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Searched refs:taxids (Results 1 – 25 of 87) sorted by relevance

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/dports/biology/py-goatools/goatools-1.1.6/goatools/anno/init/
H A Dreader_genetogo.py30 def __init__(self, taxid=None, taxids=None): argument
31 self.taxids = self._init_taxids(taxid, taxids)
34 def _init_taxids(taxid, taxids): argument
37 if taxids is not None:
38 if taxids is True:
40 if isinstance(taxids, int):
41 ret.add(taxids)
43 ret.update(taxids)
53 def init_associations(self, fin_anno, taxids=None, namespaces=None): argument
67 get_all_taxids = taxids is True
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/dports/biology/py-goatools/goatools-1.1.6/goatools/anno/
H A Dgenetogo_reader.py58 taxids = set(taxid).intersection(self.taxid2asscs.keys())
59 if taxids:
66 taxids = self._get_taxids(kws.get('taxids'), kws.get('taxid'))
67 assert taxids, "NO TAXIDS FOUND"
117 def get_taxid2asscs(self, taxids=None, **kws): argument
122 for taxid in self._get_taxids(taxids):
145 def _get_taxids(self, taxids=None, taxid=None): argument
148 if taxids is None and taxid is not None:
149 taxids = [taxid]
150 return taxid_keys if taxids is None else set(taxids).intersection(taxid_keys)
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/
H A DBlast_def_line.cpp109 TLinks taxids = GetLinks(); // see ASN.1 spec comment in GetTaxIds() local
111 ITERATE(TLinks, it, taxids) retval.insert(TAX_ID_FROM(int, *it)); in GetTaxIds()
113 retval.insert(taxids.begin(), taxids.end()); in GetTaxIds()
154 TLinks taxids = GetLinks(); // see ASN.1 spec comment in GetLeafTaxIds() local
156 ITERATE(TLinks, it, taxids) retval.insert(TAX_ID_FROM(int, *it)); in GetLeafTaxIds()
158 retval.insert(taxids.begin(), taxids.end()); in GetLeafTaxIds()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blastdb/
H A DBlast_def_line.cpp109 TLinks taxids = GetLinks(); // see ASN.1 spec comment in GetTaxIds() local
111 ITERATE(TLinks, it, taxids) retval.insert(TAX_ID_FROM(int, *it)); in GetTaxIds()
113 retval.insert(taxids.begin(), taxids.end()); in GetTaxIds()
154 TLinks taxids = GetLinks(); // see ASN.1 spec comment in GetLeafTaxIds() local
156 ITERATE(TLinks, it, taxids) retval.insert(TAX_ID_FROM(int, *it)); in GetLeafTaxIds()
158 retval.insert(taxids.begin(), taxids.end()); in GetLeafTaxIds()
/dports/biology/py-ete3/ete3-3.1.2/ete3/ncbi_taxonomy/
H A Dncbiquery.py193 def get_rank(self, taxids): argument
196 all_ids = set(taxids)
211 all_ids = set(taxids)
326 for sp in taxids:
401 taxids, merged_conversion = self._translate_merged(taxids)
402 if len(taxids) == 1:
432 taxids = set(map(int, taxids))
440 for sp in taxids:
505 taxids = set()
512 taxids.add(tid)
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/unit_test/
H A Ddefline_unit_test.cpp282 CBlast_def_line::TTaxIds taxids = def_line.GetLeafTaxIds(); in BOOST_AUTO_TEST_CASE() local
283 BOOST_CHECK_EQUAL(taxids.size(), 0); in BOOST_AUTO_TEST_CASE()
293 taxids = def_line.GetLeafTaxIds(); in BOOST_AUTO_TEST_CASE()
294 BOOST_CHECK_EQUAL(taxids.size(), 3); in BOOST_AUTO_TEST_CASE()
305 CBlast_def_line::TTaxIds taxids = def_line.GetLeafTaxIds(); in BOOST_AUTO_TEST_CASE() local
306 BOOST_CHECK_EQUAL(taxids.size(), 0); in BOOST_AUTO_TEST_CASE()
317 taxids = def_line.GetLeafTaxIds(); in BOOST_AUTO_TEST_CASE()
318 BOOST_CHECK_EQUAL(taxid_set.size(), taxids.size()); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuPrefTaxNodes.cpp66 CPriorityTaxNodes::CPriorityTaxNodes(const vector< TTaxId >& taxids, TaxClient& taxClient, TaxNodeI… in CPriorityTaxNodes() argument
69 unsigned int nAdded = TaxIdsToCddOrgRefSet(taxids, cddOrgRefSet, taxClient); in CPriorityTaxNodes()
73 m_loaded = (nAdded == taxids.size()); in CPriorityTaxNodes()
180 unsigned int CPriorityTaxNodes::TaxIdsToCddOrgRefSet(const vector< TTaxId >& taxids, CCdd_org_ref_s… in TaxIdsToCddOrgRefSet() argument
183 unsigned int nAdded = 0, nTaxa = taxids.size(); in TaxIdsToCddOrgRefSet()
191 if (cddOrgRef.NotEmpty() && taxClient.GetOrgRef(taxids[i], orgRef)) { in TaxIdsToCddOrgRefSet()
196 notAddedTaxids->push_back(taxids[i]); in TaxIdsToCddOrgRefSet()
