precellar.Assay

class precellar.Assay(path)

A Assay object.

A Assay object is used to annotate sequencing libraries produced by genomics assays. Genomic library structure depends on both the assay and sequencer (and kits) used to generate and bind the assay-specific construct to the sequencing adapters to generate a sequencing library. Assay is specific to both a genomics assay and sequencer and provides a standardized format for describing the structure of sequencing libraries and the resulting sequencing reads. See pachterlab/seqspec for more details.

Parameters:

path (Path | str) – The local path or url to the seqspec file.

See also

align

Attributes

description	Description of the Assay object.
doi	The doi of the Assay object.
filename	Filename of the seqspec file.
id	The assay_id of the Assay object.
name	Name of the Assay object.
sequence_kit	The sequence kit of the Assay object.
sequence_protocol	The sequence protocol of the Assay object.

Methods

add_illumina_reads(modality, *[, length, ...])	Add default Illumina reads to the Assay object.
delete_read(read_id)	Delete a read from the Assay object.
modalities()	Return all modality names in the Assay object.
save(out)	Save the Assay object to a yaml file.
to_yaml()	Convert the Assay object to a yaml string.
update_read(read_id, *[, modality, ...])	Update read information in the Assay object.
validate(modality, out_dir, *[, tolerance])