| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/simulate/ |
| H A D | popgensim.py | 125 leaf.num_genes = samples_per_pop
138 num_genes=None, argument
212 if num_genes is not None:
213 if isinstance(num_genes, list):
214 if len(num_genes) < num_pops:
218 samples = num_genes
220 samples = [num_genes for tax in range(num_pops)]
|
| /dports/biology/py-goatools/goatools-1.1.6/goatools/cli/ |
| H A D | ncbi_gene_results_to_python.py | 125 num_genes = len(geneid2nt)
132 ofstrm.write(' # {N} items\n\n'.format(N=num_genes))
137 ofstrm.write("GENEID2NT = {{ # {N:,} items\n".format(N=num_genes))
141 log.write(" {N:9} geneids WROTE: {PY}\n".format(N=num_genes, PY=fout_py))
|
| /dports/biology/py-multiqc/multiqc-1.10/multiqc/modules/star/ |
| H A D | star.py | 175 num_genes = 0
189 num_genes += 1
193 if num_errors > 10 and num_genes == 0:
196 if num_genes > 0:
|
| /dports/science/py-DendroPy/DendroPy-4.4.0/src/dendropy/model/ |
| H A D | coalescent.py | 387 num_genes = len(tree.leaf_nodes())
390 num_genes_wt[num_genes] = n[1]
391 num_genes = num_genes - len(n[0].child_nodes()) + 1
|
| /dports/biology/py-goatools/goatools-1.1.6/goatools/ |
| H A D | associations.py | 158 num_genes = len(genes)
159 if (min_genecnt is None or num_genes >= min_genecnt) and \
160 (max_genecnt is None or num_genes <= max_genecnt):
|
| /dports/biology/py-biopython/biopython-1.79/Bio/Phylo/PAML/ |
| H A D | _parse_codeml.py | 47 num_genes = int(num_genes_res.group(1))
48 for n in range(num_genes):
|
| /dports/biology/py-orange3-bioinformatics/Orange3-Bioinformatics-4.3.1/orangecontrib/bioinformatics/widgets/ |
| H A D | OWGenes.py | 380 num_genes = len(self.gene_matcher.genes)
386 … '{} genes with match conflicts\n'.format(num_genes, known_genes, num_genes - known_genes)
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/igblast/ |
| H A D | igblast.cpp | 379 int num_genes = (m_IgOptions->m_IsProtein) ? 1 : 3; in Run() local
380 if (num_genes > 1) { in Run()
382 for (int gene = 1; gene < num_genes; ++gene) { in Run()
396 num_genes = 1; in Run()
423 for (int gene = 0; gene < num_genes; ++gene) { in Run()
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/igblast/ |
| H A D | igblast.cpp | 379 int num_genes = (m_IgOptions->m_IsProtein) ? 1 : 3; in Run() local
380 if (num_genes > 1) { in Run()
382 for (int gene = 1; gene < num_genes; ++gene) { in Run()
396 num_genes = 1; in Run()
423 for (int gene = 0; gene < num_genes; ++gene) { in Run()
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/validator/ |
| H A D | single_feat_validator.cpp | 2002 size_t num_genes = 0; in x_ValidateGeneXRef() local
2043 if (len < max || num_genes == 0) { in x_ValidateGeneXRef()
2044 num_genes = 1; in x_ValidateGeneXRef()
2055 num_genes++; in x_ValidateGeneXRef()
2067 if (num_genes > 1 && in x_ValidateGeneXRef()
2070 if (m_Imp.IsSmallGenomeSet() && num_genes == num_trans_spliced) { in x_ValidateGeneXRef()
2075 + NStr::SizetToString(num_genes) in x_ValidateGeneXRef()
2080 + NStr::SizetToString(num_genes) in x_ValidateGeneXRef()
2083 } else if (num_genes == 1 in x_ValidateGeneXRef()
|
| /dports/math/py-point-annotator/point-annotator-2.0.0/pointannotator/tests/ |
| H A D | test_annotate_samples.py | 240 array(self.data), self.markers, num_genes=15)
|
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/blastinput/ |
| H A D | blast_args.cpp | 1557 int num_genes = (m_IsProtein) ? 1 : 3; in SetArgumentDescriptions() local
1560 for (int gene=0; gene<num_genes; ++gene) { in SetArgumentDescriptions()
1808 int num_genes = (m_IsProtein) ? 1: 3; in ExtractAlgorithmOptions() local
1809 for (int gene=0; gene< num_genes; ++gene) { in ExtractAlgorithmOptions()
|
| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/blastinput/ |
| H A D | blast_args.cpp | 1557 int num_genes = (m_IsProtein) ? 1 : 3; in SetArgumentDescriptions() local
1560 for (int gene=0; gene<num_genes; ++gene) { in SetArgumentDescriptions()
1808 int num_genes = (m_IsProtein) ? 1: 3; in ExtractAlgorithmOptions() local
1809 for (int gene=0; gene< num_genes; ++gene) { in ExtractAlgorithmOptions()
|
| /dports/biology/ncbi-toolkit/ncbi/sequin/ |
| H A D | sequin7.c | 8858 PrompT num_genes; member
9010 Int4 num_genes; in RemoveGeneByFeatChangeNotify() local
9031 num_genes = ValNodeLen (dlg->feature_list); in RemoveGeneByFeatChangeNotify()
9032 sprintf (num_genes_txt, num_genes_fmt, num_genes, num_genes == 1 ? "" : "s"); in RemoveGeneByFeatChangeNotify()
9033 SetTitle (dlg->num_genes, num_genes_txt); in RemoveGeneByFeatChangeNotify()
9246 …dlg->num_genes = StaticPrompt (g, "0 genes to be removed", 200, dialogTextHeight, systemFont, 'l'); in RemoveGeneByUnderlyingFeatureType()
|
| /dports/biology/ncbi-toolkit/ncbi/api/ |
| H A D | sqnutil4.c | 8369 Int4 num_genes; in AddProductEnding() local
8372 num_genes = 0; in AddProductEnding()
8378 num_genes = 2; in AddProductEnding()
8384 num_genes = 2; in AddProductEnding()
8388 num_genes = 1; in AddProductEnding()
8434 if (num_genes > 1) in AddProductEnding()
|