/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/ |
H A D | Species.pm | 180 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 …]
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/dports/biology/py-biopython/biopython-1.79/Tests/UniProt/ |
H A D | gp_information.goa_yeast.28.gpi | 17 ! 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 …]
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H A D | goa_yeast.gaf | 516 …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 …]
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H A D | gene_association.goa_yeast.1.gaf | 4 … 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 …]
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/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/t/ |
H A D | 11-taxon.t | 1 # $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 …]
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/dports/biology/python-nexus/python-nexus-1.63/nexus/handlers/ |
H A D | taxa.py | 33 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 …]
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/dports/biology/p5-Bio-Phylo/Bio-Phylo-v2.0.1/lib/Bio/Phylo/Parsers/ |
H A D | Ubiometa.pm | 27 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 …]
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H A D | Ubiosearch.pm | 57 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);
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/dports/biology/p5-Bio-DB-NCBIHelper/Bio-DB-NCBIHelper-1.7.7/lib/Bio/DB/Taxonomy/ |
H A D | entrez.pm | 331 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 …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/Taxonomy/ |
H A D | list.pm | 362 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 …]
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/dports/biology/checkm/CheckM-1.0.18/checkm/ |
H A D | taxonParser.py | 43 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 …]
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/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/datamodel/ |
H A D | charmatrixmodel.py | 755 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 …]
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H A D | taxonmodel.py | 605 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 …]
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/dports/biology/python-nexus/python-nexus-1.63/nexus/tools/ |
H A D | multistatise.py | 21 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)
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H A D | binarise.py | 57 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])
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H A D | sites.py | 92 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 …]
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/dports/biology/checkm/CheckM-1.0.18/scripts/ |
H A D | simComparePlots.py | 459 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 …]
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/index/ |
H A D | Makefile.am | 145 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 …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/DB/ |
H A D | Taxonomy.pm | 273 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 …]
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/dports/biology/p5-Bio-NEXUS/Bio-NEXUS-0.78/exec/ |
H A D | nexfix.pl | 185 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";
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/dports/print/texlive-base/texlive-20150521-source/utils/asymptote/doc/ |
H A D | diatom.asy | 39 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 …]
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/dports/math/asymptote/asymptote-2.67/doc/ |
H A D | diatom.asy | 39 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 …]
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/dports/biology/emboss/EMBOSS-6.6.0/test/ |
H A D | .embossrc | 43 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 …]
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/dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/dataio/ |
H A D | phylipwriter.py | 87 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
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | server.dasregistry | 102 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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