dynast.preprocessing.consensus
Module Contents
Functions
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Call a single consensus alignment given a list of aligned reads. |
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Attributes
- dynast.preprocessing.consensus.BASES = ['A', 'C', 'G', 'T']
- dynast.preprocessing.consensus.BASE_IDX
- dynast.preprocessing.consensus.call_consensus_from_reads(reads, header, quality=27, tags=None)
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) – List of reads to call a consensus sequence from
header (pysam.AlignmentHeader) – header to use when creating the new pysam alignment
quality (int, optional) – quality threshold, defaults to 27
tags (dict, optional) – additional tags to set, defaults to None
- Returns
(New pysam alignment of the consensus sequence)
- Return type
pysam.AlignedSegment
- dynast.preprocessing.consensus.call_consensus_from_reads_process(reads, header, tags, strand=None, quality=27)
- dynast.preprocessing.consensus.consensus_worker(args_q, results_q, *args, **kwargs)
- dynast.preprocessing.consensus.call_consensus(bam_path, out_path, gene_infos, strand='forward', umi_tag=None, barcode_tag=None, gene_tag='GX', barcodes=None, quality=27, add_RS_RI=False, temp_dir=None, n_threads=8)