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| <h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.reads.html">reads</a></h1> |
| <h2>Instance Methods</h2> |
| <p class="toc_element"> |
| <code><a href="#search">search(body, x__xgafv=None)</a></code></p> |
| <p class="firstline">Gets a list of reads for one or more read group sets.</p> |
| <p class="toc_element"> |
| <code><a href="#search_next">search_next(previous_request, previous_response)</a></code></p> |
| <p class="firstline">Retrieves the next page of results.</p> |
| <h3>Method Details</h3> |
| <div class="method"> |
| <code class="details" id="search">search(body, x__xgafv=None)</code> |
| <pre>Gets a list of reads for one or more read group sets. |
| |
| For the definitions of read group sets and other genomics resources, see |
| [Fundamentals of Google |
| Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| |
| Reads search operates over a genomic coordinate space of reference sequence |
| & position defined over the reference sequences to which the requested |
| read group sets are aligned. |
| |
| If a target positional range is specified, search returns all reads whose |
| alignment to the reference genome overlap the range. A query which |
| specifies only read group set IDs yields all reads in those read group |
| sets, including unmapped reads. |
| |
| All reads returned (including reads on subsequent pages) are ordered by |
| genomic coordinate (by reference sequence, then position). Reads with |
| equivalent genomic coordinates are returned in an unspecified order. This |
| order is consistent, such that two queries for the same content (regardless |
| of page size) yield reads in the same order across their respective streams |
| of paginated responses. |
| |
| Implements |
| [GlobalAllianceApi.searchReads](https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/readmethods.avdl#L85). |
| |
| Args: |
| body: object, The request body. (required) |
| The object takes the form of: |
| |
| { # The read search request. |
| "end": "A String", # The end position of the range on the reference, 0-based exclusive. If |
| # specified, `referenceName` must also be specified. |
| "readGroupIds": [ # The IDs of the read groups within which to search for reads. All specified |
| # read groups must belong to the same read group sets. Must specify one of |
| # `readGroupSetIds` or `readGroupIds`. |
| "A String", |
| ], |
| "pageSize": 42, # The maximum number of results to return in a single page. If unspecified, |
| # defaults to 256. The maximum value is 2048. |
| "start": "A String", # The start position of the range on the reference, 0-based inclusive. If |
| # specified, `referenceName` must also be specified. |
| "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. |
| "referenceName": "A String", # The reference sequence name, for example `chr1`, `1`, or `chrX`. If set to |
| # `*`, only unmapped reads are returned. If unspecified, all reads (mapped |
| # and unmapped) are returned. |
| "readGroupSetIds": [ # The IDs of the read groups sets within which to search for reads. All |
| # specified read group sets must be aligned against a common set of reference |
| # sequences; this defines the genomic coordinates for the query. Must specify |
| # one of `readGroupSetIds` or `readGroupIds`. |
| "A String", |
| ], |
| } |
| |
| x__xgafv: string, V1 error format. |
| Allowed values |
| 1 - v1 error format |
| 2 - v2 error format |
| |
| Returns: |
| An object of the form: |
| |
| { # The read search response. |
| "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. |
| "alignments": [ # The list of matching alignments sorted by mapped genomic coordinate, |
| # if any, ascending in position within the same reference. Unmapped reads, |
| # which have no position, are returned contiguously and are sorted in |
| # ascending lexicographic order by fragment name. |
| { # A read alignment describes a linear alignment of a string of DNA to a |
| # reference sequence, in addition to metadata |
| # about the fragment (the molecule of DNA sequenced) and the read (the bases |
| # which were read by the sequencer). A read is equivalent to a line in a SAM |
| # file. A read belongs to exactly one read group and exactly one |
| # read group set. |
| # |
| # For more genomics resource definitions, see [Fundamentals of Google |
| # Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics) |
| # |
| # ### Reverse-stranded reads |
| # |
| # Mapped reads (reads having a non-null `alignment`) can be aligned to either |
| # the forward or the reverse strand of their associated reference. Strandedness |
| # of a mapped read is encoded by `alignment.position.reverseStrand`. |
