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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 0669410c6b2c48884ae31671b9d710a9ff6346c6 / . / docs / dyn / genomics_v1.referencesets.html
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75<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.referencesets.html">referencesets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="#get">get(referenceSetId, x__xgafv=None)</a></code></p>
79<p class="firstline">Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).</p>
80<p class="toc_element">
81 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
82<p class="firstline">Searches for reference sets which match the given criteria. Implements [GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).</p>
83<h3>Method Details</h3>
84<div class="method">
85 <code class="details" id="get">get(referenceSetId, x__xgafv=None)</code>
86 <pre>Gets a reference set. Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
87
88Args:
89 referenceSetId: string, The ID of the reference set. (required)
90 x__xgafv: string, V1 error format.
91
92Returns:
93 An object of the form:
94
95 { # A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.
96 "description": "A String", # Free text description of this reference set.
97 "sourceUri": "A String", # The URI from which the references were obtained.
98 "referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
99 "A String",
100 ],
101 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
102 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
103 "A String",
104 ],
105 "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format.
106 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
107 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to model. Note that contained references may specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not belong to the modeled species, e.g. EBV in a human reference genome.
108 }</pre>
109</div>
110
111<div class="method">
112 <code class="details" id="search">search(body, x__xgafv=None)</code>
113 <pre>Searches for reference sets which match the given criteria. Implements [GlobalAllianceApi.searchReferenceSets](http://ga4gh.org/documentation/api/v0.5.1/ga4gh_api.html#/schema/org.ga4gh.searchReferenceSets).
114
115Args:
116 body: object, The request body. (required)
117 The object takes the form of:
118
119{
120 "md5checksums": [ # If present, return references for which the `md5checksum` matches. See `ReferenceSet.md5checksum` for details.
121 "A String",
122 ],
123 "assemblyId": "A String", # If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).
124 "accessions": [ # If present, return references for which the accession matches any of these strings. Best to give a version number, for example `GCF_000001405.26`. If only the main accession number is given then all records with that main accession will be returned, whichever version. Note that different versions will have different sequences.
125 "A String",
126 ],
127 "pageSize": 42, # Specifies the maximum number of results to return in a single page.
128 "pageToken": "A String", # The continuation token, which is used to page through large result sets. To get the next page of results, set this parameter to the value of `nextPageToken` from the previous response.
129 }
130
131 x__xgafv: string, V1 error format.
132
133Returns:
134 An object of the form:
135
136 {
137 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets. Provide this value in a subsequent request to return the next page of results. This field will be empty if there aren't any additional results.
138 "referenceSets": [ # The matching references sets.
139 { # A reference set is a set of references which typically comprise a reference assembly for a species, such as `GRCh38` which is representative of the human genome. A reference set defines a common coordinate space for comparing reference-aligned experimental data. A reference set contains 1 or more references.
140 "description": "A String", # Free text description of this reference set.
141 "sourceUri": "A String", # The URI from which the references were obtained.
142 "referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
143 "A String",
144 ],
145 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
146 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
147 "A String",
148 ],
149 "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The checksum is computed by sorting all lower case hexidecimal string `reference.md5checksum` (for all reference in this set) in ascending lexicographic order, concatenating, and taking the MD5 of that value. The resulting value is represented in lower case hexadecimal format.
150 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
151 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) indicating the species which this assembly is intended to model. Note that contained references may specify a different `ncbiTaxonId`, as assemblies may contain reference sequences which do not belong to the modeled species, e.g. EBV in a human reference genome.
152 },
153 ],
154 }</pre>
155</div>
156
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