/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blast_sra_input/unit_test/ |
H A D | blastsrainput_unit_test.cpp | 86 vector<string> accessions = {"SRR4423739"}; in BOOST_AUTO_TEST_CASE() local 88 CSraInputSource input_source(accessions, kCheckForPairs); in BOOST_AUTO_TEST_CASE() 121 vector<string> accessions = {"SRR4423739"}; in BOOST_AUTO_TEST_CASE() local 122 CSraInputSource input_source(accessions, kCheckForPairs); in BOOST_AUTO_TEST_CASE() 149 vector<string> accessions = {"SRR3720856", "SRR5196091"}; in BOOST_AUTO_TEST_CASE() local 151 CSraInputSource input_source(accessions); in BOOST_AUTO_TEST_CASE() 160 BOOST_REQUIRE(fid->GetSeqIdString().find(accessions.front()) != string::npos); in BOOST_AUTO_TEST_CASE() 164 BOOST_REQUIRE(lid->GetSeqIdString().find(accessions.back()) != string::npos); in BOOST_AUTO_TEST_CASE() 171 vector<string> accessions = {"SRR3720856", "SRR5196091"}; in BOOST_AUTO_TEST_CASE() local 173 CSraInputSource input_source(accessions, kCheckForPairs); in BOOST_AUTO_TEST_CASE() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/pubseq_gateway/server/test/ |
H A D | threaded_get_blobs.py | 23 def process(accessions): argument 26 for accession in accessions: 88 accessions = [] 94 accessions.append(line) 95 if len(accessions) >= processes: 96 process(accessions) 97 accessions = [] 102 if accessions: 103 process(accessions) 104 accessions = []
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/ |
H A D | PSPathogenReferenceTaxonProperties.java | 18 private final Map<String, Long> accessions; field in PSPathogenReferenceTaxonProperties 21 accessions = new HashMap<>(SVUtils.hashMapCapacity(1)); in PSPathogenReferenceTaxonProperties() 30 accessions.put(name, length); in addAccession() 35 return accessions.containsKey(name); in hasAccession() 39 if (accessions.containsKey(name)) { in getAccessionLength() 40 return accessions.get(name); in getAccessionLength() 53 return accessions.keySet(); in getAccessions()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/driver-tool/ |
H A D | support2.hpp | 307 for (auto const &acc : accessions) { in print_unsafe_output_file_message() 317 std::vector < ncbi::String > accessions; member 378 for ( auto & value : accessions ) in show() 416 (void)(acc_index); (void)(accessions); in populate_common_argv_builder() 465 for (auto & Acc : accessions) { in check() 502 tool_options . populate_argv_builder( builder, (int)accessions.size(), accessions ); in run() 504 auto argv = builder.generate_argv(accessions); in run() 556 if (accessions.empty()) { in run() 568 auto all_sources = sratools::data_sources::preload(convert(accessions)); in run() 581 for (auto const &acc : accessions) { in run() [all …]
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H A D | fastq-dump.cpp | 69 static ParseArgsResult parse_fastq_dump_args(ParamList ¶ms, ArgsList &accessions) in parse_fastq_dump_args() argument 136 accessions.push_back(arg); in parse_fastq_dump_args() 176 ArgsList accessions; in running_as_fastq_dump() local 177 auto const parseResult = parse_fastq_dump_args(params, accessions); in running_as_fastq_dump() 187 , params, accessions); in running_as_fastq_dump()
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H A D | imp_sra_pileup.cpp | 131 … ArgvBuilder & builder, int acc_index, std::vector<ncbi::String> const &accessions ) const override in populate_argv_builder() 133 populate_common_argv_builder(builder, acc_index, accessions); in populate_argv_builder() 137 if (accessions.size() > 1) { in populate_argv_builder() 139 print_unsafe_output_file_message("sra-pileup", ".pileup", accessions); in populate_argv_builder() 140 builder . add_option( "-o", accessions[acc_index] + ".pileup" ); in populate_argv_builder() 192 return ToolExec::run(TOOL_NAME, realpath.fullpath(), theirArgv0, *this, accessions); in run()
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H A D | imp_fasterq_dump.cpp | 163 … ArgvBuilder & builder, int acc_index, std::vector<ncbi::String> const &accessions ) const override in populate_argv_builder() 165 populate_common_argv_builder(builder, acc_index, accessions); in populate_argv_builder() 168 if (accessions.size() > 1) { in populate_argv_builder() 170 print_unsafe_output_file_message("fasterq-dump", ".fastq", accessions); in populate_argv_builder() 172 builder . add_option( "-o", accessions[acc_index] + ".fastq" ); in populate_argv_builder() 214 return ToolExec::run(TOOL_NAME, realpath.fullpath(), theirArgv0, *this, accessions); in run()
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H A D | imp_srapath.cpp | 103 … ArgvBuilder & builder, int acc_index, std::vector<ncbi::String> const &accessions ) const override in populate_argv_builder() 105 (void)(acc_index); (void)(accessions); in populate_argv_builder() 107 populate_common_argv_builder(builder, acc_index, accessions); in populate_argv_builder() 138 … return ToolExecNoSDL::run(TOOL_NAME, realpath.fullpath(), theirArgv0, *this, accessions); in run()
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H A D | imp_prefetch.cpp | 134 … ArgvBuilder & builder, int acc_index, std::vector<ncbi::String> const &accessions ) const override in populate_argv_builder() 136 (void)(acc_index); (void)(accessions); in populate_argv_builder() 138 populate_common_argv_builder(builder, acc_index, accessions); in populate_argv_builder() 190 … return ToolExecNoSDL::run(TOOL_NAME, realpath.fullpath(), theirArgv0, *this, accessions); in run()
