/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/tasks/ |
H A D | genetic_code.bf | 6 /** @module genetic_code */ 10 genetic_code.nucleotides = "ACGT"; 16 genetic_code.stop_code = 10; 28 genetic_code.singleAALetterToFullName = { 56 * genetic_code.DefineCodonToAAGivenCode 75 function genetic_code.CountSense(code) { 164 return {^"terms.genetic_code.synonymous" : SS, ^"terms.genetic_code.nonsynonymous" : NS}; 169 * genetic_code.DefineCodonToAAMapping 187 * genetic_code.IsStop 188 * @name genetic_code.IsStop [all …]
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/sequence/ |
H A D | _rna.py | 216 def translate(self, genetic_code=1, *args, **kwargs): argument 281 if not isinstance(genetic_code, skbio.GeneticCode): 282 genetic_code = skbio.GeneticCode.from_ncbi(genetic_code) 283 return genetic_code.translate(self, *args, **kwargs) 286 def translate_six_frames(self, genetic_code=1, *args, **kwargs): argument 412 if not isinstance(genetic_code, skbio.GeneticCode): 413 genetic_code = skbio.GeneticCode.from_ncbi(genetic_code) 414 return genetic_code.translate_six_frames(self, *args, **kwargs)
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/ |
H A D | Nuc_translator.pm | 131 my ($genetic_code) = @_; 133 &use_specified_genetic_code($genetic_code); 595 foreach my $genetic_code (sort keys %expected_translation_tables) { 596 my $expected_translation = $expected_translation_tables{$genetic_code}; 603 print "$genetic_code\tOK\n"; 606 print "\n$genetic_code\tERROR:\n" 622 my $genetic_code = $ARGV[0]; 624 if ($genetic_code eq "TEST") { 628 if ($genetic_code) { 629 print "\nTranslation table for $genetic_code:\n\n"; [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/ |
H A D | orf.cpp | 124 int genetic_code, in FindForwardOrfs() argument 133 objects::CGen_code_table::GetTransTable(genetic_code); in FindForwardOrfs() 229 int genetic_code, in s_FindOrfs() argument 303 objects::CGen_code_table::GetTransTable(genetic_code); in GetStartCodons() 339 int genetic_code, in FindOrfs() argument 345 genetic_code, allowable_starts, longest_orfs, max_seq_gap); in FindOrfs() 354 int genetic_code, in FindOrfs() argument 360 genetic_code, allowable_starts, longest_orfs, max_seq_gap); in FindOrfs() 369 int genetic_code, in FindOrfs() argument 390 int genetic_code, in FindStrongKozakUOrfs() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/ |
H A D | orf.hpp | 79 int genetic_code = 1, 87 int genetic_code = 1, 95 int genetic_code = 1, 102 static vector<string> GetStartCodons(int genetic_code, bool include_atg, bool include_alt); 114 int genetic_code = 1, 139 MakeCDSAnnot(const TLocVec& orfs, int genetic_code = 1,
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/libv3/models/ |
H A D | codon.bf | 1 LoadFunctionLibrary ("../tasks/genetic_code.bf"); 8 * @param {String} genetic_code 11 function models.codon.MapCode (genetic_code) { 13 …turn {terms.sense_codons : utility.UniqueValues (genetic_code.ComputeCodonCodeToStringMap (genetic… 14 …terms.stop_codons : utility.UniqueValues (genetic_code.ComputeCodonCodeToStringMapStop (genetic_c… 15 terms.translation_table : genetic_code.DefineCodonToAAGivenCode (genetic_code) }; 151 …* @param {String} type - terms.genetic_code.synonymous or terms.genetic_code.nonsynonymous or call… 167 if (type == utility.getGlobalValue("terms.genetic_code.synonymous")) { 170 if (type == utility.getGlobalValue("terms.genetic_code.non_synonymous")) {
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/SelectionAnalyses/modules/ |
H A D | selection_lib.ibf | 10 * @param {AssociativeList} genetic_code 34 …on.substitution_mapper (matrix, tree, ambig_lookup, pairwise_counts, code_to_codon, genetic_code) { 39 aa_mapping = genetic_code.DefineCodonToAAMapping (genetic_code); 40 integer_mapping = genetic_code.DefineIntegerToAAMapping (genetic_code, TRUE); 82 …ub_count")]) [s] = (pairwise_counts[utility.getGlobalValue("terms.genetic_code.OPS")])[parent_… 83 …us_sub_count")]) [s] = (pairwise_counts[utility.getGlobalValue("terms.genetic_code.OPN")])[parent_…
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/ |
H A D | TransDecoder.Predict | 31 my $genetic_code = "Universal"; 182 'G=s' => \$genetic_code, 214 if ($genetic_code) { 215 $genetic_code = " --genetic_code $genetic_code"; 361 …gff3_file_to_proteins.pl --gff3 $gff3_file --fasta $transcripts_file $genetic_code > $best_pep_fil… 367 …roteins.pl --gff3 $gff3_file --fasta $transcripts_file --seqType CDS $genetic_code > $best_cds_fil…
