/datawraps.json"
response = urllib2.urlopen(loc)
js = json.loads(response.read())
return js | python | def listRemoteDatawraps(location = conf.pyGeno_REMOTE_LOCATION) :
"""Lists all the datawraps availabe from a remote a remote location."""
loc = location + "/datawraps.json"
response = urllib2.urlopen(loc)
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"""Import a genome available from http://pygeno.iric.ca (might work)."""
try :
dw = listRemoteDatawraps()["Flat"]["Reference genomes"][name]
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raise AttributeError("There's no remote genome datawrap by the name of: '%s'" % name)
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"""Import a genome available from http://pygeno.iric.ca (might work)."""
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"""Import a SNP set available from http://pygeno.iric.ca (might work)."""
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dw = listRemoteDatawraps()["Flat"]["SNPs"]
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"""Lists all the datawraps pyGeno comes with"""
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l["Genomes"].append(f)
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/SNPs")) :
if f.find("... | python | def listDatawraps() :
"""Lists all the datawraps pyGeno comes with"""
l = {"Genomes" : [], "SNPs" : []}
for f in os.listdir(os.path.join(this_dir, "bootstrap_data/genomes")) :
if f.find(".tar.gz") > -1 :
l["Genomes"].append(f)
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for vv in v :
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printf('\n') | python | def printDatawraps() :
"""print all available datawraps for bootstraping"""
l = listDatawraps()
printf("Available datawraps for boostraping\n")
for k, v in l.iteritems() :
printf(k)
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path = os.path.join(this_dir, "bootstrap_data", "genomes/" + name)
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"""Import a genome shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties."""
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"""Import a SNP set shipped with pyGeno. Most of the datawraps only contain URLs towards data provided by third parties."""
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tariqdaouda/pyGeno | pyGeno/tools/ProgressBar.py | ProgressBar.log | def log(self) :
"""logs stats about the progression, without printing anything on screen"""
self.logs['epochDuration'].append(self.lastEpochDuration)
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self.logs['remtime'].append(self.remtime) | python | def log(self) :
"""logs stats about the progression, without printing anything on screen"""
self.logs['epochDuration'].append(self.lastEpochDuration)
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"""The default filter mixes applied all SNPs and ignores Insertions and Deletions."""
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pos = snp.start
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | aux_insertTree | def aux_insertTree(childTree, parentTree):
"""This a private (You shouldn't have to call it) recursive function that inserts a child tree into a parent tree."""
if childTree.x1 != None and childTree.x2 != None :
parentTree.insert(childTree.x1, childTree.x2, childTree.name, childTree.referedObject)
for c in childT... | python | def aux_insertTree(childTree, parentTree):
"""This a private (You shouldn't have to call it) recursive function that inserts a child tree into a parent tree."""
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parentTree.insert(childTree.x1, childTree.x2, childTree.name, childTree.referedObject)
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | aux_moveTree | def aux_moveTree(offset, tree):
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for c in tree.children:
aux_moveTree(offset, c) | python | def aux_moveTree(offset, tree):
"""This a private recursive (You shouldn't have to call it) function that translates tree(and it's children) to a given x1"""
if tree.x1 != None and tree.x2 != None :
tree.x1, tree.x2 = tree.x1+offset, tree.x2+offset
for c in tree.children:
aux_moveTree(offset, c) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.insert | def insert(self, x1, x2, name = '', referedObject = []) :
"""Insert the segment in it's right place and returns it.
If there's already a segment S as S.x1 == x1 and S.x2 == x2. S.name will be changed to 'S.name U name' and the
referedObject will be appended to the already existing list"""
if x1 > x2 :
xx... | python | def insert(self, x1, x2, name = '', referedObject = []) :
"""Insert the segment in it's right place and returns it.
