index int64 0 731k | package stringlengths 2 98 ⌀ | name stringlengths 1 76 | docstring stringlengths 0 281k ⌀ | code stringlengths 4 8.19k | signature stringlengths 2 42.8k ⌀ | embed_func_code listlengths 768 768 |
|---|---|---|---|---|---|---|
720,768 | ete3.nexml._nexml | insert_meta | null | def insert_meta(self, index, value): self.meta[index] = value
| (self, index, value) | [
0.002475359244272113,
0.00852924957871437,
-0.057923823595047,
-0.005597190000116825,
0.057389963418245316,
0.043509602546691895,
-0.0020770495757460594,
0.04297574236989021,
0.01101920660585165,
-0.0031677091028541327,
-0.031114036217331886,
0.03433388099074364,
0.013980462215840816,
-0.0... |
720,769 | ete3.nexml._nexml | insert_otus | null | def insert_otus(self, index, value): self.otus[index] = value
| (self, index, value) | [
0.00027457362739369273,
-0.007001492660492659,
-0.00002812425918818917,
-0.010321165435016155,
0.0033498520497232676,
0.025332985445857048,
-0.0624270997941494,
0.000733453780412674,
-0.005333033390343189,
-0.029971906915307045,
-0.025798602029681206,
-0.023884400725364685,
-0.01595167629420... |
720,770 | ete3.nexml._nexml | insert_trees | null | def insert_trees(self, index, value): self.trees[index] = value
| (self, index, value) | [
-0.011008141562342644,
0.018760235980153084,
-0.02670634351670742,
-0.022050024941563606,
-0.005428152624517679,
0.07989970594644547,
-0.03274605795741081,
0.02157764509320259,
-0.008798077702522278,
0.005056996829807758,
0.00015671312576159835,
-0.0015141466865316033,
-0.014947454445064068,... |
720,771 | ete3.nexml._nexml | set_about | null | def set_about(self, about): self.about = about
| (self, about) | [
-0.029354680329561234,
0.03134599328041077,
0.05537906289100647,
0.0018014074303209782,
0.01244569756090641,
-0.02140660025179386,
0.03404112905263901,
0.05198010057210922,
-0.009905058890581131,
0.011415708810091019,
-0.01496058702468872,
-0.0029976963996887207,
0.0394485704600811,
0.0626... |
720,772 | ete3.nexml._nexml | set_anyAttributes_ | null | def set_anyAttributes_(self, anyAttributes_): self.anyAttributes_ = anyAttributes_
| (self, anyAttributes_) | [
-0.006853841710835695,
0.01517177652567625,
0.062159761786460876,
0.021165141835808754,
-0.03846028447151184,
-0.02198708988726139,
0.0018964720657095313,
0.006999394856393337,
0.06041312590241432,
0.017183834686875343,
-0.02525775507092476,
0.018065717071294785,
0.0223638154566288,
0.0472... |
720,773 | ete3.nexml._nexml | set_characters | null | def set_characters(self, characters): self.characters = characters
| (self, characters) | [
0.009645731188356876,
0.038047049194574356,
0.04886500537395477,
0.03332466259598732,
-0.03414521738886833,
0.03282228112220764,
-0.02681044302880764,
0.02763100154697895,
0.07555823028087616,
0.011111011728644371,
-0.008406522683799267,
0.01868860423564911,
0.018336936831474304,
0.0890220... |
720,774 | ete3.nexml._nexml | set_generator | null | def set_generator(self, generator): self.generator = generator
| (self, generator) | [
0.04045358672738075,
-0.003447156399488449,
-0.00488292844966054,
0.04809945076704025,
-0.02220776677131653,
0.04194800555706024,
-0.04153095558285713,
0.056648921221494675,
0.027542496100068092,
0.021408425644040108,
0.02227727510035038,
0.02472742833197117,
0.005886448547244072,
0.072427... |
720,775 | ete3.nexml._nexml | set_meta | null | def set_meta(self, meta): self.meta = meta
| (self, meta) | [
-0.022338449954986572,
0.03865538164973259,
-0.007345214486122131,
0.0325300432741642,
0.036648206412792206,
0.010252154432237148,
0.023480461910367012,
0.052324920892715454,
0.023393945768475533,
0.016316931694746017,
-0.044884536415338516,
0.03503900766372681,
0.022061597555875778,
0.005... |
720,776 | ete3.nexml._nexml | set_otus | null | def set_otus(self, otus): self.otus = otus
| (self, otus) | [
-0.008297473192214966,
0.002090591238811612,
0.04810630902647972,
0.022495757788419724,
-0.03215162828564644,
-0.024260807782411575,
-0.05018284171819687,
-0.003127775387838483,
-0.01462224218994379,
-0.008574344217777252,
-0.019900092855095863,
-0.03952331468462944,
-0.004425607621669769,
... |
720,777 | ete3.nexml._nexml | set_trees | null | def set_trees(self, trees): self.trees = trees
| (self, trees) | [
-0.022778261452913284,
0.03861233964562416,
0.019205529242753983,
0.002950019668787718,
-0.06890507787466049,
0.04857573285698891,
-0.02834702655673027,
0.014123192988336086,
0.0038473960012197495,
0.045757804065942764,
0.017561737447977066,
-0.011355583555996418,
-0.0016165353590622544,
0... |
720,778 | ete3.nexml._nexml | set_version | null | def set_version(self, version): self.version = version
| (self, version) | [
0.040002889931201935,
0.03202945366501808,
-0.008681712672114372,
0.04309047386050224,
0.04807811230421066,
-0.015336137264966965,
-0.021019330248236656,
0.041054703295230865,
0.018372828140854836,
0.04186901077628136,
-0.03365807235240936,
-0.0272793248295784,
-0.02096843533217907,
0.0297... |
720,779 | ete3.nexml._nexml | validate_Nexml1_0 | null | def validate_Nexml1_0(self, value):