| # |
| # If we consider the reference to be a forward-stranded coordinate space of |
| # `[0, reference.length)` with `0` as the left-most position and |
| # `reference.length` as the right-most position, reads are always aligned left |
| # to right. That is, `alignment.position.position` always refers to the |
| # left-most reference coordinate and `alignment.cigar` describes the alignment |
| # of this read to the reference from left to right. All per-base fields such as |
| # `alignedSequence` and `alignedQuality` share this same left-to-right |
| # orientation; this is true of reads which are aligned to either strand. For |
| # reverse-stranded reads, this means that `alignedSequence` is the reverse |
| # complement of the bases that were originally reported by the sequencing |
| # machine. |
| # |
| # ### Generating a reference-aligned sequence string |
| # |
| # When interacting with mapped reads, it's often useful to produce a string |
| # representing the local alignment of the read to reference. The following |
| # pseudocode demonstrates one way of doing this: |
| # |
| # out = "" |
| # offset = 0 |
| # for c in read.alignment.cigar { |
| # switch c.operation { |
| # case "ALIGNMENT_MATCH", "SEQUENCE_MATCH", "SEQUENCE_MISMATCH": |
| # out += read.alignedSequence[offset:offset+c.operationLength] |
| # offset += c.operationLength |
| # break |
| # case "CLIP_SOFT", "INSERT": |
| # offset += c.operationLength |
| # break |
| # case "PAD": |
| # out += repeat("*", c.operationLength) |
| # break |
| # case "DELETE": |
| # out += repeat("-", c.operationLength) |
| # break |
| # case "SKIP": |
| # out += repeat(" ", c.operationLength) |
| # break |
| # case "CLIP_HARD": |
| # break |
| # } |
| # } |
| # return out |
| # |
| # ### Converting to SAM's CIGAR string |
| # |
| # The following pseudocode generates a SAM CIGAR string from the |
| # `cigar` field. Note that this is a lossy conversion |
| # (`cigar.referenceSequence` is lost). |
| # |
| # cigarMap = { |
| # "ALIGNMENT_MATCH": "M", |
| # "INSERT": "I", |
| # "DELETE": "D", |
| # "SKIP": "N", |
| # "CLIP_SOFT": "S", |
| # "CLIP_HARD": "H", |
| # "PAD": "P", |
| # "SEQUENCE_MATCH": "=", |
| # "SEQUENCE_MISMATCH": "X", |
| # } |
| # cigarStr = "" |
| # for c in read.alignment.cigar { |
| # cigarStr += c.operationLength + cigarMap[c.operation] |
| # } |
| # return cigarStr |
| "info": { # A map of additional read alignment information. This must be of the form |
| # map<string, string[]> (string key mapping to a list of string values). |
| "a_key": [ |
| "", |
| ], |
| }, |
| "duplicateFragment": True or False, # The fragment is a PCR or optical duplicate (SAM flag 0x400). |
| "readGroupSetId": "A String", # The ID of the read group set this read belongs to. A read belongs to |
| # exactly one read group set. |
| "alignedQuality": [ # The quality of the read sequence contained in this alignment record |
| # (equivalent to QUAL in SAM). |
| # `alignedSequence` and `alignedQuality` may be shorter than the full read |
| # sequence and quality. This will occur if the alignment is part of a |
| # chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR |
| # for this read will begin/end with a hard clip operator that will indicate |
| # the length of the excised sequence. |
| 42, |
| ], |
| "failedVendorQualityChecks": True or False, # Whether this read did not pass filters, such as platform or vendor quality |
| # controls (SAM flag 0x200). |
| "fragmentName": "A String", # The fragment name. Equivalent to QNAME (query template name) in SAM. |
| "id": "A String", # The server-generated read ID, unique across all reads. This is different |
| # from the `fragmentName`. |
| "properPlacement": True or False, # The orientation and the distance between reads from the fragment are |
| # consistent with the sequencing protocol (SAM flag 0x2). |
| "readGroupId": "A String", # The ID of the read group this read belongs to. A read belongs to exactly |
| # one read group. This is a server-generated ID which is distinct from SAM's |
| # RG tag (for that value, see |
| # ReadGroup.name). |
| "supplementaryAlignment": True or False, # Whether this alignment is supplementary. Equivalent to SAM flag 0x800. |
| # Supplementary alignments are used in the representation of a chimeric |
| # alignment. In a chimeric alignment, a read is split into multiple |
| # linear alignments that map to different reference contigs. The first |
| # linear alignment in the read will be designated as the representative |
| # alignment; the remaining linear alignments will be designated as |
| # supplementary alignments. These alignments may have different mapping |
