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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/
H A DSpecies.pm180 my $taxon = $self->taxon;
212 unless ($taxon->rank) {
217 $taxon->db_handle($db);
223 foreach my $node ($self->tree->get_lineage_nodes($taxon), $taxon) {
578 sub id {shift->taxon->id(@_)}
622 sub taxon { subroutine
623 my ($self, $taxon) = @_;
624 if (!$self->{taxon} || $taxon) {
626 $self->{taxon} = $taxon;
628 $self->{taxon};
[all …]
/dports/biology/py-biopython/biopython-1.79/Tests/UniProt/
H A Dgp_information.goa_yeast.28.gpi17 ! Taxon required 1 13 taxon:9606
29 E2QC18 ORF YJR025c-a E2QC18_YEAST protein taxon:559292 db_subset=TrEMBL
30 E9PAD6 Chromosome IX cosmid 9168 E9PAD6_YEAST protein taxon:559292 db_subset=TrEMBL
31 E9PAD8 Chromosome IX lambda clone 4554 E9PAD8_YEAST protein taxon:559292 db_subset=TrEMBL
33 E9PAE4 Putative uncharacterized protein E9PAE4_YEAST protein taxon:559292 db_subset=TrEMBL
34 E9PAE7 Putative uncharacterized protein E9PAE7_YEAST protein taxon:559292 db_subset=TrEMBL
35 E9PAE8 Putative uncharacterized protein E9PAE8_YEAST protein taxon:559292 db_subset=TrEMBL
36 E9PAF1 Putative uncharacterized protein E9PAF1_YEAST protein taxon:559292 db_subset=TrEMBL
130 P00163 COB Cytochrome b CYB_YEAST|COB|CYTB|Q0105 protein taxon:559292 db_subset=Swiss-Prot
152 P00724 SUC2 Invertase 2 INV2_YEAST|SUC2|YIL162W protein taxon:559292 db_subset=Swiss-Prot
[all …]
H A Dgoa_yeast.gaf516 …74 GO_REF:0000015 ND F Protein ECM12 ECM12_YEAST|ECM12|YHR021W-A protein taxon:559292 20020927 SG…
517 …75 GO_REF:0000015 ND C Protein ECM12 ECM12_YEAST|ECM12|YHR021W-A protein taxon:559292 20020927 SG…
518 …50 GO_REF:0000015 ND P Protein ECM12 ECM12_YEAST|ECM12|YHR021W-A protein taxon:559292 20121106 SG…
567 …:11979277 IMP C THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20070724 SG…
568 …:11979277 IPI C THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20070724 SG…
569 …:11060033 IMP C THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20070724 SG…
570 …:11060033 IPI C THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20070724 SG…
571 …:24084588 IMP P THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20140726 SG…
572 …:12093753 IDA F THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20021118 SG…
573 …:11060033 IMP P THO complex subunit THP2 THP2_YEAST|THP2|YHR167W protein taxon:559292 20030221 SG…
[all …]
H A Dgene_association.goa_yeast.1.gaf4 … TAS P Tropomyosin-1 TPM1_YEAST|YNL079C|N2332|TPM1|D6W1A0|Q45TY1 protein taxon:559292 20010118 SG…
8 …391144 IMP P Myosin-2 MYO2_YEAST|CDC66|YOR326W|MYO2|O6167|D6W323 protein taxon:559292 20061019 SG…
26 …978821 IGI P Myosin-2 MYO2_YEAST|CDC66|YOR326W|MYO2|O6167|D6W323 protein taxon:559292 20061019 SG…
27 …:8603912 IMP P Thioredoxin-1 TRX1_YEAST|YLR043C|TRX2|TRX1|D6VY45 protein taxon:559292 20010118 SG…
28 …:9015301 IMP P Thioredoxin-1 TRX1_YEAST|YLR043C|TRX2|TRX1|D6VY45 protein taxon:559292 20010118 SG…
79 …PMID:10652251 TAS P Tropomyosin-2 TPM2_YEAST|YIL138C|TPM2|D6VVE8 protein taxon:559292 20010118 SG…
81 …PMID:10652251 TAS P Tropomyosin-2 TPM2_YEAST|YIL138C|TPM2|D6VVE8 protein taxon:559292 20010118 SG…