# Validate type Nexml1_0, a restriction on xs:decimal.
pass
| (self, value) | [
0.046775512397289276,
0.01729719527065754,
0.09661371260881424,
-0.017340699210762978,
0.009483874775469303,
-0.0050334143452346325,
-0.0028168847784399986,
-0.040510933846235275,
0.048550475388765335,
0.0003382436989340931,
0.040476132184267044,
0.03057461977005005,
0.04124180227518082,
0... |
720,780 | ete3.nexml._nexml_tree | NexmlTree |
Special PhyloTree object with nexml support
| class NexmlTree(PhyloTree):
"""
Special PhyloTree object with nexml support
"""
def __repr__(self):
return "NexML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
return self.nexml_edge.get_length()
def _set_dist(self, value):
try:
self.nexml_edge.set_le... | (newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0) | [
0.027712291106581688,
-0.02000338025391102,
0.006903205532580614,
0.014761321246623993,
-0.0031855208799242973,
0.0002539588895160705,
-0.07567663490772247,
0.026657911017537117,
0.030696386471390724,
-0.03274546563625336,
0.014164501801133156,
-0.013090227730572224,
0.02797091193497181,
0... |
720,786 | ete3.nexml._nexml_tree | __init__ | null | def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.... | (self, newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0) | [
0.02968907542526722,
0.008843844756484032,
0.04727652668952942,
-0.0005094551597721875,
-0.02835862524807453,
0.0015844652662053704,
-0.07333876192569733,
0.02866845577955246,
0.05329088866710663,
0.004806932993233204,
0.01622055098414421,
0.03236819803714752,
0.006934741046279669,
0.04490... |
720,790 | ete3.nexml._nexml_tree | __repr__ | null | def __repr__(self):
return "NexML ETE tree <%s>" %hex(hash(self))
| (self) | [
0.033452026546001434,
-0.029804611578583717,
0.09066437184810638,
0.018028663471341133,
0.027494579553604126,
-0.03598785027861595,
-0.039982642978429794,
-0.02554929070174694,
0.04710378870368004,
-0.020043427124619484,
0.009196702390909195,
-0.019748160615563393,
-0.005979159381240606,
0... |
720,795 | ete3.nexml._nexml_tree | _get_dist | null | def _get_dist(self):
return self.nexml_edge.get_length()
| (self) | [
0.005383345298469067,
0.017748216167092323,
0.026933548972010612,
0.050939902663230896,
0.05733262747526169,
0.04044238105416298,
0.013677061535418034,
0.0008453534101136029,
0.03495809808373451,
0.04821458458900452,
-0.010817158967256546,
-0.020052960142493248,
0.021617494523525238,
0.012... |
720,798 | ete3.nexml._nexml_tree | _get_name | null | def _get_name(self):
return self.nexml_node.get_label()
| (self) | [
0.035192135721445084,
-0.016168413683772087,
0.05889296159148216,
0.027782343327999115,
-0.015599102713167667,
0.016816550865769386,
0.020442619919776917,
0.03860799968242645,
0.1232513040304184,
-0.036821238696575165,
-0.015169930644333363,
-0.030777791514992714,
0.03969406709074974,
0.01... |
720,801 | ete3.nexml._nexml_tree | _get_support | null | def _get_support(self):
return self._nexml_support.content
| (self) | [
0.04784660413861275,
-0.0551261268556118,
0.03561154380440712,
0.016378918662667274,
0.04244677349925041,
0.04186578094959259,
0.001062130555510521,
0.02961363084614277,
0.07197496294975281,
0.026059312745928764,
0.05136675015091896,
-0.027323829010128975,
0.005160598084330559,
0.017344394... |
720,806 | ete3.nexml._nexml_tree | _set_children | null | def _set_children(self, value):
if isinstance(value, Children) and \
len(set([type(n)==type(self) for n in value]))<2:
self._children = value
else:
raise ValueError("children:wrong type")
| (self, value) | [
0.02042686939239502,
0.019032122567296028,
-0.01565118320286274,
0.014000439085066319,
-0.07471608370542526,
0.0633462443947792,
0.012437968514859676,
0.042160212993621826,
0.02722405642271042,
-0.004159966483712196,
0.0538831502199173,
0.0414540097117424,
0.05642547458410263,
-0.009807368... |
720,807 | ete3.nexml._nexml_tree | _set_dist | null | def _set_dist(self, value):
try:
self.nexml_edge.set_length(value)
except ValueError:
raise
| (self, value) | [
0.03122369945049286,
0.0833079144358635,
0.004435375332832336,
0.021380353718996048,
-0.0004849881515838206,
0.045208968222141266,
-0.01354089006781578,
0.009491199627518654,
0.017791807651519775,
0.04027890786528587,
-0.021631887182593346,
0.018596714362502098,
0.0500384122133255,
0.01063... |
720,809 | ete3.nexml._nexml_tree | _set_name | null | def _set_name(self, value):
try:
self.nexml_node.set_label(value)
except ValueError:
raise
| (self, value) | [
0.020823754370212555,
0.002605109941214323,
0.022313611581921577,
0.03053351491689682,
-0.06575922667980194,
0.0201558880507946,
0.012398353777825832,
0.05842981114983559,
0.10103631019592285,
-0.019590768963098526,
-0.007457849569618702,
-0.004392510745674372,
0.07726708799600601,
0.02178... |
720,812 | ete3.nexml._nexml_tree | _set_support | null | def _set_support(self, value):
try:
self._nexml_support.content = float(value)
except ValueError:
raise
| (self, value) | [
0.060750823467969894,
0.007256811019033194,
0.043307848274707794,
0.052961405366659164,
0.005654819775372744,
0.02659721113741398,
-0.026647143065929413,
0.029975954443216324,
0.004183901008218527,
0.03718283399939537,
0.04840093106031418,
-0.0022552702575922012,
0.03804832696914673,
0.014... |
720,820 | ete3.nexml._nexml_tree | build | null | def build(self, node):
self.nexml_tree = FloatTree()
tree = self.nexml_tree
tree.build(node)
# This detects the outgroup of the tree even if the root tag
# is not set in any node
rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge])
nodeid2node = {rootid.pop(): sel... | (self, node) | [
-0.0015981666510924697,
-0.013137049041688442,
0.02000025473535061,
0.024753166362643242,
-0.02604595758020878,
0.014049608260393143,
-0.04315644130110741,
0.030646776780486107,
0.05121738091111183,
-0.03908794745802879,
0.004686371423304081,
0.010770098306238651,
0.004914510995149612,
0.0... |
720,832 | ete3.nexml._nexml_tree | export | null | def export(self, outfile=sys.stdout, level=0, namespace_='', name_='FloatTree', namespacedef_=''):
if self.nexml_tree:
info = [(n.nexml_edge, n.nexml_node) for n in self.traverse()]
self.nexml_node.set_root(True)
self.nexml_tree.set_edge([i[0] for i in info])
self.nexml_tree.set_node... | (self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0, namespace_='', name_='FloatTree', namespacedef_='') | [
-0.038538653403520584,
-0.0019651970360428095,
0.00437275692820549,
-0.02516159974038601,
0.03257559984922409,
0.003844133112579584,
-0.08238565921783447,
-0.0016422721091657877,
-0.005671091843396425,
-0.009316161274909973,
-0.003238096134737134,
-0.06872548907995224,
0.0011158603010699153,... |
720,833 | ete3.nexml._nexml_tree | exportChildren | null | def exportChildren(self, outfile, level, namespace_='', name_='FloatTree'):
sorted_nodes = []
sorted_edges = []
for n in self.traverse():
# process node
node_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'node', n.nexml_node)
sorted_nodes... | (self, outfile, level, namespace_='', name_='FloatTree') | [
-0.03906552866101265,
-0.015095136128365993,
-0.07359441369771957,
0.00852870661765337,
0.01006342377513647,
0.04108181223273277,
-0.06131667643785477,
-0.02133301831781864,
0.0032112044282257557,
0.0025743641890585423,
0.013483908027410507,
-0.02052290365099907,
0.0264277383685112,
0.0075... |
720,874 | ete3.phylo.phylotree | link_to_alignment | null | def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
... | (self, alignment, alg_format='fasta', **kwargs) | [
0.01571555808186531,
0.07549049705266953,
-0.006998743396252394,
0.019047047942876816,
-0.006924613378942013,
0.028082186356186867,
-0.047443196177482605,
-0.03232067823410034,
0.04440822824835777,
0.014721345156431198,
-0.023599501699209213,
-0.011442182585597038,
0.061676155775785446,
0.... |
720,886 | ete3.nexml._nexml_tree | set_nexml_project | null | def set_nexml_project(self, nexml_obj):
self.nexml_project = nexml_obj
| (self, nexml_obj) | [
-0.0109806964173913,
0.016734160482883453,
-0.015278252772986889,
-0.0002584563917480409,
-0.025364356115460396,
-0.01859351061284542,
0.007652282249182463,
0.06756811589002609,
0.061954982578754425,
0.025452060624957085,
0.001747526926919818,
-0.02801305428147316,
0.047430992126464844,
0.... |
720,898 | ete3.phylo.phylotree | PhyloNode |
.. currentmodule:: ete3
Extends the standard :class:`TreeNode` instance. It adds
specific attributes and methods to work with phylogentic trees.
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same information.
:argument alignment: fi... | class PhyloNode(TreeNode):
"""
.. currentmodule:: ete3
Extends the standard :class:`TreeNode` instance. It adds
specific attributes and methods to work with phylogentic trees.
