/dports/biology/py-goatools/goatools-1.1.6/goatools/anno/init/ |
H A D | reader_genetogo.py | 30 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 [all …]
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/dports/biology/py-goatools/goatools-1.1.6/goatools/anno/ |
H A D | genetogo_reader.py | 58 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) [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/ |
H A D | Blast_def_line.cpp | 109 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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/blastdb/ |
H A D | Blast_def_line.cpp | 109 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()
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/dports/biology/py-ete3/ete3-3.1.2/ete3/ncbi_taxonomy/ |
H A D | ncbiquery.py | 193 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) [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/blastdb/unit_test/ |
H A D | defline_unit_test.cpp | 282 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuPrefTaxNodes.cpp | 66 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/ |
H A D | seqdboidlist.cpp | 658 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/ |
H A D | seqdboidlist.cpp | 658 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() [all …]
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/dports/biology/py-goatools/goatools-1.1.6/goatools/ |
H A D | associations.py | 58 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)
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/Taxonomy/ |
H A D | flatfile.pm | 432 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);
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/blast_format/ |
H A D | build_archive_unit_test.cpp | 160 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/blast_format/ |
H A D | build_archive_unit_test.cpp | 160 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/structure/cd_utils/ |
H A D | cuPrefTaxNodes.hpp | 84 …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…
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/blastdb_format/ |
H A D | blastdb_dataextract.cpp | 391 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/blastdb_format/ |
H A D | blastdb_dataextract.cpp | 391 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() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/seqdb_reader/ |
H A D | seqdb_unit_test.cpp | 1957 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/seqdb_reader/ |
H A D | seqdb_unit_test.cpp | 1957 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() [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/ |
H A D | Taxonomy.pm | 338 my $iid = $TAXON_IIDS->{taxids}->{$dbh}->{$taxid}; 353 $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid; 366 $TAXON_IIDS->{taxids}->{$dbh}->{$taxid} = $iid;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqfeat/ |
H A D | prepare_taxtable.sh | 3 cut -f 3 top900_orgn_nucl.txt > taxids.txt 4 cat taxids.txt |
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqfeat/ |
H A D | prepare_taxtable.sh | 3 cut -f 3 top900_orgn_nucl.txt > taxids.txt 4 cat taxids.txt |
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/unit_test/ |
H A D | writedb_lmdb_unit_test.cpp | 75 …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()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/unit_test/ |
H A D | writedb_lmdb_unit_test.cpp | 75 …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()
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | taxblast.c | 202 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() [all …]
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/dports/www/dolibarr13/dolibarr-13.0.5/htdocs/core/triggers/ |
H A D | interface_80_modStripe_Stripe.class.php | 148 $taxids = $customer->allTaxIds($customer->id); 149 if (is_array($taxids->data)) { 150 foreach ($taxids->data as $taxidobj) {
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