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74
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.</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.</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>
86<h3>Method Details</h3>
87<div class="method">
88    <code class="details" id="get">get(referenceSetId, x__xgafv=None)</code>
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).
97
98Args:
99  referenceSetId: string, The ID of the reference set. (required)
100  x__xgafv: string, V1 error format.
101    Allowed values
102      1 - v1 error format
103      2 - v2 error format
104
105Returns:
106  An object of the form:
107
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)
116    "description": "A String", # Free text description of this reference set.
117    "sourceUri": "A String", # The URI from which the references were obtained.
118    "referenceIds": [ # The IDs of the reference objects that are part of this set.
119        # `Reference.md5checksum` must be unique within this set.
120      "A String",
121    ],
122    "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
123    "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
124        # with a version number, for example `NC_000001.11`.
125      "A String",
126    ],
127    "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The
128        # checksum is computed by sorting all lower case hexidecimal string
129        # `reference.md5checksum` (for all reference in this set) in
130        # ascending lexicographic order, concatenating, and taking the MD5 of that
131        # value. The resulting value is represented in lower case hexadecimal format.
132    "id": "A String", # The server-generated reference set ID, unique across all reference sets.
133    "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
134        # indicating the species which this reference set is intended to model. Note
135        # that contained references may specify a different `ncbiTaxonId`, as
136        # assemblies may contain reference sequences which do not belong to the
137        # modeled species, for example EBV in a human reference genome.
138  }</pre>
139</div>
140
141<div class="method">
142    <code class="details" id="search">search(body, x__xgafv=None)</code>
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)
151
152Args:
153  body: object, The request body. (required)
154    The object takes the form of:
155
156{
157    "md5checksums": [ # If present, return reference sets for which the
158        # md5checksum matches exactly.
159      "A String",
160    ],
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`.
168      "A String",
169    ],
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).
174  }
175
176  x__xgafv: string, V1 error format.
177    Allowed values
178      1 - v1 error format
179      2 - v2 error format
180
181Returns:
182  An object of the form:
183
184    {
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.
188    "referenceSets": [ # The matching references sets.
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)
197        "description": "A String", # Free text description of this reference set.
198        "sourceUri": "A String", # The URI from which the references were obtained.
199        "referenceIds": [ # The IDs of the reference objects that are part of this set.
200            # `Reference.md5checksum` must be unique within this set.
201          "A String",
202        ],
203        "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
204        "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
205            # with a version number, for example `NC_000001.11`.
206          "A String",
207        ],
208        "md5checksum": "A String", # Order-independent MD5 checksum which identifies this reference set. The
209            # checksum is computed by sorting all lower case hexidecimal string
210            # `reference.md5checksum` (for all reference in this set) in
211            # ascending lexicographic order, concatenating, and taking the MD5 of that
212            # value. The resulting value is represented in lower case hexadecimal format.
213        "id": "A String", # The server-generated reference set ID, unique across all reference sets.
214        "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human)
215            # indicating the species which this reference set is intended to model. Note
216            # that contained references may specify a different `ncbiTaxonId`, as
217            # assemblies may contain reference sequences which do not belong to the
218            # modeled species, for example EBV in a human reference genome.
219      },
220    ],
221  }</pre>
222</div>
223
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
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