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same informa... | (newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0, **kargs) | [
0.05849064141511917,
0.002407805295661092,
0.015042549930512905,
0.0278386902064085,
-0.013195035047829151,
-0.018097247928380966,
-0.05181439593434334,
0.018506640568375587,
0.027418801560997963,
-0.03841991350054741,
-0.025613274425268173,
-0.005080665927380323,
0.038608863949775696,
0.0... |
720,904 | ete3.phylo.phylotree | __init__ | null | def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0, **kargs):
# _update names?
self._name = "NoName"
self._species = "Unknown"
self._speciesFunction = None
# Caution! native __init__ has to be called after setting
# _spe... | (self, newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0, **kargs) | [
0.018697939813137054,
0.030553845688700676,
0.051369559019804,
0.00020179363491479307,
-0.04420171305537224,
0.005371359176933765,
-0.02088811621069908,
0.04626518487930298,
0.051297158002853394,
-0.01803726702928543,
-0.0085842190310359,
0.045142944902181625,
0.004599819891154766,
0.02879... |
721,122 | ete3.phyloxml | Phyloxml | null | class Phyloxml(_phyloxml.Phyloxml):
def __repr__(self):
return "PhyloXML project <%s>" %hex(hash(self))
def __init__(self, *args, **kargs):
_phyloxml.Phyloxml.__init__(self, *args, **kargs)
def build_from_file(self, fname):
doc = _phyloxml.parsexml_(fname)
rootNode = doc.ge... | (*args, **kargs) | [
0.02525591105222702,
-0.02064330503344536,
0.04268551245331764,
-0.01780768483877182,
0.0108037069439888,
-0.05845155566930771,
-0.081212118268013,
0.05516223609447479,
0.008719527162611485,
-0.018743440508842468,
0.03419756144285202,
0.004435380455106497,
0.03665509819984436,
0.0610603243... |
721,123 | ete3.phyloxml | __init__ | null | def __init__(self, *args, **kargs):
_phyloxml.Phyloxml.__init__(self, *args, **kargs)
| (self, *args, **kargs) | [
0.0016043162904679775,
-0.026018062606453896,
0.07123120874166489,
-0.011674100533127785,
-0.052908629179000854,
-0.020451487973332405,
-0.06533308327198029,
0.07189431041479111,
0.052908629179000854,
-0.0025411671958863735,
0.024953607469797134,
0.02921142615377903,
0.029316125437617302,
... |
721,124 | ete3.phyloxml | __repr__ | null | def __repr__(self):
return "PhyloXML project <%s>" %hex(hash(self))
| (self) | [
0.03668028861284256,
-0.04348056763410568,
0.03520346060395241,
0.030326493084430695,
0.02208373323082924,
-0.08325189352035522,
-0.032352838665246964,
0.004696656949818134,
0.046812016516923904,
-0.015103143639862537,
0.002069276524707675,
-0.0137379365041852,
0.02041800692677498,
0.08565... |
721,125 | ete3.phyloxml._phyloxml | add_phylogeny | null | def add_phylogeny(self, value): self.phylogeny.append(value)
| (self, value) | [
-0.02043156884610653,
0.02115466073155403,
0.05297073349356651,
-0.001011068350635469,
-0.021625511348247528,
0.023004433140158653,
-0.07452897727489471,
-0.004876670427620411,
-0.0025581500958651304,
0.008584622293710709,
0.015479224734008312,
0.00603698194026947,
0.03470844030380249,
0.0... |
721,127 | ete3.phyloxml._phyloxml | buildAttributes | null | def buildAttributes(self, node, attrs, already_processed):
pass
| (self, node, attrs, already_processed) | [
0.0012546307407319546,
0.034549176692962646,
0.03873196244239807,
0.017916826531291008,
-0.006550016347318888,
0.03649235889315605,
0.0056936973705887794,
0.0036640570033341646,
0.06257715076208115,
-0.008151497691869736,
0.022478371858596802,
0.050950974225997925,
0.0804281085729599,
0.06... |
721,128 | ete3.phyloxml._phyloxml | buildChildren | null | def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
if nodeName_ == 'phylogeny':
obj_ = Phylogeny.factory()
obj_.build(child_)
self.phylogeny.append(obj_)
| (self, child_, node, nodeName_, fromsubclass_=False) | [
-0.02405525930225849,
-0.009127543307840824,
0.009745744056999683,
-0.03089182637631893,
-0.056510768830776215,
0.04516497626900673,
-0.016491398215293884,
0.053528860211372375,
0.03107365034520626,
0.006550194229930639,
0.05149243772029877,
0.08487524837255478,
0.037492021918296814,
0.026... |
721,129 | ete3.phyloxml | build_from_file | null | def build_from_file(self, fname):
doc = _phyloxml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _phyloxml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'phyloxml'
rootClass = self.__class__
self.build(rootNode)
| (self, fname) | [
0.003172517055645585,
-0.006072324700653553,
0.011981024406850338,
0.006604108028113842,
-0.031343378126621246,
-0.003767932066693902,
-0.011408334597945213,
0.050687551498413086,
0.016153475269675255,
-0.004226992838084698,
0.009408467449247837,
0.04039732366800308,
-0.008131279610097408,
... |
721,130 | ete3.phyloxml | export | null | def export(self, outfile=stdout, level=0):
namespace = 'xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd"'
return super(Phyloxml, self).export(outfile=outfile, level=level, namespacedef_=namespace)
| (self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0) | [
-0.026294374838471413,
0.004825344309210777,
0.06339611113071442,
-0.0523415207862854,
0.051423247903585434,
-0.04404175281524658,
-0.04912756755948067,
0.015054368413984776,
0.005990843754261732,
-0.01723526418209076,
-0.021597057580947876,
-0.03704875707626343,
0.015363401733338833,
0.02... |
721,131 | ete3.phyloxml._phyloxml | exportAttributes | null | def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Phyloxml'):
pass
| (self, outfile, level, already_processed, namespace_='phy:', name_='Phyloxml') | [
0.0036912676878273487,
0.035300008952617645,
0.05140116810798645,
-0.011582283303141594,
0.040406085550785065,
-0.0438782162964344,
-0.04020184278488159,
-0.020951934158802032,
-0.00585922272875905,
-0.0012914118124172091,
-0.026381393894553185,
-0.017803186550736427,
0.06784273684024811,
... |
721,132 | ete3.phyloxml._phyloxml | exportChildren | null | def exportChildren(self, outfile, level, namespace_='phy:', name_='Phyloxml', fromsubclass_=False):
for phylogeny_ in self.phylogeny:
phylogeny_.export(outfile, level, namespace_, name_='phylogeny')
| (self, outfile, level, namespace_='phy:', name_='Phyloxml', fromsubclass_=False) | [
-0.018226394429802895,
-0.009707729332149029,
-0.008381124585866928,
-0.02505907416343689,
-0.004299263935536146,
0.0005202153697609901,
-0.04940825700759888,
-0.02587544545531273,
-0.0034074659924954176,
0.02209528721868992,
0.01219233963638544,
-0.016833238303661346,
0.0687527284026146,
... |
721,133 | ete3.phyloxml._phyloxml | exportLiteral | null | def exportLiteral(self, outfile, level, name_='Phyloxml'):
level += 1
self.exportLiteralAttributes(outfile, level, [], name_)
if self.hasContent_():
self.exportLiteralChildren(outfile, level, name_)
| (self, outfile, level, name_='Phyloxml') | [
0.011569696478545666,
-0.051144789904356,
0.07785603404045105,
0.005288757849484682,
0.04776274412870407,
0.001725532696582377,
-0.015650581568479538,
-0.010698302648961544,
-0.028039906173944473,
-0.037927210330963135,
0.01546077337116003,
0.006871934048831463,
0.005840928293764591,
-0.00... |
721,134 | ete3.phyloxml._phyloxml | exportLiteralAttributes | null | def exportLiteralAttributes(self, outfile, level, already_processed, name_):
pass
| (self, outfile, level, already_processed, name_) | [
