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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blast_sra_input/unit_test/
H A Dblastsrainput_unit_test.cpp86 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/pubseq_gateway/server/test/
H A Dthreaded_get_blobs.py23 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 = []
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/
H A DPSPathogenReferenceTaxonProperties.java18 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()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/driver-tool/
H A Dsupport2.hpp307 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()
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H A Dfastq-dump.cpp69 static ParseArgsResult parse_fastq_dump_args(ParamList &params, 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()
H A Dimp_sra_pileup.cpp131 … 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()
H A Dimp_fasterq_dump.cpp163 … 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()
H A Dimp_srapath.cpp103 … 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()
H A Dimp_prefetch.cpp134 … 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()
H A Dimp_sam_dump.cpp244 … 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()
/dports/converters/p5-Boulder/Boulder-1.30/Boulder/
H A DGenbank.pm1054 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 $accessions = join "\n",@accessions;
1252 my @accessions;
1255 push @accessions,$_;
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/dports/science/py-pyteomics/pyteomics-4.5/pyteomics/openms/
H A Didxml.py359 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
/dports/science/py-pyteomics/pyteomics-4.5/pyteomics/
H A Dmzid.py381 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
/dports/biology/p5-BioPerl/BioPerl-1.7.7/examples/db/
H A Dest_tissue_query.pl47 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;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/
H A Dvaliderror_feat.cpp408 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/test/driver-tool/expected/
H A DDRX000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A DERP000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A DSRA000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A DSRP000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A DSRS000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A DSRX000001.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
H A Ddrive.stderr2 …atic expansion of container accessions is not currently available. See the above link(s) for infor…
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_SwissProt.py145 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)
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/dports/biology/py-biopython/biopython-1.79/Bio/KEGG/Enzyme/
H A D__init__.py285 accessions = data[4:].split()
286 row = (database, accessions)
290 database, accessions = row
291 accessions.extend(data.split())
292 row = (database, accessions)
/dports/biology/mothur/mothur-1.46.1/source/classifier/
H A Dphylotree.cpp180 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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