pbcore.io.align package

Submodules

pbcore.io.align.BamAlignment module

class pbcore.io.align.BamAlignment.BamAlignment(bamReader, pysamAlignedRead, rowNumber=None)

Bases: AlignmentRecordMixin

DeletionQV(aligned=True, orientation='native')
DeletionTag(aligned=True, orientation='native')
property HoleNumber
IPD(aligned=True, orientation='native')
InsertionQV(aligned=True, orientation='native')
property MapQV
MergeQV(aligned=True, orientation='native')
PulseWidth(aligned=True, orientation='native')
SubstitutionQV(aligned=True, orientation='native')
property barcode
property barcodeName
baseFeature(featureName, aligned=True, orientation='native')

Retrieve the base feature as indicated. - aligned : whether gaps should be inserted to reflect the alignment - orientation: “native” or “genomic”

Note that this function assumes the the feature is stored in native orientation in the file, so it is not appropriate to use this method to fetch the read or the qual, which are oriented genomically in the file.

clippedTo(refStart, refEnd)

Return a new BamAlignment that refers to a subalignment of this alignment, as induced by clipping to reference coordinates refStart to refEnd.

Warning

This function takes time linear in the length of the alignment.

property hasPbi
property hqRegionSnr

Return the per-channel SNR averaged over the HQ region.

Note

This capability was not available in cmp.h5 files, so use of this property can result in code that won’t work on legacy data.

property identity
property isCCS
property isForwardStrand
property isMapped
property isReverseStrand
property isTranscript
property isUnmapped
property mapQV
property movieName
property numPasses
property qEnd
property qId
property qLen
property qName
property qStart
property queryEnd
property queryName
property queryStart
read(aligned=True, orientation='native')
property readGroupInfo
readPositions(aligned=True, orientation='native')

Returns an array of read positions.

If aligned is True, the array has the same length as the alignment and readPositions[i] = read position of the i’th column in the oriented alignment.

If aligned is False, the array has the same length as the mapped reference segment and readPositions[i] = read position of the i’th base in the oriented reference segment.

property readScore

Return the “read score”, a de novo prediction (not using any alignment) of the accuracy (between 0 and 1) of this read.

Note

This capability was not available in cmp.h5 files, so use of this property can result in code that won’t work on legacy data.

property readType
property reader
reference(aligned=True, orientation='native')
property referenceId
property referenceInfo
property referenceName
referencePositions(aligned=True, orientation='native')

Returns an array of reference positions.

If aligned is True, the array has the same length as the alignment and referencePositions[i] = reference position of the i’th column in the oriented alignment.

If aligned is False, the array has the same length as the read and referencePositions[i] = reference position of the i’th base in the oriented read.

property scrapType
property sequencingChemistry
property tId
transcript(orientation='native', style='gusfield')

A text representation of the alignment moves (see Gusfield). This can be useful in pretty-printing an alignment.

unrolledCigar(orientation='native')

Run-length decode the CIGAR encoding, and orient. Clipping ops are removed.

property zScore

pbcore.io.align.BamIO module

class pbcore.io.align.BamIO.BamReader(fname, referenceFastaFname=None)

Bases: _BamReaderBase, AlignmentReaderMixin

Reader for a BAM with a bam.bai (SAMtools) index, but not a bam.pbi (PacBio) index. Supports basic BAM operations.

property index
readsInRange(winId, winStart, winEnd, justIndices=False)
class pbcore.io.align.BamIO.IndexedBamReader(fname, referenceFastaFname=None, sharedIndex=None)

Bases: _BamReaderBase, IndexedAlignmentReaderMixin

A IndexedBamReader is a BAM reader class that uses the bam.pbi (PacBio BAM index) file to enable random access by “row number” and to provide access to precomputed semantic information about the BAM records

atRowNumber(rn)
property identity

Fractional alignment sequence identities as numpy array.

property index
readsInRange(winId, winStart, winEnd, justIndices=False)

pbcore.io.align.BlasrIO module

class pbcore.io.align.BlasrIO.M4Reader(f)

Bases: ReaderBase

Reader for -m 4 formatted alignment summary information from BLASR

class pbcore.io.align.BlasrIO.M4Record

Bases: object

Record for alignment summary record output from BLASR -m 4 option

classmethod fromString(s)
class pbcore.io.align.BlasrIO.M5Reader(f)

Bases: ReaderBase

Reader for -m 5 formatted alignment summary information from BLASR

class pbcore.io.align.BlasrIO.M5Record

Bases: object

Record for alignment summary record output from BLASR -m 5 option

classmethod fromString(s)

pbcore.io.align.PacBioBamIndex module

class pbcore.io.align.PacBioBamIndex.PacBioBamIndex(pbiFilename, chunk_start=None, chunk_size=None, to_virtual_offset=None)

Bases: PbIndexBase

The PacBio BAM index is a companion file allowing modest semantic queries on PacBio BAM files without iterating over the entire file. By convention, the PacBio BAM index has extension “bam.pbi”.

property columnNames
property hasBarcodeInfo
property hasCoordinateSortedInfo
property hasMappingInfo
property identity
property isChunk
rangeQuery(winId, winStart, winEnd)
property version

Module contents