-0.0007991113816387951,
-0.012736224569380283,
0.06634069979190826,
0.017675435170531273,
0.04598917067050934,
-0.010217062197625637,
-0.008172824047505856,
-0.012620590627193451,
-0.010902605019509792,
-0.023770982399582863,
-0.019376901909708977,
0.00678521953523159,
0.025026433169841766,
... |
721,135 | ete3.phyloxml._phyloxml | exportLiteralChildren | null | def exportLiteralChildren(self, outfile, level, name_):
showIndent(outfile, level)
outfile.write('phylogeny=[\n')
level += 1
for phylogeny_ in self.phylogeny:
showIndent(outfile, level)
outfile.write('model_.Phylogeny(\n')
phylogeny_.exportLiteral(outfile, level, name_='Phylogeny... | (self, outfile, level, name_) | [
-0.012763936072587967,
-0.02210911549627781,
0.03727659583091736,
-0.014455961063504219,
-0.0081434091553092,
0.007852727547287941,
-0.049493879079818726,
-0.030595269054174423,
0.0013547040289267898,
0.006156364921480417,
0.017406156286597252,
-0.0031410912051796913,
0.019905146211385727,
... |
721,136 | ete3.phyloxml._phyloxml | factory | null | def factory(*args_, **kwargs_):
if Phyloxml.subclass:
return Phyloxml.subclass(*args_, **kwargs_)
else:
return Phyloxml(*args_, **kwargs_)
| (*args_, **kwargs_) | [
0.04442374035716057,
-0.06838376820087433,
0.06543589383363724,
-0.0624537467956543,
-0.060465648770332336,
0.002515117172151804,
-0.045863401144742966,
0.06002004072070122,
0.011363017372786999,
-0.015707699581980705,
0.04620617628097534,
0.0609455332159996,
-0.0016410390380769968,
0.0286... |
721,158 | ete3.phyloxml._phyloxml | get_phylogeny | null | def get_phylogeny(self): return self.phylogeny
| (self) | [
0.0029563545249402523,
0.012597584165632725,
0.1096649169921875,
-0.007799743674695492,
0.0056480905041098595,
-0.009621708653867245,
-0.04414359852671623,
-0.006077553611248732,
0.041228458285331726,
-0.007465716917067766,
0.008654331788420677,
-0.02967199496924877,
0.014922757633030415,
... |
721,159 | ete3.phyloxml._phyloxml | hasContent_ | null | def hasContent_(self):
if (
self.phylogeny
):
return True
else:
return False
| (self) | [
0.046880919486284256,
-0.028572794049978256,
0.05192911624908447,
0.008438901975750923,
0.04587128013372421,
0.0306425541639328,
-0.0149679034948349,
0.021219253540039062,
-0.00023255885753314942,
-0.004707443527877331,
0.031517576426267624,
0.020024513825774193,
0.04846268892288208,
-0.01... |
721,160 | ete3.phyloxml._phyloxml | insert_phylogeny | null | def insert_phylogeny(self, index, value): self.phylogeny[index] = value
| (self, index, value) | [
-0.005786124151200056,
0.020704666152596474,
0.047847773879766464,
-0.03436093404889107,
-0.019806673750281334,
0.021416284143924713,
-0.06075853854417801,
0.0071966503746807575,
-0.004115094896405935,
0.010453992523252964,
-0.009640716016292572,
0.014867712743580341,
0.02136545442044735,
... |
721,161 | ete3.phyloxml._phyloxml | set_phylogeny | null | def set_phylogeny(self, phylogeny): self.phylogeny = phylogeny
| (self, phylogeny) | [
-0.009787989780306816,
0.057618577033281326,
0.10697667300701141,
-0.0015531074022874236,
-0.060485851019620895,
-0.007180988322943449,
-0.0494263619184494,
0.03689910098910332,
0.006617773324251175,
0.03304193168878555,
0.0022293918300420046,
0.007803937885910273,
0.05929115414619446,
0.0... |
721,162 | ete3.phyloxml._phyloxml_tree | PhyloxmlTree | PhyloTree object supporting phyloXML format. | class PhyloxmlTree(PhyloTree):
''' PhyloTree object supporting phyloXML format. '''
def __repr__(self):
return "PhyloXML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
v = self.phyloxml_clade.get_branch_length_attr()
if v is None:
v = self.phyloxml_clade.get_branc... | (phyloxml_clade=None, phyloxml_phylogeny=None, **kargs) | [
0.020665304735302925,
-0.015631206333637238,
0.03504034876823425,
0.01588621735572815,
-0.013950024731457233,
-0.03500256687402725,
-0.06607608497142792,
0.013987804763019085,
0.004533521831035614,
-0.024235453456640244,
0.01536675076931715,
-0.007943108677864075,
0.04148172587156296,
0.04... |
721,168 | ete3.phyloxml._phyloxml_tree | __init__ | null | def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_l... | (self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs) | [
-0.011571533046662807,
0.014730632305145264,
0.07525046169757843,
0.004308266099542379,
-0.04678306728601456,
-0.01654977723956108,
-0.04305604100227356,
0.03411117568612099,
0.04135225713253021,
-0.010568784549832344,
0.03105856105685234,
0.026302164420485497,
0.023214057087898254,
0.0327... |
721,172 | ete3.phyloxml._phyloxml_tree | __repr__ | null | def __repr__(self):
return "PhyloXML ETE tree <%s>" %hex(hash(self))
| (self) | [
0.041431937366724014,
-0.03225971385836601,
0.08572365343570709,
0.017891064286231995,
0.025023076683282852,
-0.05074365809559822,
-0.043698836117982864,
-0.009808696806430817,
0.033811669796705246,
-0.026086775586009026,
0.013749613426625729,
-0.025110265240073204,
0.005235664546489716,
0... |
721,176 | ete3.phyloxml._phyloxml_tree | _get_children | null | def _get_children(self):
return self.phyloxml_clade.clade
| (self) | [
0.00220271828584373,
-0.011842850595712662,
0.051137618720531464,
-0.01902112178504467,
-0.01750081405043602,
0.05659690499305725,
0.011385031044483185,
0.018070928752422333,
0.0993037298321724,
-0.004370884504169226,
0.02019590511918068,
-0.0024899356067180634,
0.04177390784025192,
0.0404... |
721,177 | ete3.phyloxml._phyloxml_tree | _get_dist | null | def _get_dist(self):
v = self.phyloxml_clade.get_branch_length_attr()
if v is None:
v = self.phyloxml_clade.get_branch_length()
if v is None:
self._set_dist(self._dist)
v = self.phyloxml_clade.get_branch_length_attr()
return float(v)
| (self) | [
0.03263923153281212,
0.04785923659801483,
0.024837233126163483,
0.03972560912370682,
0.0487668514251709,
0.002090132562443614,
0.009844131767749786,
-0.03562388941645622,
-0.025779755786061287,
0.04154083877801895,
-0.013535681180655956,
-0.005554778501391411,
-0.003287922590970993,
0.0161... |
721,180 | ete3.phyloxml._phyloxml_tree | _get_name | null | def _get_name(self):
return self.phyloxml_clade.get_name()
| (self) | [
0.029273875057697296,
0.00780607620254159,
0.07314115017652512,
0.0178847536444664,
-0.00891625415533781,
-0.026888079941272736,
0.010056908242404461,
0.02828124538064003,
0.09403862059116364,
-0.04708896949887276,
-0.010318126529455185,
-0.00904686376452446,
0.01149360928684473,
0.0305103... |
721,183 | ete3.phyloxml._phyloxml_tree | _get_support | null | def _get_support(self):
if len(self.phyloxml_clade.confidence) == 0:
_c = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(_c)
return float(self.phyloxml_clade.confidence[0].valueOf_)
| (self) | [
0.024887897074222565,
-0.021233996376395226,
0.038469381630420685,
0.06687329709529877,
0.0224404726177454,
-0.008333309553563595,
-0.030920282006263733,
-0.024405306205153465,
0.012840362265706062,
-0.00014178798301145434,
0.04560483247041702,
-0.03733184561133385,
0.0024905132595449686,
... |
721,189 | ete3.phyloxml._phyloxml_tree | _set_dist | null | def _set_dist(self, value):
try:
self.phyloxml_clade.set_branch_length(float(value))
self.phyloxml_clade.set_branch_length_attr(float(value))
except ValueError:
raise
| (self, value) | [
0.04712548851966858,
0.0868573859333992,
0.011384053155779839,
0.02518656849861145,