| # quality scores. In each linear alignment in a chimeric alignment, the read |
| # will be hard clipped. The `alignedSequence` and |
| # `alignedQuality` fields in the alignment record will only |
| # represent the bases for its respective linear alignment. |
| "numberReads": 42, # The number of reads in the fragment (extension to SAM flag 0x1). |
| "fragmentLength": 42, # The observed length of the fragment, equivalent to TLEN in SAM. |
| "secondaryAlignment": True or False, # Whether this alignment is secondary. Equivalent to SAM flag 0x100. |
| # A secondary alignment represents an alternative to the primary alignment |
| # for this read. Aligners may return secondary alignments if a read can map |
| # ambiguously to multiple coordinates in the genome. By convention, each read |
| # has one and only one alignment where both `secondaryAlignment` |
| # and `supplementaryAlignment` are false. |
| "alignedSequence": "A String", # The bases of the read sequence contained in this alignment record, |
| # **without CIGAR operations applied** (equivalent to SEQ in SAM). |
| # `alignedSequence` and `alignedQuality` may be |
| # shorter than the full read sequence and quality. This will occur if the |
| # alignment is part of a chimeric alignment, or if the read was trimmed. When |
| # this occurs, the CIGAR for this read will begin/end with a hard clip |
| # operator that will indicate the length of the excised sequence. |
| "readNumber": 42, # The read number in sequencing. 0-based and less than numberReads. This |
| # field replaces SAM flag 0x40 and 0x80. |
| "alignment": { # A linear alignment can be represented by one CIGAR string. Describes the # The linear alignment for this alignment record. This field is null for |
| # unmapped reads. |
| # mapped position and local alignment of the read to the reference. |
| "position": { # An abstraction for referring to a genomic position, in relation to some # The position of this alignment. |
| # already known reference. For now, represents a genomic position as a |
| # reference name, a base number on that reference (0-based), and a |
| # determination of forward or reverse strand. |
| "position": "A String", # The 0-based offset from the start of the forward strand for that reference. |
| "reverseStrand": True or False, # Whether this position is on the reverse strand, as opposed to the forward |
| # strand. |
| "referenceName": "A String", # The name of the reference in whatever reference set is being used. |
| }, |
| "cigar": [ # Represents the local alignment of this sequence (alignment matches, indels, |
| # etc) against the reference. |
| { # A single CIGAR operation. |
| "referenceSequence": "A String", # `referenceSequence` is only used at mismatches |
| # (`SEQUENCE_MISMATCH`) and deletions (`DELETE`). |
| # Filling this field replaces SAM's MD tag. If the relevant information is |
| # not available, this field is unset. |
| "operation": "A String", |
| "operationLength": "A String", # The number of genomic bases that the operation runs for. Required. |
| }, |
| ], |
| "mappingQuality": 42, # The mapping quality of this alignment. Represents how likely |
| # the read maps to this position as opposed to other locations. |
| # |
| # Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to |
| # the nearest integer. |
| }, |
| "nextMatePosition": { # An abstraction for referring to a genomic position, in relation to some # The mapping of the primary alignment of the |
| # `(readNumber+1)%numberReads` read in the fragment. It replaces |
| # mate position and mate strand in SAM. |
| # already known reference. For now, represents a genomic position as a |
| # reference name, a base number on that reference (0-based), and a |
| # determination of forward or reverse strand. |
| "position": "A String", # The 0-based offset from the start of the forward strand for that reference. |
| "reverseStrand": True or False, # Whether this position is on the reverse strand, as opposed to the forward |
| # strand. |
| "referenceName": "A String", # The name of the reference in whatever reference set is being used. |
| }, |
| }, |
| ], |
| }</pre> |
| </div> |
| |
| <div class="method"> |
| <code class="details" id="search_next">search_next(previous_request, previous_response)</code> |
| <pre>Retrieves the next page of results. |
| |
| Args: |
| previous_request: The request for the previous page. (required) |
| previous_response: The response from the request for the previous page. (required) |
| |
| Returns: |
| A request object that you can call 'execute()' on to request the next |
| page. Returns None if there are no more items in the collection. |
| </pre> |
| </div> |
| |
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