82 …D:12882345 IMP P Prohibitin-1 PHB1_YEAST|PHB|PHB1|YGR132C|D6VUR4 protein taxon:559292 20080204 SG…
262 …49 PMID:11959996 TAS F Exportin-T XPOT_YEAST|YKL205W|LOS1|D6VWZ8 protein taxon:559292 20020917 SG…
276 …000054 PMID:20368619 IMP P Zuotin ZUO1_YEAST|YGR285C|ZUO1|D6VV62 protein taxon:559292 20101019 SG…
[all …]
/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/t/
H A D11-taxon.t1 # $Id: 11-taxon.t 1247 2010-03-04 15:47:17Z rvos $
9 ok( my $taxon = new Bio::Phylo::Taxa::Taxon, '1 initialize object' );
10 $taxon->VERBOSE( -level => 0 );
11 ok( $taxon->set_desc('This is a taxon description'), '2 enter description' );
13 eval { $taxon->set_name(':') };
14 ok( $taxon->get_name eq ':', '4 enter bad name' );
18 eval { $taxon->set_data('BAD!') };
23 eval { $taxon->set_nodes('BAD!') };
26 ok( $taxon->get_nodes, '12 get nodes' );
27 eval { $taxon->set_data( new Bio::Phylo::Forest ) };
[all …]
/dports/biology/python-nexus/python-nexus-1.63/nexus/handlers/
H A Dtaxa.py33 for taxon in taxa:
35 taxon = TAXON_PLACEHOLDER.sub('', taxon)
37 annot = TAXON_ANNOTATION.match(taxon)
39 taxon, annot = annot.groups()
41 taxon = QUOTED_PATTERN.sub('\\1', taxon)
43 if taxon and taxon not in self.taxa:
44 yield (taxon, annot)
75 self.taxa.append(taxon)
77 self.annotations[taxon] = annot
100 for idx, taxon in enumerate(self.taxa, 1):
[all …]
/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/lib/Bio/Phylo/Parsers/
H A DUbiometa.pm27 my ( $self, $taxon ) = @_;
28 $taxon->set_name( $taxon->get_meta_object('dc:subject') );
29 $taxon->set_desc(
30 $taxon->get_meta_object('dc:type')
32 . $taxon->get_meta_object('gla:rank')
34 . $taxon->get_meta_object('ubio:lexicalStatus')
70 my $taxon = $fac->create_taxon;
73 $self->_copy_namespaces($elt,$taxon);
83 $taxon->add_meta( $fac->create_meta(
93 $self->_rss_prettify($taxon);
[all …]
H A DUbiosearch.pm57 my $taxon = $fac->create_taxon;
58 $self->_elt_handler( $elt, $taxon );
61 if ( my $name = $taxon->get_meta_object($DCSUB) ) {
62 $taxon->set_name( $name );
71 if ( my ($meta) = @{ $taxon->get_meta($DCID) } ) {
74 $taxon->add_meta( $fac->create_meta(
79 $taxon->set_guid( $id );
80 $taxon->remove_meta( $meta );
81 $taxon->add_meta( $fac->create_meta( '-triple' => { $DCID => $id } ) );
87 $taxa->insert($taxon);
/dports/biology/p5-Bio-DB-NCBIHelper/Bio-DB-NCBIHelper-1.7.7/lib/Bio/DB/Taxonomy/
H A Dentrez.pm331 for my $taxon ( $root->children('Taxon') ) {
516 my ($self, $taxon) = @_;
517 $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
518 …row("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_hand…
543 my ($self, $taxon) = @_;
544 $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
545 …row("The supplied Taxon must belong to this database") unless $taxon->db_handle && $taxon->db_hand…
636 my $taxon = Bio::Taxon->new();
649 $taxon->{'db_handle'} = $self;
651 $self->_handle_internal_id($taxon);
[all …]
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/Taxonomy/
H A Dlist.pm362 my $taxon;
366 $taxon = Bio::Taxon->new(
372 $taxon->rank($rank);
377 $taxon->{'db_handle'} = $self;
