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Using references

Working with references

from cirro import DataPortal

portal = DataPortal()

Finding a list of available reference types

for ref_type in portal.list_reference_types():
    print(str(ref_type))
Name: Barcode files (general)
Description: List of line-separated barcodes
Name: CRISPR sgRNA Library
Description: Describes the set of sgRNA guides used in the screen, along with the genes which each guide targets.
Name: Barcode files (bbi-sci)
Description: List of line-separated barcodes
Name: STAR files (bbi-sci)
Description: BBI-sci: genome to star maps
Name: Gene files (bbi-sci)
Description: BBI-sci: genome to gene model maps
Name: Garnett files (bbi-sci)
Description: BBI-sci
Name: Hash Lists (bbi-sci)
Description: BBI-sci
Name: Reference Genome (BWA)
Description: Genome sequence indexed for alignment with the BWA algorithm.
Name: Reference Genome (FASTA)
Description: Genome fasta file
Name: Genome Regions (BED)
Description: Table of genomic regions in BED format
Name: CellRanger Feature Reference (CSV)
Description: Reference file used for Feature Barcodes on the 10X platform (e.g. Antibody Capture, CRISPR Guide Capture
Name: VirScan Library
Description: VirScan library CSV (oligo, organism, peptide) and Table of public epitopes (peptide_translate).

Finding available references within the project

# List the CRISPR sgRNA Library references which are available in your project
project = portal.get_project_by_name("Test Project")
print(project.list_references(reference_type="CRISPR sgRNA Library").description())
BroadGPP-Brunello
# Select the CRISPR Library
library = project.get_reference_by_name("BroadGPP-Brunello")
print(str(library))
BroadGPP-Brunello
# Use the absolute path in the process parameter
library.absolute_path
's3://z-9a31492a-e679-43ce-9f06-d84213c8f7f7/resources/data/references/crispr_libraries/BroadGPP-Brunello/library.csv'