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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / 46a8071fe1d1a112dcc791f61c20fd8306b4061f / . / docs / dyn / genomics_v1beta.readsets.html
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74
75<h1><a href="genomics_v1beta.html">Genomics API</a> . <a href="genomics_v1beta.readsets.html">readsets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
78 <code><a href="genomics_v1beta.readsets.coveragebuckets.html">coveragebuckets()</a></code>
79</p>
80<p class="firstline">Returns the coveragebuckets Resource.</p>
81
82<p class="toc_element">
83 <code><a href="#delete">delete(readsetId)</a></code></p>
84<p class="firstline">Deletes a readset.</p>
85<p class="toc_element">
86 <code><a href="#export">export(body)</a></code></p>
87<p class="firstline">Exports readsets to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, and some custom tags will be converted to strings.</p>
88<p class="toc_element">
89 <code><a href="#get">get(readsetId)</a></code></p>
90<p class="firstline">Gets a readset by ID.</p>
91<p class="toc_element">
92 <code><a href="#import_">import_(body)</a></code></p>
93<p class="firstline">Creates readsets by asynchronously importing the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.</p>
94<p class="toc_element">
95 <code><a href="#patch">patch(readsetId, body)</a></code></p>
96<p class="firstline">Updates a readset. This method supports patch semantics.</p>
97<p class="toc_element">
98 <code><a href="#search">search(body)</a></code></p>
99<p class="firstline">Gets a list of readsets matching the criteria.</p>
100<p class="toc_element">
101 <code><a href="#update">update(readsetId, body)</a></code></p>
102<p class="firstline">Updates a readset.</p>
103<h3>Method Details</h3>
104<div class="method">
105 <code class="details" id="delete">delete(readsetId)</code>
106 <pre>Deletes a readset.
107
108Args:
109 readsetId: string, The ID of the readset to be deleted. The caller must have WRITE permissions to the dataset associated with this readset. (required)
110</pre>
111</div>
112
113<div class="method">
114 <code class="details" id="export">export(body)</code>
115 <pre>Exports readsets to a BAM file in Google Cloud Storage. Note that currently there may be some differences between exported BAM files and the original BAM file at the time of import. In particular, comments in the input file header will not be preserved, and some custom tags will be converted to strings.
116
117Args:
118 body: object, The request body. (required)
119 The object takes the form of:
120
121{ # The readset export request.
122 "readsetIds": [ # The IDs of the readsets to export.
123 "A String",
124 ],
125 "exportUri": "A String", # A Google Cloud Storage URI where the exported BAM file will be created. The currently authenticated user must have write access to the new file location. An error will be returned if the URI already contains data.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]126 "referenceNames": [ # The reference names to export. If this is not specified, all reference sequences, including unmapped reads, are exported. Use * to export only unmapped reads.
127 "A String",
128 ],
129 "projectId": "A String", # The Google Developers Console project number that owns this export.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]130 }
131
132
133Returns:
134 An object of the form:
135
136 { # The readset export response.
137 "jobId": "A String", # A job ID that can be used to get status information.
138 }</pre>
139</div>
140
141<div class="method">
142 <code class="details" id="get">get(readsetId)</code>
143 <pre>Gets a readset by ID.
144
145Args:
146 readsetId: string, The ID of the readset. (required)
147
148Returns:
149 An object of the form:
150
151 { # A Readset is a collection of Reads.
152 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
153 { # The header section of the BAM/SAM file.
154 "programs": [ # (@PG) Programs.
155 {
156 "commandLine": "A String", # (CL) Command line.
157 "prevProgramId": "A String", # (PP) Previous program ID.
158 "id": "A String", # (ID) Program record identifier.
159 "version": "A String", # (VN) Program version.
160 "name": "A String", # (PN) Program name.
161 },
162 ],
163 "readGroups": [ # (@RG) Read group.
164 {
165 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
166 "predictedInsertSize": 42, # (PI) Predicted median insert size.
167 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
168 "description": "A String", # (DS) Description.
169 "processingProgram": "A String", # (PG) Programs used for processing the read group.
170 "platformUnit": "A String", # (PU) Platform unit.
171 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
172 "library": "A String", # (LS) Library.
173 "sample": "A String", # (SM) Sample.
174 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
175 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
176 "id": "A String", # (ID) Read group identifier.
177 },
178 ],
179 "filename": "A String", # The name of the file from which this data was imported.
180 "headers": [ # (@HD) The header line.
181 {
182 "sortingOrder": "A String", # (SO) Sorting order of alignments.
183 "version": "A String", # (VN) BAM format version.
184 },
185 ],
186 "comments": [ # (@CO) One-line text comments.
187 "A String",
188 ],
189 "refSequences": [ # (@SQ) Reference sequence dictionary.
