You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
355 lines
16 KiB
355 lines
16 KiB
<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.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>
|
|
|
|
</body></html> |