382 return $taxon;
420 my ($self, $taxon) = @_;
422 $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
424 unless $taxon->db_handle && $taxon->db_handle eq $self;
444 my ($self, $taxon) = @_;
445 $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
[all …]
/dports/biology/checkm/CheckM-1.0.18/checkm/
H A DtaxonParser.py43 taxon = lineSplit[1]
51 taxonMarkerSets[rank][taxon] = ms
70 for taxon in sorted(taxonMarkerSets[rank]):
71 markerSet = taxonMarkerSets[rank][taxon]
79 def markerSet(self, rank, taxon, markerFile): argument
87 elif taxon not in taxonMarkerSets[rank]:
91 markerSet = taxonMarkerSets[rank][taxon]
95 for i, taxon in enumerate(taxonomy):
100 taxon = taxonomy[1] + ' ' + taxonomy[0]
102 markerSet = taxonMarkerSets[rank][taxon]
[all …]
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/datamodel/
H A Dcharmatrixmodel.py755 taxon = key
817 other._taxon_sequence_map[taxon] = self._taxon_sequence_map[taxon]
930 taxa.add(taxon)
967 if taxon is None:
970 taxon = key
971 return taxon
1120 s = [self[taxon] for taxon in self]
1422 self._taxon_sequence_map[taxon].extend(other_matrix._taxon_sequence_map[taxon])
1467 for taxon in taxa:
1480 for taxon in taxa:
[all …]
H A Dtaxonmodel.py605 memo[id(taxon)] = taxon
776 def append(self, taxon): argument
826 self.add_taxon(taxon)
827 return taxon
890 def remove(self, taxon): argument
941 for taxon in taxa:
985 for taxon in taxa:
1233 if taxon is not None:
1234 return taxon
1238 return taxon
[all …]
/dports/biology/python-nexus/python-nexus-1.63/nexus/tools/
H A Dmultistatise.py21 for taxon in nexus_obj.data.matrix:
22 states[taxon] = []
23 sequence = nexus_obj.data.matrix[taxon]
31 states[taxon].append(chr(65 + site_idx))
34 for taxon in states:
35 if not states[taxon]:
36 nexout.add(taxon, charlabel, '?')
38 for s in states[taxon]:
39 nexout.add(taxon, charlabel, s)
H A Dbinarise.py57 for taxon, value in char.items():
58 char[taxon] = [
61 states.update(char[taxon])
65 for taxon, values in char.items():
66 newdata[taxon] = ['0' for _ in range(num_states)]
69 newdata[taxon][states.index(value)] = '1'
70 newdata[taxon] = "".join(newdata[taxon])
71 assert len(newdata[taxon]) == num_states
107 for taxon, state in recoding.items():
111 n.add(taxon, new_label, state[j])
H A Dsites.py92 for taxon, sites in nexus_obj.data:
93 tally[taxon] = tally.get(taxon, 0)
96 tally[taxon] += 1
128 for taxon, data in nexus_obj.data:
129 nexout.add(taxon, new_sitepos, data[sitepos])
157 for taxon, state in data.items():
159 tally[site][state].append(taxon)
185 for taxon, characters in nexus_obj.data:
186 tally[taxon] = {}
189 tally[taxon][char] = tally[taxon].get(char, [])
[all …]
/dports/biology/checkm/CheckM-1.0.18/scripts/
H A DsimComparePlots.py459 taxon = taxonomy[r]
465 if taxon == 'unclassified':
468 taxon = rankPrefixes[r] + taxon
470 taxaByRank[r].add(taxon)
509 for taxon in orderedTaxa:
524 for taxon in orderedTaxa:
603 taxon = taxonomy[r]
605 if taxon == 'unclassified':
608 taxaByRank[r].add(taxon)
644 for taxon in orderedTaxa:
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/index/
H A DMakefile.am145 taxon.ent \
