1 | #! /bin/bash
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38 |
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39 | echo '{"id":"abc123","xref":{"dataSource":"ensembl","identifier":"ENSG00000132031"}}' |\
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40 | ./bin/bridgedb xrefs -f "json" \
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41 | Human ".xref.dataSource" ".xref.identifier" \
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42 | ensembl uniprot |\
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43 | jq .
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44 |
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45 | echo '[{"xrefDataSource": "Entrez Gene", "xrefIdentifier": "1234"}]' |\
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46 | ./bin/bridgedb xrefs -f "json" \
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47 | Human ".[].xrefDataSource" ".[].xrefIdentifier" \
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48 | ensembl ncbigene uniprot wikidata
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49 |
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50 | ./bin/bridgedb xrefs -f "json" -i ".[].type" \
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51 | Human ".[].xrefDataSource" ".[].xrefIdentifier" \
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52 | ensembl ncbigene uniprot wikidata \
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53 | < "./test/inputs/nest0-array.json" |\
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54 | jq .
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55 |
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56 | ./bin/bridgedb xrefs -f "json" \
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57 | Human ".[].xrefDataSource" ".[].xrefIdentifier" \
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58 | ensembl ncbigene uniprot wikidata \
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59 | < ./test/inputs/nest0-array.json |\
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60 | jq .
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61 |
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62 | ./bin/bridgedb xrefs -f "json" \
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63 | Human ".entitiesById[].xrefDataSource" ".entitiesById[].xrefIdentifier" \
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64 | ensembl ncbigene uniprot wikidata \
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65 | < ./test/inputs/nest1-object.json |\
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66 | jq .
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67 |
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68 | ./bin/bridgedb xrefs -f "json" \
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69 | Human ".entitiesById[].xrefDataSource" ".entitiesById[].xrefIdentifier" \
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70 | ensembl ncbigene uniprot wikidata \
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71 | < ./test/inputs/nest1-object.json |\
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72 | jq .
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73 |
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74 |
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75 |
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76 | echo '{"id":"abc123","xref":{"dataSource":"ensembl","identifier":"ENSG00000132031"}}' |\
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77 | ./bin/bridgedb xrefs -f "json" \
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78 | -i ".xref.alternates" \
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79 | Human \
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80 | ".xref.dataSource" \
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81 | ".xref.identifier" \
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82 | ensembl uniprot
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83 |
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84 | echo '[{"xrefDataSource": "Entrez Gene", "xrefIdentifier": "1234"}]' |\
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85 | ./bin/bridgedb xrefs -f "json" \
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86 | -i ".[]" \
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87 | Human \
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88 | ".[].xrefDataSource" \
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89 | ".[].xrefIdentifier" \
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90 | ensembl ncbigene uniprot wikidata
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91 |
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92 | ./bin/bridgedb xrefs -f "json" -i ".[].type" \
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93 | Human \
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94 | ".[].xrefDataSource" \
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95 | ".[].xrefIdentifier" \
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96 | ensembl ncbigene uniprot wikidata \
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97 | < "./test/inputs/nest0-array.json" |\
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98 | jq .
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99 |
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100 | ./bin/bridgedb xrefs -f "json" -i ".[]" \
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101 | Human ".[].xrefDataSource" ".[].xrefIdentifier" \
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102 | ensembl ncbigene uniprot wikidata \
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103 | < ./test/inputs/nest0-array.json |\
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104 | jq .
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105 |
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106 | ./bin/bridgedb xrefs -f "json" -i ".entitiesById[].type" \
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107 | Human ".entitiesById[].xrefDataSource" ".entitiesById[].xrefIdentifier" \
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108 | ensembl ncbigene uniprot wikidata \
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109 | < ./test/inputs/nest1-object.json |\
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110 | jq .
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111 |
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112 | ./bin/bridgedb xrefs -f "json" -i ".entitiesById" \
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113 | Human ".entitiesById[].xrefDataSource" ".entitiesById[].xrefIdentifier" \
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114 | ensembl ncbigene uniprot wikidata \
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115 | < ./test/inputs/nest1-object.json |\
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116 | jq .
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