-0.017672058194875717,
0.004733278416097164,
-0.03606965392827988,
-0.0260675810277462,
-0.03714068979024887,
0.027656856924295425,
-0.013750691898167133,
0.027242261916399002,
0.03207919001579285,
0.033616... |
721,191 | ete3.phyloxml._phyloxml_tree | _set_name | null | def _set_name(self, value):
try:
self.phyloxml_clade.set_name(value)
except ValueError:
raise
| (self, value) | [
0.019627878442406654,
0.03571517765522003,
0.02650279365479946,
0.023821577429771423,
-0.07280533760786057,
-0.013010774739086628,
-0.003957372158765793,
0.03863701596856117,
0.07803027331829071,
-0.014781065285205841,
-0.006273359060287476,
0.012185784988105297,
0.05180247500538826,
0.035... |
721,194 | ete3.phyloxml._phyloxml_tree | _set_support | null | def _set_support(self, value):
self._get_support()
self.phyloxml_clade.confidence[0].valueOf_ = float(value)
| (self, value) | [
0.04298773780465126,
-0.001508900080807507,
0.04543253779411316,
0.07157831639051437,
0.0004992528120055795,
0.011731645092368126,
-0.034498848021030426,
0.009286845102906227,
0.008454933762550354,
0.027300268411636353,
0.02789449132978916,
-0.01546675618737936,
0.04964302480220795,
0.0130... |
721,202 | ete3.phyloxml._phyloxml_tree | build | null | def build(self, node):
nodetype = Tag_pattern_.match(node.tag).groups()[-1]
if nodetype == 'phylogeny':
self.phyloxml_phylogeny.buildAttributes(node, node.attrib, [])
elif nodetype == 'clade':
if "branch_length" in node.attrib:
node.attrib["branch_length_attr"] = node.attrib["bra... | (self, node) | [
-0.014092053286731243,
0.030481724068522453,
0.035517334938049316,
-0.0061365533620119095,
-0.0237803403288126,
0.0219613928347826,
-0.027169326320290565,
-0.014704751782119274,
0.028490455821156502,
-0.016858767718076706,
0.01934785395860672,
0.08217811584472656,
0.039155229926109314,
0.0... |
721,203 | ete3.phyloxml._phyloxml_tree | buildChildren | null | def buildChildren(self, child_, node, nodeName_, fromsubclass=False, nodetype=None):
if nodetype == 'phylogeny':
baseclass = self.phyloxml_phylogeny
if nodeName_ == 'clade':
self.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
elif nodetype ==... | (self, child_, node, nodeName_, fromsubclass=False, nodetype=None) | [
-0.03693888336420059,
-0.006942025385797024,
0.021520279347896576,
-0.03246310353279114,
-0.04048297181725502,
0.039058029651641846,
-0.023182712495326996,
0.04000798985362053,
0.022269288077950478,
0.007403304800391197,
0.04552507400512695,
0.06434161961078644,
0.04695001617074013,
0.0453... |
721,215 | ete3.phyloxml._phyloxml_tree | export | null | def export(self, outfile=sys.stdout, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_=''):
if not self.up:
self.phyloxml_phylogeny.clade = self.phyloxml_clade
self.phyloxml_clade.clade = self.children
self.phyloxml_phylogeny.export(outfile=outfile, level=level, name_=name_, names... | (self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_='') | [
-0.0376395620405674,
-0.007516327779740095,
0.033344514667987823,
-0.031295012682676315,
0.012163352221250534,
-0.03362966328859329,
-0.05471280962228775,
-0.0020907153375446796,
-0.01341087557375431,
-0.012501966208219528,
-0.010122760199010372,
-0.030885113403201103,
0.03143758699297905,
... |
721,279 | ete3.coretype.seqgroup | SeqGroup |
SeqGroup class can be used to store a set of sequences (aligned
or not).
:argument sequences: Path to the file containing the sequences or,
alternatively, the text string containing the same
information.
:argument fasta format: the format in which sequences are
encoded. Curre... | class SeqGroup(object):
"""
SeqGroup class can be used to store a set of sequences (aligned
or not).
:argument sequences: Path to the file containing the sequences or,
alternatively, the text string containing the same
information.
:argument fasta format: the format in which seque... | (sequences=None, format='fasta', fix_duplicates=True, **kwargs) | [
0.03149641305208206,
0.05511386692523956,
-0.052358176559209824,
0.030564909800887108,
-0.023636862635612488,
-0.02466539666056633,
-0.06485582888126373,
0.032854851335287094,
0.05068923532962799,
-0.05127142369747162,
-0.08236030489206314,
0.01761120930314064,
0.005428910255432129,
0.0784... |
721,280 | ete3.coretype.seqgroup | __contains__ | null | def __contains__(self, item):
return item in self.name2id
| (self, item) | [
0.05304223299026489,
-0.04652521759271622,
-0.026068061590194702,
0.021816318854689598,
-0.015003074891865253,
-0.031922921538352966,
0.021868593990802765,
-0.010150164365768433,
0.06234727427363396,
-0.042970478534698486,
-0.0292045921087265,
-0.016083436086773872,
0.043876588344573975,
-... |
721,281 | ete3.coretype.seqgroup | __init__ | null | def __init__(self, sequences=None , format="fasta", fix_duplicates=True, **kwargs):
self.parsers = {
"fasta": [read_fasta, write_fasta, {}],
"phylip": [read_phylip, write_phylip, {"interleaved":False, "relaxed":False}],
"iphylip": [read_phylip, write_phylip, {"interleaved":True, "relaxed":Fa... | (self, sequences=None, format='fasta', fix_duplicates=True, **kwargs) | [
-0.002306272741407156,
0.03999036177992821,
0.031403034925460815,
-0.011821051128208637,
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0.007518403697758913,
-0.044373854994773865,
0.04469722509384155,
0.03142099827528,
-0.005555714014917612,
-0.05781176686286926,
0.07333362847566605,
-0.025240996852517128,
0.0691... |
721,282 | ete3.coretype.seqgroup | __iter__ | null | def __iter__(self):
return self.iter_entries()
| (self) | [
0.042141638696193695,
-0.038948092609643936,
-0.08257127553224564,
-0.005946744699031115,
-0.01952343061566353,
-0.013161031529307365,
-0.01526811346411705,
0.016749655827879906,
0.11167534440755844,
0.014617880806326866,
-0.0029116414953023195,
-0.007424171548336744,
0.008329558186233044,
... |
721,283 | ete3.coretype.seqgroup | __len__ | null | def __len__(self):
return len(self.id2seq)
| (self) | [
-0.0034808041527867317,
0.024307476356625557,
0.02218078076839447,
0.0631030723452568,
0.028943011537194252,
0.017428942024707794,
0.004282468929886818,
0.002724830061197281,
0.059215206652879715,
-0.048614952713251114,
-0.03788178041577339,
-0.010600253008306026,
0.03528987243771553,
0.01... |
721,284 | ete3.coretype.seqgroup | __repr__ | null | def __repr__(self):
return "SeqGroup (%s)" %hex(self.__hash__())
| (self) | [
0.020168496295809746,
0.01756610907614231,
-0.015772797167301178,
0.04580867663025856,
0.005884563084691763,
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0.02270415425300598,
0.046943049877882004,
-0.028559524565935135,
-0.04087081551551819,
0.001129160518757999,
0.04447411745786667,
0.05... |
721,285 | ete3.coretype.seqgroup | __str__ | null | def __str__(self):
return write_fasta(self)
| (self) | [
-0.04024982824921608,
0.006624315399676561,
0.029439596459269524,
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0.0179628673940897,
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0.04366358742117882,
0.05016598105430603,
-0.0621303915977478,
-0.03186173737049103,
0.023863792419433594,
-0.006518651731312275,
0.06456... |
721,286 | ete3.coretype.seqgroup | get_entries | Returns the list of entries currently stored. | def get_entries(self):
""" Returns the list of entries currently stored."""