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H A D | TransDecoder.LongOrfs | 32 my $genetic_code='universal'; 97 'G=s' => \$genetic_code, 127 if ($genetic_code ne 'universal') { 128 &Nuc_translator::use_specified_genetic_code($genetic_code); 349 …my $pep_header = ">$model_id type:$prot_type len:$length gc:$genetic_code $acc:$start-$stop($orien…
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/util/ |
H A D | gff3_file_to_proteins.pl | 50 my $genetic_code = ''; 55 'genetic_code=s' => \$genetic_code, 66 if ($genetic_code) { 67 &Nuc_translator::use_specified_genetic_code($genetic_code);
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/dports/biology/seaview/seaview/csrc/ |
H A D | misc_acnuc.c | 81 struct genetic_code_libel genetic_code[TOTCODES] = variable 471 return genetic_code[code].libel ; in get_code_descr() 484 return genetic_code[code].target ; in get_code_target() 526 pdata = &genetic_code[code]; /* ici ecriture plus compacte mal compilee sur PC*/ in codaa() 533 return genetic_code[gc].ncbi_gc; in get_ncbi_gc_number() 542 if(genetic_code[num].ncbi_gc == ncbi_gc) return num; in get_acnuc_gc_number() 684 pdata = &genetic_code[gc]; in init_codon_to_aa() 701 pdata = &genetic_code[gc]; in stop_codon_to_aa()
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/TemplateModels/ |
H A D | chooseGeneticCode.def | 131 genetic_code.stop_code = 10; 589 if (code[_ci] == genetic_code.stop_code) { 637 return code[codon] == ^ "genetic_code.stop_code"; 677 if (genCode[_idx] != ^ "genetic_code.stop_code") { 690 if (genCode[_idx] == ^ "genetic_code.stop_code") { 699 lfunction genetic_code.partition_codon(codon) { 707 lfunction genetic_code.assemble_codon(positions) { 713 lfunction genetic_code.ComputeBranchLengthStencils(genCode) { 729 stop_code = ^ "genetic_code.stop_code"; 762 lfunction genetic_code.DefineCodonToAAMapping (code) { [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/alignment/ |
H A D | alignment.cpp | 67 genetic_code = NULL; in Alignment() 517 ASSERT(genetic_code); in isStopCodon() 523 ASSERT(genetic_code); in getNumNonstopCodons() 2787 genetic_code = aln->genetic_code; in extractSubAlignment() 2840 genetic_code = aln->genetic_code; in extractPatterns() 2880 genetic_code = aln->genetic_code; in extractPatternFreqs() 2922 genetic_code = aln->genetic_code; in extractSites() 3268 genetic_code = aln->genetic_code; in createBootstrapAlignment() 3533 genetic_code = aln.genetic_code; in buildFromPatternFreq() 3576 genetic_code = aln->genetic_code; in createGapMaskedAlignment() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
H A D | blast_aux.cpp | 109 ddc.Log("genetic_code", m_Ptr->genetic_code); in DebugDump() 588 FindGeneticCode(int genetic_code) in FindGeneticCode() argument 631 if ( !genetic_code ) { in CAutomaticGenCodeSingleton() 632 genetic_code = BLAST_GENETIC_CODE; in CAutomaticGenCodeSingleton() 639 if (GenCodeSingletonFind(genetic_code) == NULL) { in CAutomaticGenCodeSingleton() 640 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in CAutomaticGenCodeSingleton() 641 GenCodeSingletonAdd(genetic_code, gc.get()); in CAutomaticGenCodeSingleton() 653 void CAutomaticGenCodeSingleton::AddGeneticCode(int genetic_code) in AddGeneticCode() argument 656 if (GenCodeSingletonFind(genetic_code) == NULL) { in AddGeneticCode() 657 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in AddGeneticCode() [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
H A D | blast_aux.cpp | 109 ddc.Log("genetic_code", m_Ptr->genetic_code); in DebugDump() 588 FindGeneticCode(int genetic_code) in FindGeneticCode() argument 631 if ( !genetic_code ) { in CAutomaticGenCodeSingleton() 632 genetic_code = BLAST_GENETIC_CODE; in CAutomaticGenCodeSingleton() 639 if (GenCodeSingletonFind(genetic_code) == NULL) { in CAutomaticGenCodeSingleton() 640 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in CAutomaticGenCodeSingleton() 641 GenCodeSingletonAdd(genetic_code, gc.get()); in CAutomaticGenCodeSingleton() 653 void CAutomaticGenCodeSingleton::AddGeneticCode(int genetic_code) in AddGeneticCode() argument 656 if (GenCodeSingletonFind(genetic_code) == NULL) { in AddGeneticCode() 657 TAutoUint1ArrayPtr gc = FindGeneticCode(genetic_code); in AddGeneticCode() [all …]
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