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H A D | imp_sam_dump.cpp | 244 … ArgvBuilder & builder, int acc_index, std::vector<ncbi::String> const &accessions ) const override in populate_argv_builder() 246 populate_common_argv_builder(builder, acc_index, accessions); in populate_argv_builder() 276 if (accessions.size() > 1 && !(fasta || fastq)) { in populate_argv_builder() 278 print_unsafe_output_file_message("sam-dump", ".sam", accessions); in populate_argv_builder() 280 builder . add_option( "--output-file", accessions[acc_index] + ".sam" ); in populate_argv_builder() 329 return ToolExec::run(TOOL_NAME, realpath.fullpath(), theirArgv0, *this, accessions); in run()
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/dports/converters/p5-Boulder/Boulder-1.30/Boulder/ |
H A D | Genbank.pm | 1054 my @accessions = ref $self->{accession} ? @{$self->{accession}} : ($self->{accession}); 1055 $self->{accession} = \@accessions; 1127 my @accessions = $line; 1130 push @accessions,$line; 1132 return \@accessions; 1224 my @accessions = splice(@$a,0,MAX_ENTRIES); 1225 return unless @accessions; 1226 my $accessions = join "\n",@accessions; 1252 my @accessions; 1255 push @accessions,$_; [all …]
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/dports/science/py-pyteomics/pyteomics-4.5/pyteomics/openms/ |
H A D | idxml.py | 359 accessions, isd, starts, ends, scores, aa_bs, aa_as = [], [], [], [], [], [], [] 361 accessions.append(d.get('accession')) 371 if all(isinstance(acc, str) for acc in accessions): 372 accessions = sep.join(accessions) 377 if all(acc is None for acc in accessions): 378 accessions = None 381 info['accession'] = accessions
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/dports/science/py-pyteomics/pyteomics-4.5/pyteomics/ |
H A D | mzid.py | 381 prot_descr, accessions, isd, starts, ends, lengths = [], [], [], [], [], [] 384 accessions.append(d.get('accession')) 394 if all(isinstance(acc, str) for acc in accessions): 395 accessions = sep.join(accessions) 399 if all(acc is None for acc in accessions): 400 accessions = None 404 info['accession'] = accessions
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/examples/db/ |
H A D | est_tissue_query.pl | 47 my %accessions; # cache results 61 tie %accessions, "DB_File", $cache, O_RDWR|O_CREAT,0660, $DB_HASH; 140 if( $tissue = $accessions{$id} ) { 155 $accessions{$seq->display_id} = $tissue;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
H A D | validerror_feat.cpp | 408 vector<string> accessions; in GetAccessionsFromInferenceString() local 410 accessions.clear(); in GetAccessionsFromInferenceString() 413 return accessions; in GetAccessionsFromInferenceString() 428 return accessions; in GetAccessionsFromInferenceString() 434 return accessions; in GetAccessionsFromInferenceString() 444 NStr::Split(remainder, ",", accessions, 0); in GetAccessionsFromInferenceString() 446 NStr::Split(remainder, ",", accessions, 0); in GetAccessionsFromInferenceString() 448 return accessions; in GetAccessionsFromInferenceString() 478 for (size_t i = 0; i < accessions.size(); i++) { in ValidateInference() 479 NStr::TruncateSpacesInPlace (accessions[i]); in ValidateInference() [all …]
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/dports/biology/sra-tools/sra-tools-2.11.0/test/driver-tool/expected/ |
H A D | DRX000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | ERP000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | SRA000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | SRP000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | SRS000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | SRX000001.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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H A D | drive.stderr | 2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_SwissProt.py | 145 self.assertEqual(records[0].accessions, record.accessions) 260 self.assertEqual(records[0].accessions, record.accessions) 483 self.assertEqual(records[0].accessions, record.accessions) 631 self.assertEqual(records[0].accessions, record.accessions) 734 self.assertEqual(records[0].accessions, record.accessions) 827 self.assertEqual(records[0].accessions, record.accessions) 964 self.assertEqual(records[0].accessions, record.accessions) 1763 self.assertEqual(records[0].accessions, record.accessions) 1862 self.assertEqual(records[0].accessions, record.accessions) 2175 self.assertEqual(records[0].accessions, record.accessions) [all …]
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/dports/biology/py-biopython/biopython-1.79/Bio/KEGG/Enzyme/ |
H A D | __init__.py | 285 accessions = data[4:].split() 286 row = (database, accessions) 290 database, accessions = row 291 accessions.extend(data.split()) 292 row = (database, accessions)
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/dports/biology/mothur/mothur-1.46.1/source/classifier/ |
H A D | phylotree.cpp | 180 if (seqTaxonomy == "") { names = tree[currentNode].accessions; } in getSeqs() 201 tree[0].accessions.push_back(seqName); in addSeqToTree() 216 tree[currentNode].accessions.push_back(seqName); in addSeqToTree() 228 tree[currentNode].accessions.push_back(seqName); in addSeqToTree() 256 tree[0].accessions.push_back(seqName); in addSeqToTree() 278 tree[currentNode].accessions.push_back(seqName); in addSeqToTree() 290 tree[currentNode].accessions.push_back(seqName); in addSeqToTree() 338 totals.push_back(tree[genusIndex[j]].accessions.size()); in getGenusTotals() 586 …niqueTaxonomies.end(); it2++) { outTree << *it2 << '\t' << tree[*it2].accessions.size() << endl; } in printTreeNodes()
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