keys = list(self.id2seq.keys())
seqs = list(self.id2seq.values())
comments = [self.id2comment.get(x, []) for x in keys]
names = [self.id2name[x] for x in keys]
return list(zip(names, seqs, comments))
| (self) | [
0.03436722233891487,
0.027724355459213257,
-0.07118663191795349,
-0.020477592945098877,
0.02062399312853813,
0.021063189953565598,
0.010979942977428436,
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0.10972622781991959,
-0.025930965319275856,
-0.0571323037147522,
-0.028547851368784904,
-0.028017153963446617,
0.0... |
721,287 | ete3.coretype.seqgroup | get_seq | Returns the sequence associated to a given entry name. | def get_seq(self, name):
""" Returns the sequence associated to a given entry name."""
return self.id2seq[self.name2id[name]]
| (self, name) | [
0.06268345564603806,
0.0492800809442997,
-0.03387795761227608,
0.031039398163557053,
-0.023632269352674484,
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0.0028469576500356197,
0.10171785205602646,
-0.07141748815774918,
-0.08129365742206573,
0.026235681027173996,
0.016645044088363647,
0.036... |
721,288 | ete3.coretype.seqgroup | iter_entries | Returns an iterator over all sequences in the
collection. Each item is a tuple with the sequence name,
sequence, and sequence comments | def iter_entries(self):
""" Returns an iterator over all sequences in the
collection. Each item is a tuple with the sequence name,
sequence, and sequence comments """
for i, seq in six.iteritems(self.id2seq):
yield self.id2name[i], seq, self.id2comment.get(i, [])
| (self) | [
0.03572949394583702,
0.023769909515976906,
-0.036494459956884384,
-0.009767306037247181,
-0.01836850494146347,
-0.000314557139063254,
-0.011483813636004925,
0.0022634121123701334,
0.10396070033311844,
-0.003745533060282469,
-0.06395859271287918,
0.022725077345967293,
0.0022564155515283346,
... |
721,289 | ete3.coretype.seqgroup | set_seq | Updates or adds a sequence | def set_seq(self, name, seq, comments = None):
"""Updates or adds a sequence """
if comments is None:
comments = []
name = name.strip()
seq = seq.replace(" ", "")
seq = seq.replace("\t", "")
seq = seq.replace("\n", "")
seq = seq.replace("\r", "")
seqid = self.name2id.get(name, ma... | (self, name, seq, comments=None) | [
0.02151615358889103,
0.06900740414857864,
-0.008718820288777351,
0.04423551633954048,
-0.07304168492555618,
-0.007949122227728367,
-0.03804254159331322,
0.04359852150082588,
0.03991812840104103,
-0.013474137522280216,
-0.09462860971689224,
-0.00039480195846408606,
-0.004494328051805496,
0.... |
721,290 | ete3.coretype.seqgroup | write | Returns the text representation of the sequences in the
supplied given format (default=FASTA). If "oufile" argument is
used, the result is written into the given path. | def write(self, format="fasta", outfile=None):
""" Returns the text representation of the sequences in the
supplied given format (default=FASTA). If "oufile" argument is
used, the result is written into the given path."""
format = format.lower()
if format in self.parsers:
write = self.parser... | (self, format='fasta', outfile=None) | [
-0.003135968931019306,
0.027643468230962753,
0.018376821652054787,
-0.027834711596369743,
0.024653105065226555,
0.009084095247089863,
-0.03371112048625946,
0.0042138900607824326,
0.05636485666036606,
-0.024931278079748154,
-0.01945474185049534,
0.029781924560666084,
-0.029277736321091652,
... |
721,291 | ete3.coretype.tree | TreeNode |
TreeNode (Tree) class is used to store a tree structure. A tree
consists of a collection of TreeNode instances connected in a
hierarchical way. Trees can be loaded from the New Hampshire Newick
format (newick).
:argument newick: Path to the file containing the tree or, alternatively,
the te... | class TreeNode(object):
"""
TreeNode (Tree) class is used to store a tree structure. A tree
consists of a collection of TreeNode instances connected in a
hierarchical way. Trees can be loaded from the New Hampshire Newick
format (newick).
:argument newick: Path to the file containing the tree o... | (newick=None, format=0, dist=None, support=None, name=None, quoted_node_names=False) | [
0.043274518102407455,
-0.030937859788537025,
-0.01807737536728382,
0.01721145585179329,
-0.027581091970205307,
-0.001172597287222743,
-0.036069225519895554,
0.05033014714717865,
0.009273874573409557,
-0.01824842020869255,
0.000863913563080132,
0.01411125622689724,
0.0064409333281219006,
0.... |
721,296 | ete3.coretype.tree | __init__ | null | def __init__(self, newick=None, format=0, dist=None, support=None,
name=None, quoted_node_names=False):
self._children = []
self._up = None
self._dist = DEFAULT_DIST
self._support = DEFAULT_SUPPORT
self._img_style = None
self.features = set([])
# Add basic features
self.feat... | (self, newick=None, format=0, dist=None, support=None, name=None, quoted_node_names=False) | [
0.04643934965133667,
0.01347808726131916,
-0.0026533594354987144,
-0.0247142743319273,
-0.03464268893003464,
0.013424708507955074,
-0.013531466014683247,
0.04868125170469284,
0.003827687818557024,
0.05295153707265854,
0.029020145535469055,
0.05177720636129379,
0.00495530990883708,
0.037827... |
721,300 | ete3.coretype.tree | __repr__ | null | def __repr__(self):
return "Tree node '%s' (%s)" %(self.name, hex(self.__hash__()))
| (self) | [
0.02457979880273342,
-0.0006728317821398377,
0.08713886141777039,
0.02644318901002407,
0.026951385661959648,
-0.026765046641230583,
-0.022953568026423454,
0.016075968742370605,
0.02813717909157276,
-0.02483389712870121,
0.0019205615390092134,
-0.013340173289179802,
0.014331158250570297,
0.... |
721,477 | ete3.webplugin.webapp | WebTreeApplication | Provides a basic WSGI application object which can handle ETE
tree visualization and interactions. Please, see the
webplugin example provided with the ETE installation package
(http://pypi.python.org/pypi/ete3). | class WebTreeApplication(object):
""" Provides a basic WSGI application object which can handle ETE
tree visualization and interactions. Please, see the
webplugin example provided with the ETE installation package
(http://pypi.python.org/pypi/ete3)."""
def __init__(self):
# Red... | () | [
0.04609548673033714,
-0.05325394123792648,
-0.028757955878973007,
0.02784763276576996,
0.019954711198806763,
0.0025357173290103674,
-0.053419455885887146,
0.029771726578474045,
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-0.027164889499545097,
0.02999930828809738,
-0.021351231262087822,
-0.034033697098493576,
0... |
721,478 | ete3.webplugin.webapp | __call__ | This function is executed when the application is called
by the WSGI apache module. It is, therefore, in charge of
answering web requests. | def __call__(self, environ, start_response):
""" This function is executed when the application is called
by the WSGI apache module. It is, therefore, in charge of
answering web requests."""
path = environ['PATH_INFO'].split("/")
start_response('202 OK', [('content-type', 'text/plain')])
if envi... | (self, environ, start_response) | [
0.042244862765073776,
-0.03935994580388069,
-0.0035103182308375835,
-0.0011335402959957719,
0.023240726441144943,
0.0020602946169674397,
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0.0150398975238204,
-0.03001927211880684,
-0.03387255221605301,
0.047570861876010895,
0.011317750439047813,
-0.0008107523899525404,
... |
721,479 | ete3.webplugin.webapp | __init__ | null | def __init__(self):
# Redirects normal output msgs to stderr, since stdout in web
# application is for the browser
sys.stdout = sys.stderr
self.TreeConstructor = None
self.NODE_TARGET_ACTIONS = ["node", "face"]
self.TREE_TARGET_ACTIONS = ["layout", "search"]
self.actions = []
self._layou... | (self) | [
0.01868549734354019,
-0.03160852938890457,
-0.01786363683640957,
-0.03141959756612778,
0.008676758967339993,
0.017712490633130074,
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0.04239661991596222,
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-0.0025931086856871843,
0.039751552045345306,
0.030588291585445404,
-0.022898707538843155,
0.... |
721,480 | ete3.webplugin.webapp | _dump_tree_to_file | null | def _dump_tree_to_file(self, t, treeid):
tree_path = os.path.join(self.CONFIG["temp_dir"], treeid+".pkl")
six.moves.cPickle.dump(t, open(tree_path, "wb"))
#open(tree_path, "w").write(t.write(features=[]))
| (self, t, treeid) | [
0.02049744874238968,
0.026584256440401077,
0.015138979069888592,
0.006932195741683245,
0.03176931291818619,
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0.023324085399508476,
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-0.04463657736778259,
-0.002997881965711713,
-0.03891393914818764,
-0.06995491683483124,
0.017... |
721,481 | ete3.webplugin.webapp | _get_html_map | null | def _get_html_map(self, img_map, treeid, mapid, tree):
