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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 860a6378c538d8e2e424c7be150b41ba28120387 / . / 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>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]84<p class="firstline">Gets a reference. 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.getReference](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L158).</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>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]87<p class="firstline">Searches for references 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.searchReferences](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/referencemethods.avdl#L146).</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]88<h3>Method Details</h3>
89<div class="method">
90 <code class="details" id="get">get(referenceId, x__xgafv=None)</code>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]91 <pre>Gets a reference. 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.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]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
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]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. 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]101 "name": "A String", # The name of this reference, for example `22`.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]102 "sourceUri": "A String", # The URI from which the sequence was obtained. Typically specifies a FASTA format file.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]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.
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.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]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>
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]115 <pre>Searches for references 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.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]116
117Args:
118 body: object, The request body. (required)
119 The object takes the form of:
120
121{
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]122 "md5checksums": [ # If present, return references for which the md5checksum matches exactly.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]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.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]127 "accessions": [ # If present, return references 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 `GCF_000001405.26`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]128 "A String",
129 ],
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]130 "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]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.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]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. 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]142 "name": "A String", # The name of this reference, for example `22`.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]143 "sourceUri": "A String", # The URI from which the sequence was obtained. Typically specifies a FASTA format file.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]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.
Jon Wayne Parrott36e41bc2016-02-19 16:02:29 -0800[diff] [blame]148 "ncbiTaxonId": 42, # ID from http://www.ncbi.nlm.nih.gov/taxonomy. For example, 9606 for human.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]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>
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