202 …rgRefSetToTaxIds(const CCdd_org_ref_set& cddOrgRefSet, vector< TTaxId >& taxids, vector<int>* notA… in CddOrgRefSetToTaxIds() argument
214 taxids.push_back(taxId); in CddOrgRefSetToTaxIds()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/
H A Dseqdboidlist.cpp658 set<TTaxId> taxids; in s_ProcessTaxIdFilters() local
659 taxids = list->GetTaxIdsList(); in s_ProcessTaxIdFilters()
660 if(taxids.size() == 0){ in s_ProcessTaxIdFilters()
665 common.resize(taxids.size()); in s_ProcessTaxIdFilters()
666 vector<TTaxId>::iterator itr = set_intersection(taxids.begin(), taxids.end(), in s_ProcessTaxIdFilters()
672 taxids.clear(); in s_ProcessTaxIdFilters()
673 taxids.insert(common.begin(), common.end()); in s_ProcessTaxIdFilters()
677 difference.resize(taxids.size()); in s_ProcessTaxIdFilters()
678 vector<TTaxId>::iterator itr = set_difference(taxids.begin(), taxids.end(), in s_ProcessTaxIdFilters()
684 taxids.clear(); in s_ProcessTaxIdFilters()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/
H A Dseqdboidlist.cpp658 set<TTaxId> taxids; in s_ProcessTaxIdFilters() local
659 taxids = list->GetTaxIdsList(); in s_ProcessTaxIdFilters()
660 if(taxids.size() == 0){ in s_ProcessTaxIdFilters()
665 common.resize(taxids.size()); in s_ProcessTaxIdFilters()
666 vector<TTaxId>::iterator itr = set_intersection(taxids.begin(), taxids.end(), in s_ProcessTaxIdFilters()
672 taxids.clear(); in s_ProcessTaxIdFilters()
673 taxids.insert(common.begin(), common.end()); in s_ProcessTaxIdFilters()
677 difference.resize(taxids.size()); in s_ProcessTaxIdFilters()
678 vector<TTaxId>::iterator itr = set_difference(taxids.begin(), taxids.end(), in s_ProcessTaxIdFilters()
684 taxids.clear(); in s_ProcessTaxIdFilters()
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/dports/biology/py-goatools/goatools-1.1.6/goatools/
H A Dassociations.py58 def get_assoc_ncbi_taxids(taxids, force_dnld=False, loading_bar=True, **kws): argument
67 return read_ncbi_gene2go(fin, taxids, **kws)
105 def read_ncbi_gene2go(fin_gene2go, taxids=None, namespace='BP', **kws): argument
112 obj = Gene2GoReader(fin_gene2go, taxids=taxids)
123 t2asscs_ret = obj.get_taxid2asscs(taxids, **kws)
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/Taxonomy/
H A Dflatfile.pm432 my $taxids = $name2id{$lc_name} || '';
433 my %taxids = map { $_ => 1 } split(SEPARATOR, $taxids);
434 unless (exists $taxids{$taxid}) {
435 $taxids{$taxid} = 1;
436 $name2id{$lc_name} = join(SEPARATOR, keys %taxids);
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_format/
H A Dbuild_archive_unit_test.cpp160 set<TTaxId> taxids; in BOOST_AUTO_TEST_CASE() local
161 taxids.insert(TAX_ID_CONST(9606)); in BOOST_AUTO_TEST_CASE()
162 taxids.insert(TAX_ID_CONST(9479)); in BOOST_AUTO_TEST_CASE()
163 gilist->AddTaxIds(taxids); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_format/
H A Dbuild_archive_unit_test.cpp160 set<TTaxId> taxids; in BOOST_AUTO_TEST_CASE() local
161 taxids.insert(TAX_ID_CONST(9606)); in BOOST_AUTO_TEST_CASE()
162 taxids.insert(TAX_ID_CONST(9479)); in BOOST_AUTO_TEST_CASE()
163 gilist->AddTaxIds(taxids); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/
H A DcuPrefTaxNodes.hpp84 …CPriorityTaxNodes(const vector< TTaxId >& taxids, TaxClient& taxClient, TaxNodeInputType inputType…
137 …rgRefSetToTaxIds(const CCdd_org_ref_set& cddOrgRefSet, vector< TTaxId >& taxids, vector<int>* notA…
138 …static unsigned int TaxIdsToCddOrgRefSet(const vector< TTaxId >& taxids, CCdd_org_ref_set& cddOrgR…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/blastdb_format/
H A Dblastdb_dataextract.cpp391 set<TTaxId> taxids; in ExtractLeafTaxIds() local
392 x_ExtractLeafTaxIds(taxids); in ExtractLeafTaxIds()
393 if (taxids.empty()) { in ExtractLeafTaxIds()
420 set<TTaxId> taxids; in ExtractLeafCommonTaxonomicNames() local
421 x_ExtractLeafTaxIds(taxids); in ExtractLeafCommonTaxonomicNames()
424 ITERATE(set<TTaxId>, taxid_iter, taxids) { in ExtractLeafCommonTaxonomicNames()
456 set<TTaxId> taxids; in ExtractLeafScientificNames() local
457 x_ExtractLeafTaxIds(taxids); in ExtractLeafScientificNames()
460 ITERATE(set<TTaxId>, taxid_iter, taxids) { in ExtractLeafScientificNames()
770 taxids.clear(); in x_ExtractLeafTaxIds()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/blastdb_format/