# Scans for node-enabled actions.
nid2actions = {}
nid2face_actions = {}
for n in tree.traverse():
for aindex, (action, target, handler, checker, html_generator) in enumerate(self.actions):
if target == "node" and (not checker or... | (self, img_map, treeid, mapid, tree) | [
0.03442675620317459,
-0.0410948321223259,
0.010910547338426113,
0.007623334880918264,
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0.00991782732307911,
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-0.0012807016028091311,
0.02157759666442871,
0.01257756631821394,
-0.016866862773895264,
0.0... |
721,482 | ete3.webplugin.webapp | _get_tree_img | null | def _get_tree_img(self, treeid, pre_drawing_action=None):
img_url = os.path.join(self.CONFIG["temp_url"], treeid+".png?"+str(time.time()))
img_path = os.path.join(self.CONFIG["temp_dir"], treeid+".png")
t = self._treeid2tree[treeid]
tree_index = self._treeid2index[treeid]
if pre_drawing_action:
... | (self, treeid, pre_drawing_action=None) | [
0.03824102133512497,
-0.05613625422120094,
0.02199322171509266,
0.0016976274782791734,
0.00019724140292964876,
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0.07318717986345291,
-0.0083864601328969,
-0.0058638290502130985,
-0... |
721,483 | ete3.webplugin.webapp | _load_tree | null | def _load_tree(self, treeid, tree=None, cache_file=None):
# if a tree is given, it overwrites previous versions
if tree and isinstance(tree, str):
tree = self._tree(tree)
self._treeid2tree[treeid] = tree
self._load_tree_index(treeid)
elif tree:
self._treeid2tree[treeid] = tre... | (self, treeid, tree=None, cache_file=None) | [
0.04914212226867676,
0.026345422491431236,
0.007492823526263237,
0.03847666084766388,
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0.01465777587145567,
0.06302843242883682,
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-0.06322129815816879,
0.026229703798890114,
-0.0050916485488414764,
-0.07560326159000397,
0.0121... |
721,484 | ete3.webplugin.webapp | _load_tree_from_path | null | def _load_tree_from_path(self, pkl_path):
tree_path = os.path.join(self.CONFIG["temp_dir"], pkl_path)
if os.path.exists(tree_path):
print(six.moves.cPickle.load(open(tree_path)))
t = self._treeid2tree[treeid] = six.moves.cPickle.load(open(tree_path))
self._load_tree_index(treeid)
... | (self, pkl_path) | [
0.06628867238759995,
0.007120133377611637,
-0.03093225695192814,
0.04545824974775314,
0.012452168390154839,
0.031540580093860626,
0.023816730827093124,
0.05002988502383232,
-0.007622459903359413,
-0.03602004051208496,
0.0455319881439209,
0.011714808642864227,
-0.05250003933906555,
-0.00628... |
721,485 | ete3.webplugin.webapp | _load_tree_index | null | def _load_tree_index(self, treeid):
if not self._treeid2index.get(treeid, {}):
tree_index = self._treeid2index[treeid] = {}
t = self._treeid2tree[treeid]
for n in t.traverse():
if hasattr(n, "_nid"):
tree_index[str(n._nid)] = n
return True
else:
... | (self, treeid) | [
0.01990736834704876,
0.011348294094204903,
0.0008750492124818265,
0.034163378179073334,
0.01771063171327114,
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0.008504384197294712,
0.029587600380182266,
-0.014265124686062336,
-0.06719648838043213,
-0.003422718495130539,
-0.019597455859184265,
-0.037554193288087845,
-0... |
721,486 | ete3.webplugin.webapp | register_action | Adds a new web interactive function associated to tree
nodes. | def register_action(self, name, target, handler, checker, html_generator):
""" Adds a new web interactive function associated to tree
nodes. """
self.actions.append([name, target, handler, checker, html_generator])
| (self, name, target, handler, checker, html_generator) | [
-0.024743320420384407,
-0.019829628989100456,
0.0050929272547364235,
0.009495140053331852,
0.028205635026097298,
0.0649096816778183,
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0.04424070566892624,
-0.010623015463352203,
-0.008970546536147594,
0.07267366349697113,
0.00973120704293251,
0.05130523070693016,
0.01... |
721,487 | ete3.webplugin.webapp | set_default_layout_fn | Fix the layout function used to render the tree. | def set_default_layout_fn(self, layout_fn):
""" Fix the layout function used to render the tree. """
self._layout = layout_fn
| (self, layout_fn) | [
0.014152485877275467,
-0.01259123906493187,
0.07331949472427368,
-0.007603690959513187,
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0.04418748617172241,
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0.04138568416237831,
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-0.03483688831329346,
0.016785506159067154,
-0.01253216527402401,
0.0036625992506742477,
-0.... |
721,488 | ete3.webplugin.webapp | set_external_app_handler | Sets a custom function that will extend current WSGI
application. | def set_external_app_handler(self, handler):
""" Sets a custom function that will extend current WSGI
application."""
self._external_app_handler = handler
| (self, handler) | [
-0.0025434433482587337,
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0.05832521617412567,
0.020910916849970818,
0.025136180222034454,
0.03436548262834549,
0.04192125052213669,
0.012228411622345448,
0.003788239322602749,
-0.0038773014675825834,
-0.05779498815536499,
0.02397630363702774,
-0.0... |
721,489 | ete3.webplugin.webapp | set_external_tree_renderer | If the tree needs to be processed every time is going to
be drawn, the task can be delegated. | def set_external_tree_renderer(self, handler):
""" If the tree needs to be processed every time is going to
be drawn, the task can be delegated. """
self._custom_tree_renderer = handler
| (self, handler) | [
0.005686530377715826,
-0.0018707321723923087,
0.01323966309428215,
0.07406943291425705,
0.005855846218764782,
0.06220907345414162,
-0.02547169104218483,
0.06409219652414322,
0.018335653468966484,
-0.0015424248995259404,
0.06785843521356583,
-0.028246818110346794,
0.047177139669656754,
-0.0... |
721,490 | ete3.webplugin.webapp | set_tree_loader | Delegate tree constructor. It allows to customize the Tree
class used to create new tree instances. | def set_tree_loader(self, TreeConstructor):
""" Delegate tree constructor. It allows to customize the Tree
class used to create new tree instances. """
self._tree = TreeConstructor
| (self, TreeConstructor) | [
-0.023414360359311104,
0.043746501207351685,
0.04203026369214058,
-0.011715936474502087,
-0.029456209391355515,
0.04745917394757271,
0.013449684716761112,
0.062204789370298386,
-0.015323533676564693,
0.0026334587018936872,
0.05863221734762192,
0.0015498660504817963,
-0.0063483212143182755,
... |
721,491 | ete3.webplugin.webapp | set_tree_size | Fix the size of tree image | def set_tree_size(self, w, h, units="px"):
""" Fix the size of tree image """
self._width = w
self._height = h
self._size_units = units
| (self, w, h, units='px') | [
0.02826567180454731,
-0.010640386492013931,
0.03857998177409172,
-0.021847115829586983,
-0.08203394711017609,
0.028540262952446938,
-0.02146955393254757,
-0.002797391964122653,
-0.06243504211306572,
0.028643235564231873,
0.01265691127628088,
-0.007152227684855461,
0.06040993705391884,
0.02... |
721,492 | ete3.webplugin.webapp | set_tree_style | Fix a :class:`TreeStyle` instance to render tree images. | def set_tree_style(self, handler):
""" Fix a :class:`TreeStyle` instance to render tree images. """
self._tree_style = handler
| (self, handler) | [
-0.01989370584487915,
-0.010564827360212803,
0.03342142328619957,
-0.00165075424592942,
-0.020537076517939568,
0.010767997242510319,
-0.004368149675428867,
0.05045382305979729,
0.04740627482533455,
0.021519063040614128,
0.009201896376907825,
-0.009591305628418922,
0.03545312210917473,
-0.0... |
721,497 | ete3.ncbi_taxonomy.ncbiquery | is_taxadb_up_to_date | Check if a valid and up-to-date taxa.sqlite database exists
If dbfile= is not specified, DEFAULT_TAXADB is assumed
| def is_taxadb_up_to_date(dbfile=DEFAULT_TAXADB):
"""Check if a valid and up-to-date taxa.sqlite database exists
If dbfile= is not specified, DEFAULT_TAXADB is assumed
"""
db = sqlite3.connect(dbfile)
try:
r = db.execute('SELECT version FROM stats;')
version = r.fetchone()[0]
ex... | (dbfile='/root/.etetoolkit/taxa.sqlite') | [
0.02971409261226654,
0.0026223636232316494,
-0.013102775439620018,
0.0014581246068701148,
0.07689855247735977,
-0.0016593232285231352,
-0.03515775874257088,
-0.018862932920455933,
-0.026513000950217247,
-0.04253654554486275,
-0.014486297965049744,
0.058306898921728134,
-0.0064519187435507774... |
721,515 | pydal.base | DAL |
An instance of this class represents a database connection
Args:
uri(str): contains information for connecting to a database.
