`dynast.preprocessing.consensus`

Module Contents

Functions

`call_consensus_from_reads`(reads: List[pysam.AlignedSegment], header: pysam.AlignmentHeader, quality: int = 27, tags: Optional[Dict[str, Any]] = None) → pysam.AlignedSegment	Call a single consensus alignment given a list of aligned reads.
`call_consensus_from_reads_process`(reads, header, tags, strand=None, quality=27)	Helper function to call `call_consensus_from_reads()` from a subprocess.
`consensus_worker`(args_q, results_q, args, *kwargs)	Multiprocessing worker.
`call_consensus`(bam_path: str, out_path: str, gene_infos: dict, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', umi_tag: Optional[str] = None, barcode_tag: Optional[str] = None, gene_tag: str = 'GX', barcodes: Optional[List[str]] = None, quality: int = 27, add_RS_RI: bool = False, temp_dir: Optional[str] = None, n_threads: int = 8) → str	Call consensus sequences from BAM.

Attributes

`BASES`
`BASE_IDX`

dynast.preprocessing.consensus.BASES = ['A', 'C', 'G', 'T'][source]

dynast.preprocessing.consensus.BASE_IDX[source]

dynast.preprocessing.consensus.call_consensus_from_reads(reads: List[pysam.AlignedSegment], header: pysam.AlignmentHeader, quality: int = 27, tags: Optional[Dict[str, Any]] = None) → pysam.AlignedSegment[source]

Call a single consensus alignment given a list of aligned reads.

Reads must map to the same contig. Results are undefined otherwise. Additionally, consensus bases are called only for positions that match to the reference (i.e. no insertions allowed).

This function only sets the minimal amount of attributes such that the alignment is valid. These include: * read name – SHA256 hash of the provided read names * read sequence and qualities * reference name and ID * reference start * mapping quality (MAPQ) * cigarstring * MD tag * NM tag * Not unmapped, paired, duplicate, qc fail, secondary, nor supplementary

The caller is expected to further populate the alignment with additional tags, flags, and name.

Parameters

reads: List of reads to call a consensus sequence from
header: header to use when creating the new pysam alignment
quality: quality threshold
tags: additional tags to set

Returns

New pysam alignment of the consensus sequence

dynast.preprocessing.consensus.call_consensus_from_reads_process(reads, header, tags, strand=None, quality=27)[source]: Helper function to call call_consensus_from_reads() from a subprocess.

dynast.preprocessing.consensus.consensus_worker(args_q, results_q, *args, **kwargs)[source]: Multiprocessing worker.

dynast.preprocessing.consensus.call_consensus(bam_path: str, out_path: str, gene_infos: dict, strand: typing_extensions.Literal[forward, reverse, unstranded] = 'forward', umi_tag: Optional[str] = None, barcode_tag: Optional[str] = None, gene_tag: str = 'GX', barcodes: Optional[List[str]] = None, quality: int = 27, add_RS_RI: bool = False, temp_dir: Optional[str] = None, n_threads: int = 8) → str[source]

Call consensus sequences from BAM.