H A D | blast_options_api.c | 89 BLAST_GeneticCodeFind(db_options->genetic_code, &gc); in SBlastOptionsNew() 90 GenCodeSingletonAdd(db_options->genetic_code, gc); in SBlastOptionsNew() 324 options->db_options->genetic_code = gc; in SBlastOptionsSetDbGeneticCode() 329 BLAST_GeneticCodeFind(options->db_options->genetic_code, &gcode); in SBlastOptionsSetDbGeneticCode() 330 GenCodeSingletonAdd(options->db_options->genetic_code, gcode); in SBlastOptionsSetDbGeneticCode()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
H A D | blast_util.h | 180 const Uint1* genetic_code); 290 Int4 nucl_length, const Uint1* genetic_code, 309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
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/dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
H A D | blast_util.h | 180 const Uint1* genetic_code); 290 Int4 nucl_length, const Uint1* genetic_code, 309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
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H A D | blast_util.c | 429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument 446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation() 1004 if (genetic_code == NULL) in s_BlastGetTranslationTable() 1029 genetic_code[codon]; in s_BlastGetTranslationTable() 1036 genetic_code[codon]; in s_BlastGetTranslationTable() 1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument 1070 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations() 1071 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations() 1093 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations() 1140 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
H A D | blast_util.h | 180 const Uint1* genetic_code); 290 Int4 nucl_length, const Uint1* genetic_code, 309 Int4 nucl_length, Int2 frame, const Uint1* genetic_code,
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/dports/biology/p5-Bio-DB-NCBIHelper/Bio-DB-NCBIHelper-1.7.7/bin/ |
H A D | bp_query_entrez_taxa | 54 print " genetic_code ", $node->genetic_code, "\n"; 70 print " genetic_code ", $node->genetic_code, "\n";
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
H A D | blast_util.c | 429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument 446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation() 1004 if (genetic_code == NULL) in s_BlastGetTranslationTable() 1029 genetic_code[codon]; in s_BlastGetTranslationTable() 1036 genetic_code[codon]; in s_BlastGetTranslationTable() 1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument 1072 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations() 1073 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations() 1095 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations() 1142 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
H A D | blast_util.c | 429 Int4 nt_length, Int2 frame, Uint1* prot_seq, const Uint1* genetic_code) in BLAST_GetTranslation() argument 446 residue = s_CodonToAA(codon, genetic_code); in BLAST_GetTranslation() 1004 if (genetic_code == NULL) in s_BlastGetTranslationTable() 1029 genetic_code[codon]; in s_BlastGetTranslationTable() 1036 genetic_code[codon]; in s_BlastGetTranslationTable() 1046 Int4 nucl_length, const Uint1* genetic_code, in BLAST_GetAllTranslations() argument 1070 translation_table = s_BlastGetTranslationTable(genetic_code, FALSE); in BLAST_GetAllTranslations() 1071 translation_table_rc = s_BlastGetTranslationTable(genetic_code, TRUE); in BLAST_GetAllTranslations() 1093 nucl_length, frame, translation_buffer+offset, genetic_code); in BLAST_GetAllTranslations() 1140 Int4 nucl_length, Int2 frame, const Uint1* genetic_code, in Blast_GetPartialTranslation() argument [all …]
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/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/libv3/ |
H A D | models-codon.bf | 6 genetic_code = { 10 mapped_code = models.codon.MapCode (genetic_code);
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | suggest.c | 225 static Char *genetic_code = NULL; variable 445 if (genetic_code == NULL) { in get_frames() 446 genetic_code = suggestRec.geneticCode; in get_frames() 462 frame[i][j] = genetic_code[val] ; in get_frames() 515 genetic_code = NULL; in ClearBatchSuggestFrames() 1071 if ( ! genetic_code){ in APT_suggest() 1075 if ( ! * genetic_code){ in APT_suggest() 1136 fix_single_unassigned(dna_seq, rev_seq, p_seq, genetic_code); in APT_suggest() 1139 fix_overlaps_by_splice_sites(dna_seq, rev_seq, p_seq, genetic_code); in APT_suggest() 1422 genetic_code = geneticCode; in Suggest_Intervals() [all …]
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