Defaults to `'sqlite://dummy.db'`
Note:
experimental: you can specify a dictionary as uri
parameter i.e. with::
... | class DAL(with_metaclass(MetaDAL, Serializable, BasicStorage)):
"""
An instance of this class represents a database connection
Args:
uri(str): contains information for connecting to a database.
Defaults to `'sqlite://dummy.db'`
Note:
experimental: you can sp... | (*args, **kwargs) | [
0.013089874759316444,
-0.01776023954153061,
-0.01976335421204567,
0.0455467626452446,
0.06555648893117905,
-0.053730614483356476,
-0.03612034022808075,
0.029607538133859634,
-0.054416172206401825,
-0.0947784036397934,
-0.04850323125720024,
0.050088584423065186,
-0.05295936018228531,
0.0426... |
721,517 | pydal.base | __call__ | null | def __call__(self, query=None, ignore_common_filters=None):
return self.where(query, ignore_common_filters)
| (self, query=None, ignore_common_filters=None) | [
-0.020695051178336143,
-0.08175314962863922,
0.011939452029764652,
0.05121554434299469,
-0.03139348328113556,
-0.023142851889133453,
0.018247248604893684,
-0.029253797605633736,
0.02490595355629921,
-0.06586811691522598,
0.02153380773961544,
0.025265421718358994,
0.03363587707281113,
-0.01... |
721,521 | pydal.base | __getitem__ | null | def __getitem__(self, key):
return self.__getattr__(str(key))
| (self, key) | [
0.04582010582089424,
-0.05270139127969742,
-0.027425896376371384,
-0.023472465574741364,
0.030171794816851616,
-0.014118216000497341,
0.03526659309864044,
0.007873780094087124,
0.09686733782291412,
-0.046845681965351105,
-0.03486959636211395,
0.04168471693992615,
0.04866525158286095,
0.008... |
721,522 | pydal.base | __init__ | null | def __init__(
self,
uri="sqlite://dummy.db",
pool_size=0,
folder=None,
db_codec="UTF-8",
check_reserved=None,
migrate=True,
fake_migrate=False,
migrate_enabled=True,
fake_migrate_all=False,
decode_credentials=False,
driver_args=None,
adapter_args=None,
attempts=5,... | (self, uri='sqlite://dummy.db', pool_size=0, folder=None, db_codec='UTF-8', check_reserved=None, migrate=True, fake_migrate=False, migrate_enabled=True, fake_migrate_all=False, decode_credentials=False, driver_args=None, adapter_args=None, attempts=5, auto_import=False, bigint_id=False, debug=False, lazy_tables=False, ... | [
0.009955660440027714,
-0.06744413077831268,
0.015996620059013367,
0.0484469048678875,
0.036345113068819046,
-0.03662331774830818,
-0.020447852090001106,
0.047572553157806396,
-0.0761478841304779,
-0.060528822243213654,
-0.049917399883270264,
0.07992348074913025,
-0.029966337606310844,
0.09... |
721,570 | pydal.objects | Field | null | class Field(Expression, Serializable):
Virtual = FieldVirtual
Method = FieldMethod
Lazy = FieldMethod # for backward compatibility
"""
Represents a database field
Example:
Usage::
a = Field(name, 'string', length=32, default=None, required=False,
requires=... | (fieldname, type='string', length=None, default=<function <lambda> at 0x7fbac9f848b0>, required=False, requires=<function <lambda> at 0x7fbac9f848b0>, ondelete='CASCADE', onupdate='CASCADE', notnull=False, unique=False, uploadfield=True, widget=None, label=None, comment=None, writable=True, readable=True, searchable=Tr... | [
0.02375727891921997,
-0.03397186100482941,
-0.013124064542353153,
0.0663110688328743,
-0.008069101721048355,
-0.05044497177004814,
0.005829429253935814,
0.012653105892241001,
-0.030476298183202744,
-0.06237594038248062,
-0.007006827276200056,
0.028927365317940712,
0.01246472168713808,
0.05... |
721,576 | pydal.objects | __getitem__ | null | def __getitem__(self, i):
if isinstance(i, slice):
start = i.start or 0
stop = i.stop
db = self.db
if start < 0:
pos0 = "(%s - %d)" % (self.len(), abs(start) - 1)
else:
pos0 = start + 1
maxint = sys.maxint if PY2 else sys.maxsize
if sto... | (self, i) | [
0.009343590587377548,
-0.0125195337459445,
-0.010536761954426765,
-0.006742299534380436,
0.015879716724157333,
-0.03102247416973114,
0.019827712327241898,
-0.0036847961600869894,
0.0279693566262722,
-0.08429409563541412,
0.022722909227013588,
0.0611325241625309,
-0.0013894751900807023,
-0.... |
721,579 | pydal.objects | __init__ | null | def __init__(
self,
fieldname,
type="string",
length=None,
default=DEFAULT,
required=False,
requires=DEFAULT,
ondelete="CASCADE",
onupdate="CASCADE",
notnull=False,
unique=False,
uploadfield=True,
widget=None,
label=None,
comment=None,
writable=True,
r... | (self, fieldname, type='string', length=None, default=<function <lambda> at 0x7fbac9f848b0>, required=False, requires=<function <lambda> at 0x7fbac9f848b0>, ondelete='CASCADE', onupdate='CASCADE', notnull=False, unique=False, uploadfield=True, widget=None, label=None, comment=None, writable=True, readable=True, searcha... | [
0.023206891492009163,
-0.0246293805539608,
-0.01810625195503235,
0.05454229190945625,
-0.01666344329714775,
-0.054461006075143814,
0.03218889236450195,
0.031843431293964386,
-0.015200311318039894,
-0.07177472859621048,
-0.043203022330999374,
0.05238823592662811,
-0.015444166027009487,
0.02... |
721,580 | pydal.objects | __invert__ | null | def __invert__(self):
if hasattr(self, "_op") and self.op == self._dialect.invert:
return self.first
return Expression(self.db, self._dialect.invert, self, type=self.type)
| (self) | [
0.030687497928738594,
-0.0686943382024765,
0.09790453314781189,
0.0192888043820858,
-0.03438074141740799,
-0.0741334781050682,
-0.014630282297730446,
-0.023586397990584373,
0.001983020221814513,
-0.013354433700442314,
-0.0032735569402575493,
0.006085458677262068,
0.014252563938498497,
0.02... |
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