146 taxon.pxac \
147 taxon.pxgc \
148 taxon.pxid \
152 taxon.pxup \
153 taxon.xac \
154 taxon.xgc \
155 taxon.xid \
156 taxon.xmgc \
157 taxon.xrnk \
[all …]
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/
H A DTaxonomy.pm273 my ($self, $taxon) = @_;
275 foreach my $desc_taxon ($self->each_Descendent($taxon)) {
330 my ($self, $taxon, $try_name) = @_;
331 $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
333 my $taxid = $taxon->id || return;
334 my $name = $taxon->scientific_name || '';
335 my $rank = $taxon->rank || 'no rank';
336 my $dbh = $try_name ? $taxon->db_handle : 'any';
362 $taxon->_creation_id($iid);
365 $iid = $taxon->internal_id;
[all …]
/dports/biology/p5-Bio-NEXUS/Bio-NEXUS-0.78/exec/
H A Dnexfix.pl185 TAXON: for my $taxon (@taxa) {
186 if ($taxon =~ /^'.*?'$/) {next TAXON;}
188 $taxon = "'$taxon'" if ($taxon =~ /$punctuation_pattern/);
197 my ($taxon, $seq) = $row =~ /\s*('.+'|\S+)\s*(.*?)\s*$/;
198 if ($taxon =~ /^'.*?'$/) { $row .="\n"; next ROW;}
199 $taxon = "'$taxon'" if ($taxon =~ /$punctuation_pattern/);
200 $row = "$taxon $seq\n";
210 my ($taxon, $seq) = $row =~ /\s*('.+'|\S+)\s*(.*?)\s*$/;
232 $row = "$taxon $seq\n";
/dports/print/texlive-base/texlive-20150521-source/utils/asymptote/doc/
H A Ddiatom.asy39 for(int taxon=0; taxon < n; ++taxon) {
40 real[] P=percentage[taxon];
42 final=taxon;
61 for(int taxon=0; taxon < n; ++taxon) {
62 real[] P=percentage[taxon];
76 label(label,rotate(angle)*TeXify(taxa[taxon]),(0,0),N);
80 int taxon=taxon;
89 if(taxon == begin[i]) {
95 } else if(taxon == end[i]) {
114 if(taxon == 0) yaxis(pic,depthlabel,Left,RightTicks(0,10),above=true);
[all …]
/dports/math/asymptote/asymptote-2.67/doc/
H A Ddiatom.asy39 for(int taxon=0; taxon < n; ++taxon) {
40 real[] P=percentage[taxon];
42 final=taxon;
61 for(int taxon=0; taxon < n; ++taxon) {
62 real[] P=percentage[taxon];
76 label(label,rotate(angle)*TeXify(taxa[taxon]),(0,0),N);
80 int taxon=taxon;
89 if(taxon == begin[i]) {
95 } else if(taxon == end[i]) {
114 if(taxon == 0) yaxis(pic,depthlabel,Left,RightTicks(0,10),above=true);
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/test/
H A D.embossrc43 taxon: "1 all"
56 taxon: "1 all"
68 taxon: "1 all"
85 taxon: "1 all"
98 taxon: "1 all"
109 taxon: "1 all"
134 taxon: "1 all"
143 taxon: "1 all"
153 taxon: "1 all"
173 taxon: "1 all"
[all …]
/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/dataio/
H A Dphylipwriter.py87 for taxon in char_matrix.taxon_namespace:
88 label = taxon.label
91 taxon_label_map[taxon] = label
97 for taxon in char_matrix.taxon_namespace:
98 label = taxon_label_map[taxon]
99 if taxon in char_matrix:
100 seq_vec = char_matrix[taxon].symbols_as_string()
112 for taxon in taxon_namespace:
113 label = taxon.label
118 taxon_label_map[taxon] = label
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dserver.dasregistry102 taxon: "31033"
163 taxon: "9606"
176 taxon: "9606"
189 taxon: "9606"
202 taxon: "7955"
239 taxon: "7955"
264 taxon: "9606"
277 taxon: "9606"
290 taxon: "9606"
303 taxon: "9606"
[all …]

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