Gitiles
Code Review Sign In
gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 46a8071fe1d1a112dcc791f61c20fd8306b4061f / . / docs / dyn / genomics_v1.references.html
blob: bd0ac736a664b32b296677ed3ff62ec8b39b48e4 [file] [log] [blame]
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1<html><body>
2<style>
3
4body, h1, h2, h3, div, span, p, pre, a {
5 margin: 0;
6 padding: 0;
7 border: 0;
8 font-weight: inherit;
9 font-style: inherit;
10 font-size: 100%;
11 font-family: inherit;
12 vertical-align: baseline;
13}
14
15body {
16 font-size: 13px;
17 padding: 1em;
18}
19
20h1 {
21 font-size: 26px;
22 margin-bottom: 1em;
23}
24
25h2 {
26 font-size: 24px;
27 margin-bottom: 1em;
28}
29
30h3 {
31 font-size: 20px;
32 margin-bottom: 1em;
33 margin-top: 1em;
34}
35
36pre, code {
37 line-height: 1.5;
38 font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace;
39}
40
41pre {
42 margin-top: 0.5em;
43}
44
45h1, h2, h3, p {
46 font-family: Arial, sans serif;
47}
48
49h1, h2, h3 {
50 border-bottom: solid #CCC 1px;
51}
52
53.toc_element {
54 margin-top: 0.5em;
55}
56
57.firstline {
58 margin-left: 2 em;
59}
60
61.method {
62 margin-top: 1em;
63 border: solid 1px #CCC;
64 padding: 1em;
65 background: #EEE;
66}
67
68.details {
69 font-weight: bold;
70 font-size: 14px;
71}
72
73</style>
74
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>
84<p class="firstline">Gets a reference. Implements [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).</p>
85<p class="toc_element">
86 <code><a href="#search">search(body, x__xgafv=None)</a></code></p>
87<p class="firstline">Searches for references which match the given criteria. Implements [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).</p>
88<h3>Method Details</h3>
89<div class="method">
90 <code class="details" id="get">get(referenceId, x__xgafv=None)</code>
91 <pre>Gets a reference. Implements [GlobalAllianceApi.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).
92
93Args:
94 referenceId: string, The ID of the reference. (required)
95 x__xgafv: string, V1 error format.
96
97Returns:
98 An object of the form:
99
100 { # A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.
101 "name": "A String", # The name of this reference, for example `22`.
102 "sourceUri": "A String", # The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair.
103 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `GCF_000001405.26`.
104 "A String",
105 ],
106 "length": "A String", # The length of this reference's sequence.
107 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.
108 "id": "A String", # The server-generated reference ID, unique across all references.
109 "md5checksum": "A String", # MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is represented in lower case hexadecimal format.
110 }</pre>
111</div>
112
113<div class="method">
114 <code class="details" id="search">search(body, x__xgafv=None)</code>
115 <pre>Searches for references which match the given criteria. Implements [GlobalAllianceApi.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).
116
117Args:
118 body: object, The request body. (required)
119 The object takes the form of:
120
121{
122 "md5checksums": [ # If present, return references for which the `md5checksum` matches. See `Reference.md5checksum` for construction details.
123 "A String",
124 ],
125 "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.
126 "referenceSetId": "A String", # If present, return only references which belong to this reference set.
127 "accessions": [ # If present, return references for which the accession matches this string. 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.
128 "A String",
129 ],
130 "pageSize": 42, # Specifies the maximum number of results to return in a single page.
131 }
132
133 x__xgafv: string, V1 error format.
134
135Returns:
136 An object of the form:
137
138 {
139 "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.
140 "references": [ # The matching references.
141 { # A reference is a canonical assembled DNA sequence, intended to act as a reference coordinate space for other genomic annotations. A single reference might represent the human chromosome 1 or mitochandrial DNA, for instance. A reference belongs to one or more reference sets.
142 "name": "A String", # The name of this reference, for example `22`.
143 "sourceUri": "A String", # The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair.
144 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `GCF_000001405.26`.
145 "A String",
146 ],
147 "length": "A String", # The length of this reference's sequence.
148 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (e.g. 9606->human) if not specified by the containing reference set.
149 "id": "A String", # The server-generated reference ID, unique across all references.
150 "md5checksum": "A String", # MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM). This value is represented in lower case hexadecimal format.
151 },
152 ],
153 }</pre>
154</div>
155
156</body></html>