Coverage for denofo/choices.py: 100%

60 statements  

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1from enum import Enum 

2 

3 

4class AnnotGenomeChoices(str, Enum): 

5 abInitio = "ab initio approach" 

6 homology = "homology-based approach" 

7 unknown = "unknown" 

8 

9 

10class ORFChoices(str, Enum): 

11 noORF = "no ORF" 

12 allORF = "all ORF" 

13 highestKoz = "highest Kozac" 

14 longestORF = "longest ORF" 

15 firstORF = "start first ORF" 

16 long_5_3_ORF = "long 5` 3` ORF" 

17 CUSTOM = "custom choice" 

18 

19 

20class GeneticContextChoices(str, Enum): 

21 intergenic = "intergenic" 

22 antisense = "antisense" 

23 intronic = "intronic" 

24 overlap_gene = "overlap gene" 

25 CUSTOM = "custom choice" 

26 

27 

28class InputDataChoices(str, Enum): 

29 ANNOT_GENOME = "annotated genome" 

30 TRANSCRIPTOME = "transcriptome" 

31 CUSTOM = "custom choice" 

32 

33 

34class TaxSpecificityChoices(str, Enum): 

35 conditSpecif = "tissue/condition-specific" 

36 speciesSpecif = "species-specific" 

37 lineageSpecif = "lineage-specific" 

38 

39 

40class HomologyDBChoices(str, Enum): 

41 NCBINR = "NCBI NR" 

42 REFSEQ = "RefSeq" 

43 TrEMBL = "UniProtKB/TrEMBL" 

44 SWISSPROT = "UniProtKB/Swiss-Prot" 

45 ENA = "ENA (by EMBL-EBI)" 

46 ENSEMBL = "Ensembl" 

47 INTERPRO = "InterPro" 

48 CUSTOM = "custom choice" 

49 

50 

51class ThresholdChoices(str, Enum): 

52 EVALUE = "e-value" 

53 COVERAGE = "coverage [%]" 

54 CUSTOM = "custom choice" 

55 

56 

57class SeqTypeChoices(str, Enum): 

58 PROT_SEQS = "protein sequences" 

59 DNA = "DNA" 

60 FRAME6 = "6-frame translation" 

61 RNA = "RNA" 

62 NCRNA = "ncRNAs" 

63 TE = "transposable elements" 

64 CUSTOM = "custom choice" 

65 

66 

67class DirectionChoices(str, Enum): 

68 FORWARD = "forward" 

69 ANY = "any direction" 

70 

71 

72class AnchorChoices(str, Enum): 

73 GENEANCHOR = "gene anchors" 

74 GENOMEALIGNMENT = "genome alignment" 

75 CUSTOM = "custom choice" 

76 

77 

78class TranslationEvidenceChoices(str, Enum): 

79 MASS_SPEC = "mass spectrometry" 

80 RIBO_PROFIL = "ribosome profiling" 

81 PERIODICITY = "periodicity" 

82 CUSTOM = "custom choice"