H A Dblastdb_dataextract.cpp391 set<TTaxId> taxids; in ExtractLeafTaxIds() local
392 x_ExtractLeafTaxIds(taxids); in ExtractLeafTaxIds()
393 if (taxids.empty()) { in ExtractLeafTaxIds()
420 set<TTaxId> taxids; in ExtractLeafCommonTaxonomicNames() local
421 x_ExtractLeafTaxIds(taxids); in ExtractLeafCommonTaxonomicNames()
424 ITERATE(set<TTaxId>, taxid_iter, taxids) { in ExtractLeafCommonTaxonomicNames()
456 set<TTaxId> taxids; in ExtractLeafScientificNames() local
457 x_ExtractLeafTaxIds(taxids); in ExtractLeafScientificNames()
460 ITERATE(set<TTaxId>, taxid_iter, taxids) { in ExtractLeafScientificNames()
770 taxids.clear(); in x_ExtractLeafTaxIds()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/seqdb_reader/
H A Dseqdb_unit_test.cpp1957 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1960 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
1966 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1969 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
1982 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1985 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
2028 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
2031 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
2037 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
2040 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/seqdb_reader/
H A Dseqdb_unit_test.cpp1957 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1960 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
1966 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1969 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
1982 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
1985 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
2028 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
2031 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
2037 sort(taxids.begin(), taxids.end()); in BOOST_AUTO_TEST_CASE()
2040 taxids.begin(), taxids.end(), in BOOST_AUTO_TEST_CASE()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/
H A DTaxonomy.pm338 my $iid = $TAXON_IIDS->{taxids}->{$dbh}->{$taxid};
353 $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid;
366 $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/
H A Dprepare_taxtable.sh3 cut -f 3 top900_orgn_nucl.txt > taxids.txt
4 cat taxids.txt |
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/
H A Dprepare_taxtable.sh3 cut -f 3 top900_orgn_nucl.txt > taxids.txt
4 cat taxids.txt |
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/unit_test/
H A Dwritedb_lmdb_unit_test.cpp75 …const TTaxId taxids[5] = { TAX_ID_CONST(9606), TAX_ID_CONST(562), TAX_ID_CONST(0), TAX_ID_CONST(2)… in BOOST_AUTO_TEST_CASE() local
79 t.insert(taxids[j]); in BOOST_AUTO_TEST_CASE()
173 …const TTaxId taxids[5] = { TAX_ID_CONST(9606), TAX_ID_CONST(562), TAX_ID_CONST(0), TAX_ID_CONST(2)… in BOOST_AUTO_TEST_CASE() local
177 t.insert(taxids[j]); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/unit_test/
H A Dwritedb_lmdb_unit_test.cpp75 …const TTaxId taxids[5] = { TAX_ID_CONST(9606), TAX_ID_CONST(562), TAX_ID_CONST(0), TAX_ID_CONST(2)… in BOOST_AUTO_TEST_CASE() local
79 t.insert(taxids[j]); in BOOST_AUTO_TEST_CASE()
173 …const TTaxId taxids[5] = { TAX_ID_CONST(9606), TAX_ID_CONST(562), TAX_ID_CONST(0), TAX_ID_CONST(2)… in BOOST_AUTO_TEST_CASE() local
177 t.insert(taxids[j]); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dtaxblast.c202 Int4Ptr taxids; member
266 orgobj->taxids = (Int4Ptr) NULL; in OrgObjNew()
303 MemFree(orgobj->taxids); in OrgObjFree()
703 Int4Ptr taxids; in FindTaxid() local
706 taxids = orgobj->taxids; in FindTaxid()
709 if (taxid==taxids[i]) in FindTaxid()
770 Int4Ptr taxids, gis, taxoffs; in GetOrgData() local
788 taxids = orgobj->taxids = (Int4Ptr) MemNew(numhits*sizeof(Int4)); in GetOrgData()
818 taxids[numorgs] = taxid; in GetOrgData()
928 taxid = orgobj->taxids[i]; in GetTreeData()
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/dports/www/dolibarr13/dolibarr-13.0.5/htdocs/core/triggers/
H A Dinterface_80_modStripe_Stripe.class.php148 $taxids = $customer->allTaxIds($customer->id);
149 if (is_array($taxids->data)) {
150 foreach ($taxids->data as $taxidobj) {

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