190 {
191 "name": "A String", # (SN) Reference sequence name.
192 "assemblyId": "A String", # (AS) Genome assembly identifier.
193 "uri": "A String", # (UR) URI of the sequence.
194 "length": 42, # (LN) Reference sequence length.
195 "species": "A String", # (SP) Species.
196 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
197 },
198 ],
199 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
200 },
201 ],
202 "id": "A String", # The Google generated ID of the readset, immutable.
203 "datasetId": "A String", # The ID of the dataset this readset belongs to.
204 "name": "A String", # The readset name, typically this is the sample name.
205 }</pre>
206</div>
207
208<div class="method">
209 <code class="details" id="import_">import_(body)</code>
210 <pre>Creates readsets by asynchronously importing the provided information. Note that currently comments in the input file header are not imported and some custom tags will be converted to strings, rather than preserving tag types. The caller must have WRITE permissions to the dataset.
211
212Args:
213 body: object, The request body. (required)
214 The object takes the form of:
215
216{ # The readset import request.
217 "sourceUris": [ # A list of URIs pointing at BAM files in Google Cloud Storage.
218 "A String",
219 ],
220 "datasetId": "A String", # Required. The ID of the dataset these readsets will belong to. The caller must have WRITE permissions to this dataset.
221 }
222
223
224Returns:
225 An object of the form:
226
227 { # The readset import response.
228 "jobId": "A String", # A job ID that can be used to get status information.
229 }</pre>
230</div>
231
232<div class="method">
233 <code class="details" id="patch">patch(readsetId, body)</code>
234 <pre>Updates a readset. This method supports patch semantics.
235
236Args:
237 readsetId: string, The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this readset. (required)
238 body: object, The request body. (required)
239 The object takes the form of:
240
241{ # A Readset is a collection of Reads.
242 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
243 { # The header section of the BAM/SAM file.
244 "programs": [ # (@PG) Programs.
245 {
246 "commandLine": "A String", # (CL) Command line.
247 "prevProgramId": "A String", # (PP) Previous program ID.
248 "id": "A String", # (ID) Program record identifier.
249 "version": "A String", # (VN) Program version.
250 "name": "A String", # (PN) Program name.
251 },
252 ],
253 "readGroups": [ # (@RG) Read group.
254 {
255 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
256 "predictedInsertSize": 42, # (PI) Predicted median insert size.
257 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
258 "description": "A String", # (DS) Description.
259 "processingProgram": "A String", # (PG) Programs used for processing the read group.
260 "platformUnit": "A String", # (PU) Platform unit.
261 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
262 "library": "A String", # (LS) Library.
263 "sample": "A String", # (SM) Sample.
264 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
265 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
266 "id": "A String", # (ID) Read group identifier.
267 },
268 ],
269 "filename": "A String", # The name of the file from which this data was imported.
270 "headers": [ # (@HD) The header line.
271 {
272 "sortingOrder": "A String", # (SO) Sorting order of alignments.
273 "version": "A String", # (VN) BAM format version.
274 },
275 ],
276 "comments": [ # (@CO) One-line text comments.
277 "A String",
278 ],
279 "refSequences": [ # (@SQ) Reference sequence dictionary.
280 {
281 "name": "A String", # (SN) Reference sequence name.
282 "assemblyId": "A String", # (AS) Genome assembly identifier.
283 "uri": "A String", # (UR) URI of the sequence.
284 "length": 42, # (LN) Reference sequence length.
285 "species": "A String", # (SP) Species.
286 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
287 },
288 ],
289 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
290 },
291 ],
292 "id": "A String", # The Google generated ID of the readset, immutable.
293 "datasetId": "A String", # The ID of the dataset this readset belongs to.
294 "name": "A String", # The readset name, typically this is the sample name.
295}
296
297
298Returns:
299 An object of the form:
300
301 { # A Readset is a collection of Reads.
302 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
303 { # The header section of the BAM/SAM file.
304 "programs": [ # (@PG) Programs.
305 {
306 "commandLine": "A String", # (CL) Command line.
307 "prevProgramId": "A String", # (PP) Previous program ID.
308 "id": "A String", # (ID) Program record identifier.
309 "version": "A String", # (VN) Program version.
310 "name": "A String", # (PN) Program name.
311 },
312 ],
313 "readGroups": [ # (@RG) Read group.
314 {
315 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
316 "predictedInsertSize": 42, # (PI) Predicted median insert size.
317 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
318 "description": "A String", # (DS) Description.
319 "processingProgram": "A String", # (PG) Programs used for processing the read group.
320 "platformUnit": "A String", # (PU) Platform unit.
321 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
322 "library": "A String", # (LS) Library.
