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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 860a6378c538d8e2e424c7be150b41ba28120387 / . / 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>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]79<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>
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>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]82<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>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]83<h3>Method Details</h3>
84<div class="method">
85 <code class="details" id="get">get(referenceSetId, x__xgafv=None)</code>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]86 <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).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]87
88Args:
89 referenceSetId: string, The ID of the reference set. (required)
90 x__xgafv: string, V1 error format.
91
92Returns:
93 An object of the form:
94
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]95 { # 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)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]96 "description": "A String", # Free text description of this reference set.
97 "sourceUri": "A String", # The URI from which the references were obtained.
98 "referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
99 "A String",
100 ],
101 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
102 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
103 "A String",
104 ],
105 "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.
106 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]107 "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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]108 }</pre>
109</div>
110
111<div class="method">
112 <code class="details" id="search">search(body, x__xgafv=None)</code>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]113 <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)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]114
115Args:
116 body: object, The request body. (required)
117 The object takes the form of:
118
119{
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]120 "md5checksums": [ # If present, return reference sets for which the md5checksum matches exactly.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]121 "A String",
122 ],
123 "assemblyId": "A String", # If present, return reference sets for which a substring of their `assemblyId` matches this string (case insensitive).
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]124 "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`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]125 "A String",
126 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]127 "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, defaults to 1024. The maximum value is 4096.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]128 "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.
129 }
130
131 x__xgafv: string, V1 error format.
132
133Returns:
134 An object of the form:
135
136 {
137 "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.
138 "referenceSets": [ # The matching references sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]139 { # 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)
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]140 "description": "A String", # Free text description of this reference set.
141 "sourceUri": "A String", # The URI from which the references were obtained.
142 "referenceIds": [ # The IDs of the reference objects that are part of this set. `Reference.md5checksum` must be unique within this set.
143 "A String",
144 ],
145 "assemblyId": "A String", # Public id of this reference set, such as `GRCh37`.
146 "sourceAccessions": [ # All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, for example `NC_000001.11`.
147 "A String",
148 ],
149 "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.
150 "id": "A String", # The server-generated reference set ID, unique across all reference sets.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]151 "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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]152 },
153 ],
154 }</pre>
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