If there's already a segment S as S.x1 == x1 and S.x2 == x2. S.name will be changed to 'S.name U name' and the
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.intersect | def intersect(self, x1, x2 = None) :
"""Returns a list of all segments intersected by [x1, x2]"""
def condition(x1, x2, tree) :
#print self.id, tree.x1, tree.x2, x1, x2
if (tree.x1 != None and tree.x2 != None) and (tree.x1 <= x1 and x1 < tree.x2 or tree.x1 <= x2 and x2 < tree.x2) :
return True
retur... | python | def intersect(self, x1, x2 = None) :
"""Returns a list of all segments intersected by [x1, x2]"""
def condition(x1, x2, tree) :
#print self.id, tree.x1, tree.x2, x1, x2
if (tree.x1 != None and tree.x2 != None) and (tree.x1 <= x1 and x1 < tree.x2 or tree.x1 <= x2 and x2 < tree.x2) :
return True
retur... | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.__radiateDown | def __radiateDown(self, x1, x2, childId, condition) :
"Radiates down: walks self.children downward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while 0 <= i :
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i -= 1
... | python | def __radiateDown(self, x1, x2, childId, condition) :
"Radiates down: walks self.children downward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while 0 <= i :
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
i -= 1
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.__radiateUp | def __radiateUp(self, x1, x2, childId, condition) :
"Radiates uo: walks self.children upward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while i < len(self.children):
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
... | python | def __radiateUp(self, x1, x2, childId, condition) :
"Radiates uo: walks self.children upward until condition is no longer verifed or there's no childrens left "
ret = []
i = childId
while i < len(self.children):
if condition(x1, x2, self.children[i]) :
ret.append(self.children[i])
else :
break
... | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.removeGaps | def removeGaps(self) :
"""Remove all gaps between regions"""
for i in range(1, len(self.children)) :
if self.children[i].x1 > self.children[i-1].x2:
aux_moveTree(self.children[i-1].x2-self.children[i].x1, self.children[i]) | python | def removeGaps(self) :
"""Remove all gaps between regions"""
for i in range(1, len(self.children)) :
if self.children[i].x1 > self.children[i-1].x2:
aux_moveTree(self.children[i-1].x2-self.children[i].x1, self.children[i]) | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.getIndexedLength | def getIndexedLength(self) :
"""Returns the total length of indexed regions"""
if self.x1 != None and self.x2 != None:
return self.x2 - self.x1
else :
if len(self.children) == 0 :
return 0
else :
l = self.children[0].x2 - self.children[0].x1
for i in range(1, len(self.children)) :
l += s... | python | def getIndexedLength(self) :
"""Returns the total length of indexed regions"""
if self.x1 != None and self.x2 != None:
return self.x2 - self.x1
else :
if len(self.children) == 0 :
return 0
else :
l = self.children[0].x2 - self.children[0].x1
for i in range(1, len(self.children)) :
l += s... | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.getFirstLevel | def getFirstLevel(self) :
"""returns a list of couples (x1, x2) of all the first level indexed regions"""
res = []
if len(self.children) > 0 :
for c in self.children:
res.append((c.x1, c.x2))
else :
if self.x1 != None :
res = [(self.x1, self.x2)]
else :
res = None
return res | python | def getFirstLevel(self) :
"""returns a list of couples (x1, x2) of all the first level indexed regions"""
res = []
if len(self.children) > 0 :
for c in self.children:
res.append((c.x1, c.x2))
else :
if self.x1 != None :
res = [(self.x1, self.x2)]
else :
res = None
return res | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.flatten | def flatten(self) :
"""Flattens the tree. The tree become a tree of depth 1 where overlapping regions have been merged together"""
if len(self.children) > 1 :
children = self.children
self.emptyChildren()
children[0].emptyChildren()
x1 = children[0].x1
x2 = children[0].x2
refObjs = [children[0... | python | def flatten(self) :
"""Flattens the tree. The tree become a tree of depth 1 where overlapping regions have been merged together"""
if len(self.children) > 1 :
children = self.children
self.emptyChildren()
children[0].emptyChildren()
x1 = children[0].x1
x2 = children[0].x2
refObjs = [children[0... | [
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tariqdaouda/pyGeno | pyGeno/tools/SegmentTree.py | SegmentTree.move | def move(self, newX1) :
"""Moves tree to a new starting position, updates x1s of children"""
if self.x1 != None and self.x2 != None :
offset = newX1-self.x1
aux_moveTree(offset, self)
elif len(self.children) > 0 :
offset = newX1-self.children[0].x1
aux_moveTree(offset, self) | python | def move(self, newX1) :
"""Moves tree to a new starting position, updates x1s of children"""
if self.x1 != None and self.x2 != None :
offset = newX1-self.x1
aux_moveTree(offset, self)
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offset = newX1-self.children[0].x1
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.encode | def encode(self, sequence):
"""Returns a tuple (binary reprensentation, default sequence, polymorphisms list)"""
polymorphisms = []
defaultSequence = ''
binSequence = array.array(self.forma.typecode)
b = 0
i = 0
trueI = 0 #not inc in case if poly
poly = set()
while i < len(sequence)-1:
b = b | ... | python | def encode(self, sequence):
"""Returns a tuple (binary reprensentation, default sequence, polymorphisms list)"""
polymorphisms = []
defaultSequence = ''
binSequence = array.array(self.forma.typecode)
b = 0
i = 0
trueI = 0 #not inc in case if poly
poly = set()
while i < len(sequence)-1:
b = b | ... | [
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.findPolymorphisms | def findPolymorphisms(self, strSeq, strict = False):
"""
Compares strSeq with self.sequence.
If not 'strict', this function ignores the cases of matching heterozygocity (ex: for a given position i, strSeq[i] = A and self.sequence[i] = 'A/G'). If 'strict' it returns all positions where strSeq differs self,sequence... | python | def findPolymorphisms(self, strSeq, strict = False):
"""
Compares strSeq with self.sequence.
If not 'strict', this function ignores the cases of matching heterozygocity (ex: for a given position i, strSeq[i] = A and self.sequence[i] = 'A/G'). If 'strict' it returns all positions where strSeq differs self,sequence... | [
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