323 "sample": "A String", # (SM) Sample.
324 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
325 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
326 "id": "A String", # (ID) Read group identifier.
327 },
328 ],
329 "filename": "A String", # The name of the file from which this data was imported.
330 "headers": [ # (@HD) The header line.
331 {
332 "sortingOrder": "A String", # (SO) Sorting order of alignments.
333 "version": "A String", # (VN) BAM format version.
334 },
335 ],
336 "comments": [ # (@CO) One-line text comments.
337 "A String",
338 ],
339 "refSequences": [ # (@SQ) Reference sequence dictionary.
340 {
341 "name": "A String", # (SN) Reference sequence name.
342 "assemblyId": "A String", # (AS) Genome assembly identifier.
343 "uri": "A String", # (UR) URI of the sequence.
344 "length": 42, # (LN) Reference sequence length.
345 "species": "A String", # (SP) Species.
346 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
347 },
348 ],
349 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
350 },
351 ],
352 "id": "A String", # The Google generated ID of the readset, immutable.
353 "datasetId": "A String", # The ID of the dataset this readset belongs to.
354 "name": "A String", # The readset name, typically this is the sample name.
355 }</pre>
356</div>
357
358<div class="method">
359 <code class="details" id="search">search(body)</code>
360 <pre>Gets a list of readsets matching the criteria.
361
362Args:
363 body: object, The request body. (required)
364 The object takes the form of:
365
366{ # The readset search request.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]367 "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.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]368 "datasetIds": [ # Restricts this query to readsets within the given datasets. At least one ID must be provided.
369 "A String",
370 ],
371 "name": "A String", # Only return readsets for which a substring of the name matches this string.
Craig Citro0e5b9bf2014-10-15 10:26:14 -0700[diff] [blame]372 "maxResults": "A String", # Specifies number of results to return in a single page. If unspecified, it will default to 128. The maximum value is 1024.
Craig Citro065b5302014-08-14 00:47:23 -0700[diff] [blame]373 }
374
375
376Returns:
377 An object of the form:
378
379 { # The readset search response.
380 "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.
381 "readsets": [ # The list of matching Readsets.
382 { # A Readset is a collection of Reads.
383 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
384 { # The header section of the BAM/SAM file.
385 "programs": [ # (@PG) Programs.
386 {
387 "commandLine": "A String", # (CL) Command line.
388 "prevProgramId": "A String", # (PP) Previous program ID.
389 "id": "A String", # (ID) Program record identifier.
390 "version": "A String", # (VN) Program version.
391 "name": "A String", # (PN) Program name.
392 },
393 ],
394 "readGroups": [ # (@RG) Read group.
395 {
396 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
397 "predictedInsertSize": 42, # (PI) Predicted median insert size.
398 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
399 "description": "A String", # (DS) Description.
400 "processingProgram": "A String", # (PG) Programs used for processing the read group.
401 "platformUnit": "A String", # (PU) Platform unit.
402 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
403 "library": "A String", # (LS) Library.
404 "sample": "A String", # (SM) Sample.
405 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
406 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
407 "id": "A String", # (ID) Read group identifier.
408 },
409 ],
410 "filename": "A String", # The name of the file from which this data was imported.
411 "headers": [ # (@HD) The header line.
412 {
413 "sortingOrder": "A String", # (SO) Sorting order of alignments.
414 "version": "A String", # (VN) BAM format version.
415 },
416 ],
417 "comments": [ # (@CO) One-line text comments.
418 "A String",
419 ],
420 "refSequences": [ # (@SQ) Reference sequence dictionary.
421 {
422 "name": "A String", # (SN) Reference sequence name.
423 "assemblyId": "A String", # (AS) Genome assembly identifier.
424 "uri": "A String", # (UR) URI of the sequence.
425 "length": 42, # (LN) Reference sequence length.
426 "species": "A String", # (SP) Species.
427 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
428 },
429 ],
430 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
431 },
432 ],
433 "id": "A String", # The Google generated ID of the readset, immutable.
434 "datasetId": "A String", # The ID of the dataset this readset belongs to.
435 "name": "A String", # The readset name, typically this is the sample name.
436 },
437 ],
438 }</pre>
439</div>
440
441<div class="method">
442 <code class="details" id="update">update(readsetId, body)</code>
443 <pre>Updates a readset.
444
445Args:
446 readsetId: string, The ID of the readset to be updated. The caller must have WRITE permissions to the dataset associated with this readset. (required)
447 body: object, The request body. (required)
448 The object takes the form of:
449
450{ # A Readset is a collection of Reads.
451 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
452 { # The header section of the BAM/SAM file.
453 "programs": [ # (@PG) Programs.
454 {
455 "commandLine": "A String", # (CL) Command line.
