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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / b8458c0b73030155b64a3c2392b2f70e5fbc3baf / . / docs / dyn / genomics_v1.references.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.references.html">references</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="genomics_v1.references.bases.html">bases()</a></code>
79</p>
80<p class="firstline">Returns the bases Resource.</p>
81
82<p class="toc_element">
83 <code><a href="#get">get(referenceId, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]84<p class="firstline">Gets a reference.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]85<p class="toc_element">
86 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]87<p class="firstline">Searches for references which match the given criteria.</p>
88<p class="toc_element">
89 <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p>
90<p class="firstline">Retrieves the next page of results.</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]91<h3>Method Details</h3>
92<div class="method">
93 <code class="details" id="get">get(referenceId, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]94 <pre>Gets a reference.
95
96For the definitions of references and other genomics resources, see
97[Fundamentals of Google
98Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
99
100Implements
101[GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]102
103Args:
104 referenceId: string, The ID of the reference. (required)
105 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]106 Allowed values
107 1 - v1 error format
108 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]109
110Returns:
111 An object of the form:
112
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]113 { # A reference is a canonical assembled DNA sequence, intended to act as a
114 # reference coordinate space for other genomic annotations. A single reference
115 # might represent the human chromosome 1 or mitochandrial DNA, for instance. A
116 # reference belongs to one or more reference sets.
117 #
118 # For more genomics resource definitions, see [Fundamentals of Google
119 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]120 "name": "A String", # The name of this reference, for example `22`.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]121 "sourceUri": "A String", # The URI from which the sequence was obtained. Typically specifies a FASTA
122 # format file.
123 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
124 # with a version number, for example `GCF_000001405.26`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]125 "A String",
126 ],
127 "length": "A String", # The length of this reference's sequence.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]128 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
129 "id": "A String", # The server-generated reference ID, unique across all references.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]130 "md5checksum": "A String", # MD5 of the upper-case sequence excluding all whitespace characters (this
131 # is equivalent to SQ:M5 in SAM). This value is represented in lower case
132 # hexadecimal format.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]133 }</pre>
134</div>
135
136<div class="method">
137 <code class="details" id="search">search(body, x__xgafv=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]138 <pre>Searches for references which match the given criteria.
139
140For the definitions of references and other genomics resources, see
141[Fundamentals of Google
142Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
143
144Implements
145[GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]146
147Args:
148 body: object, The request body. (required)
149 The object takes the form of:
150
151{
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]152 "md5checksums": [ # If present, return references for which the
153 # md5checksum matches exactly.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]154 "A String",
155 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]156 "pageToken": "A String", # The continuation token, which is used to page through large result sets.
157 # To get the next page of results, set this parameter to the value of
158 # `nextPageToken` from the previous response.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]159 "referenceSetId": "A String", # If present, return only references which belong to this reference set.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]160 "accessions": [ # If present, return references for which a prefix of any of
161 # sourceAccessions match
162 # any of these strings. Accession numbers typically have a main number and a
163 # version, for example `GCF_000001405.26`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]164 "A String",
165 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]166 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified,
167 # defaults to 1024. The maximum value is 4096.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]168 }
169
170 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]171 Allowed values
172 1 - v1 error format
173 2 - v2 error format
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]174
175Returns:
176 An object of the form:
177
178 {
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]179 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
180 # Provide this value in a subsequent request to return the next page of
181 # results. This field will be empty if there aren't any additional results.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]182 "references": [ # The matching references.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]183 { # A reference is a canonical assembled DNA sequence, intended to act as a
184 # reference coordinate space for other genomic annotations. A single reference
185 # might represent the human chromosome 1 or mitochandrial DNA, for instance. A
186 # reference belongs to one or more reference sets.
187 #
188 # For more genomics resource definitions, see [Fundamentals of Google
189 # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]190 "name": "A String", # The name of this reference, for example `22`.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]191 "sourceUri": "A String", # The URI from which the sequence was obtained. Typically specifies a FASTA
192 # format file.
193 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally
194 # with a version number, for example `GCF_000001405.26`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]195 "A String",
196 ],
197 "length": "A String", # The length of this reference's sequence.
Sai Cheemalapatie833b792017-03-24 15:06:46 -0700[diff] [blame]198 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
199 "id": "A String", # The server-generated reference ID, unique across all references.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]200 "md5checksum": "A String", # MD5 of the upper-case sequence excluding all whitespace characters (this
201 # is equivalent to SQ:M5 in SAM). This value is represented in lower case
202 # hexadecimal format.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]203 },
204 ],
205 }</pre>
206</div>
207
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]208<div class="method">
209 <code class="details" id="search_next">search_next(previous_request, previous_response)</code>
210 <pre>Retrieves the next page of results.
211
212Args:
213 previous_request: The request for the previous page. (required)
214 previous_response: The response from the request for the previous page. (required)
215
216Returns:
217 A request object that you can call 'execute()' on to request the next
218 page. Returns None if there are no more items in the collection.
219 </pre>
220</div>
221
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]222</body></html>