1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
<html><body>
<style>
body, h1, h2, h3, div, span, p, pre, a {
margin: 0;
padding: 0;
border: 0;
font-weight: inherit;
font-style: inherit;
font-size: 100%;
font-family: inherit;
vertical-align: baseline;
}
body {
font-size: 13px;
padding: 1em;
}
h1 {
font-size: 26px;
margin-bottom: 1em;
}
h2 {
font-size: 24px;
margin-bottom: 1em;
}
h3 {
font-size: 20px;
margin-bottom: 1em;
margin-top: 1em;
}
pre, code {
line-height: 1.5;
font-family: Monaco, 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', 'Lucida Console', monospace;
}
pre {
margin-top: 0.5em;
}
h1, h2, h3, p {
font-family: Arial, sans serif;
}
h1, h2, h3 {
border-bottom: solid #CCC 1px;
}
.toc_element {
margin-top: 0.5em;
}
.firstline {
margin-left: 2 em;
}
.method {
margin-top: 1em;
border: solid 1px #CCC;
padding: 1em;
background: #EEE;
}
.details {
font-weight: bold;
font-size: 14px;
}
</style>
<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.referencesets.html">referencesets</a></h1>
<h2>Instance Methods</h2>
<p class="toc_element">
<code><a href="#get">get(referenceSetId, x__xgafv=None)</a></code></p>
<p class="firstline">Gets a reference set. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).</p>
<p class="toc_element">
<code><a href="#search">search(body, x__xgafv=None)</a></code></p>
<p class="firstline">Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)</p>
<h3>Method Details</h3>
<div class="method">
<code class="details" id="get">get(referenceSetId, x__xgafv=None)</code>
<pre>Gets a reference set. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.getReferenceSet](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L83).
Args:
referenceSetId: string, The ID of the reference set. (required)
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{ # 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. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"description": "A String", # Free text description of this reference set.
"sourceUri": "A String", # The URI from which the references were obtained.
"referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
"A String",
],
"assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
"sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
"A String",
],
"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.
"id": "A String", # The server-generated reference set ID, unique across all reference sets.
"ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the species which this reference set 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, for example EBV in a human reference genome.
}</pre>
</div>
<div class="method">
<code class="details" id="search">search(body, x__xgafv=None)</code>
<pre>Searches for reference sets which match the given criteria. For the definitions of references and other genomics resources, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) Implements [GlobalAllianceApi.searchReferenceSets](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L71)
Args:
body: object, The request body. (required)
The object takes the form of:
{
"md5checksums": [ # If present, return reference sets for which the md5checksum matches exactly.
"A String",
],
"assemblyId": "A String", # If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).
"accessions": [ # If present, return reference sets for which a prefix of any of sourceAccessions match any of these strings. Accession numbers typically have a main number and a version, for example `NC_000001.11`.
"A String",
],
"pageSize": 42, # The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096.
"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.
}
x__xgafv: string, V1 error format.
Returns:
An object of the form:
{
"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.
"referenceSets": [ # The matching references sets.
{ # 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. For more genomics resource definitions, see [Fundamentals of Google Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
"description": "A String", # Free text description of this reference set.
"sourceUri": "A String", # The URI from which the references were obtained.
"referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
"A String",
],
"assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
"sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
"A String",
],
"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.
"id": "A String", # The server-generated reference set ID, unique across all reference sets.
"ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy (for example, 9606 for human) indicating the species which this reference set 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, for example EBV in a human reference genome.
},
],
}</pre>
</div>
</body></html>
|