456 "prevProgramId": "A String", # (PP) Previous program ID.
457 "id": "A String", # (ID) Program record identifier.
458 "version": "A String", # (VN) Program version.
459 "name": "A String", # (PN) Program name.
460 },
461 ],
462 "readGroups": [ # (@RG) Read group.
463 {
464 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
465 "predictedInsertSize": 42, # (PI) Predicted median insert size.
466 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
467 "description": "A String", # (DS) Description.
468 "processingProgram": "A String", # (PG) Programs used for processing the read group.
469 "platformUnit": "A String", # (PU) Platform unit.
470 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
471 "library": "A String", # (LS) Library.
472 "sample": "A String", # (SM) Sample.
473 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
474 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
475 "id": "A String", # (ID) Read group identifier.
476 },
477 ],
478 "filename": "A String", # The name of the file from which this data was imported.
479 "headers": [ # (@HD) The header line.
480 {
481 "sortingOrder": "A String", # (SO) Sorting order of alignments.
482 "version": "A String", # (VN) BAM format version.
483 },
484 ],
485 "comments": [ # (@CO) One-line text comments.
486 "A String",
487 ],
488 "refSequences": [ # (@SQ) Reference sequence dictionary.
489 {
490 "name": "A String", # (SN) Reference sequence name.
491 "assemblyId": "A String", # (AS) Genome assembly identifier.
492 "uri": "A String", # (UR) URI of the sequence.
493 "length": 42, # (LN) Reference sequence length.
494 "species": "A String", # (SP) Species.
495 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
496 },
497 ],
498 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
499 },
500 ],
501 "id": "A String", # The Google generated ID of the readset, immutable.
502 "datasetId": "A String", # The ID of the dataset this readset belongs to.
503 "name": "A String", # The readset name, typically this is the sample name.
504}
505
506
507Returns:
508 An object of the form:
509
510 { # A Readset is a collection of Reads.
511 "fileData": [ # File information from the original BAM import. See the BAM format specification for additional information on each field.
512 { # The header section of the BAM/SAM file.
513 "programs": [ # (@PG) Programs.
514 {
515 "commandLine": "A String", # (CL) Command line.
516 "prevProgramId": "A String", # (PP) Previous program ID.
517 "id": "A String", # (ID) Program record identifier.
518 "version": "A String", # (VN) Program version.
519 "name": "A String", # (PN) Program name.
520 },
521 ],
522 "readGroups": [ # (@RG) Read group.
523 {
524 "sequencingTechnology": "A String", # (PL) Platform/technology used to produce the reads.
525 "predictedInsertSize": 42, # (PI) Predicted median insert size.
526 "sequencingCenterName": "A String", # (CN) Name of sequencing center producing the read.
527 "description": "A String", # (DS) Description.
528 "processingProgram": "A String", # (PG) Programs used for processing the read group.
529 "platformUnit": "A String", # (PU) Platform unit.
530 "flowOrder": "A String", # (FO) Flow order. The array of nucleotide bases that correspond to the nucleotides used for each flow of each read.
531 "library": "A String", # (LS) Library.
532 "sample": "A String", # (SM) Sample.
533 "date": "A String", # (DT) Date the run was produced (ISO8601 date or date/time).
534 "keySequence": "A String", # (KS) The array of nucleotide bases that correspond to the key sequence of each read.
535 "id": "A String", # (ID) Read group identifier.
536 },
537 ],
538 "filename": "A String", # The name of the file from which this data was imported.
539 "headers": [ # (@HD) The header line.
540 {
541 "sortingOrder": "A String", # (SO) Sorting order of alignments.
542 "version": "A String", # (VN) BAM format version.
543 },
544 ],
545 "comments": [ # (@CO) One-line text comments.
546 "A String",
547 ],
548 "refSequences": [ # (@SQ) Reference sequence dictionary.
549 {
550 "name": "A String", # (SN) Reference sequence name.
551 "assemblyId": "A String", # (AS) Genome assembly identifier.
552 "uri": "A String", # (UR) URI of the sequence.
553 "length": 42, # (LN) Reference sequence length.
554 "species": "A String", # (SP) Species.
555 "md5Checksum": "A String", # (M5) MD5 checksum of the sequence in the uppercase, excluding spaces but including pads as *.
556 },
557 ],
558 "fileUri": "A String", # [Deprecated] This field is deprecated and will no longer be populated. Please use filename instead.
559 },
560 ],
561 "id": "A String", # The Google generated ID of the readset, immutable.
562 "datasetId": "A String", # The ID of the dataset this readset belongs to.
563 "name": "A String", # The readset name, typically this is the sample name.
564 }</pre>
565</div>
566
567</body></html>