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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / c30d2b5d4478b230246dcaaa9f1c533ca3304387 / . / docs / dyn / genomics_v1.referencesets.html
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Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1<html><body>
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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>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]79<p class="firstline">Gets a reference set.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]80<p class="toc_element">
81 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]82<p class="firstline">Searches for reference sets which match the given criteria.</p>
83<p class="toc_element">
84 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
85<p class="firstline">Retrieves the next page of results.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]86<h3>Method Details</h3>
87<div class="method">
88 <code class="details" id="get">get(referenceSetId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]89 <pre>Gets a reference set.
90
91For the definitions of references and other genomics resources, see
92[Fundamentals of Google
93Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
94
95Implements
96[GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]97
98Args:
99 referenceSetId: string, The ID of the reference set. (required)
100 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]101 Allowed values
102 1 - v1 error format
103 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]104
105Returns:
106 An object of the form:
107
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]108 { # A reference set is a set of references which typically comprise a reference
109 # assembly for a species, such as `GRCh38` which is representative
110 # of the human genome. A reference set defines a common coordinate space for
111 # comparing reference-aligned experimental data. A reference set contains 1 or
112 # more references.
113 #
114 # For more genomics resource definitions, see [Fundamentals of Google
115 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]116 "description": "A String", # Free text description of this reference set.
117 "sourceUri": "A String", # The URI from which the references were obtained.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]118 "referenceIds": [ # The IDs of the reference objects that are part of this set.
119 # `Reference.md5checksum` must be unique within this set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]120 "A String",
121 ],
122 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]123 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
124 # with a version number, for example `NC_000001.11`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]125 "A String",
126 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]127 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
128 # indicating the species which this reference set is intended to model. Note
129 # that contained references may specify a different `ncbiTaxonId`, as
130 # assemblies may contain reference sequences which do not belong to the
131 # modeled species, for example EBV in a human reference genome.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]132 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]133 "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The
134 # checksum is computed by sorting all lower case hexidecimal string
135 # `reference.md5checksum` (for all reference in this set) in
136 # ascending lexicographic order, concatenating, and taking the MD5 of that
137 # value. The resulting value is represented in lower case hexadecimal format.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]138 }</pre>
139</div>
140
141<div class="method">
142 <code class="details" id="search">search(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]143 <pre>Searches for reference sets which match the given criteria.
144
145For the definitions of references and other genomics resources, see
146[Fundamentals of Google
147Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
148
149Implements
150[GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]151
152Args:
153 body: object, The request body. (required)
154 The object takes the form of:
155
156{
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]157 "md5checksums": [ # If present, return reference sets for which the
158 # md5checksum matches exactly.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]159 "A String",
160 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]161 "pageToken": "A String", # The continuation token, which is used to page through large result sets.
162 # To get the next page of results, set this parameter to the value of
163 # `nextPageToken` from the previous response.
164 "accessions": [ # If present, return reference sets for which a prefix of any of
165 # sourceAccessions
166 # match any of these strings. Accession numbers typically have a main number
167 # and a version, for example `NC_000001.11`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]168 "A String",
169 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]170 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified,
171 # defaults to 1024. The maximum value is 4096.
172 "assemblyId": "A String", # If present, return reference sets for which a substring of their
173 # `assemblyId` matches this string (case insensitive).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]174 }
175
176 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]177 Allowed values
178 1 - v1 error format
179 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]180
181Returns:
182 An object of the form:
183
184 {
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]185 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
186 # Provide this value in a subsequent request to return the next page of
187 # results. This field will be empty if there aren't any additional results.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]188 "referenceSets": [ # The matching references sets.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]189 { # A reference set is a set of references which typically comprise a reference
190 # assembly for a species, such as `GRCh38` which is representative
191 # of the human genome. A reference set defines a common coordinate space for
192 # comparing reference-aligned experimental data. A reference set contains 1 or
193 # more references.
194 #
195 # For more genomics resource definitions, see [Fundamentals of Google
196 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]197 "description": "A String", # Free text description of this reference set.
198 "sourceUri": "A String", # The URI from which the references were obtained.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]199 "referenceIds": [ # The IDs of the reference objects that are part of this set.
200 # `Reference.md5checksum` must be unique within this set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]201 "A String",
202 ],
203 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]204 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
205 # with a version number, for example `NC_000001.11`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]206 "A String",
207 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]208 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
209 # indicating the species which this reference set is intended to model. Note
210 # that contained references may specify a different `ncbiTaxonId`, as
211 # assemblies may contain reference sequences which do not belong to the
212 # modeled species, for example EBV in a human reference genome.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]213 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]214 "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The
215 # checksum is computed by sorting all lower case hexidecimal string
216 # `reference.md5checksum` (for all reference in this set) in
217 # ascending lexicographic order, concatenating, and taking the MD5 of that
218 # value. The resulting value is represented in lower case hexadecimal format.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]219 },
220 ],
221 }</pre>
222</div>
223
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame^]224<div class="method">
225 <code class="details" id="search_next">search_next(previous_request, previous_response)</code>
226 <pre>Retrieves the next page of results.
227
228Args:
229 previous_request: The request for the previous page. (required)
230 previous_response: The response from the request for the previous page. (required)
231
232Returns:
233 A request object that you can call 'execute()' on to request the next
234 page. Returns None if there are no more items in the collection.
235 </pre>
236</div>
237
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]238</body></html>