Quickstart Tutorial

This section demonstrates how to preprocess long-read data and perform differential analyses.

Example Long-Read Workflow:

import altanalyze3.components.long_read.isoform_matrix as iso
import altanalyze3.components.long_read.isoform_automate as isoa

metadata_file = "/path/to/metadata.txt"
ensembl_exon_dir = "/path/to/Hs_Ensembl_exon.txt"
barcode_cluster_dirs = ["/path/to/barcode_to_clusters.txt"]

sample_dict = isoa.import_metadata(metadata_file)
isoa.pre_process_samples(metadata_file, barcode_cluster_dirs, ensembl_exon_dir)

import altanalyze3.components.long_read.comparisons as comp
gencode_gff = "/path/to/gencode.annotation.gff3"
genome_fasta = "/path/to/genome.fa"

isoa.combine_processed_samples(
   metadata_file,
   barcode_cluster_dirs,
   ensembl_exon_dir,
   gencode_gff,
   genome_fasta
)

gene_symbol_file = "/path/to/Hs_Ensembl-annotations.txt"
genome_fasta = "/path/to/genome.fa"

# Import all cell clusters in order or replace with a list of select cluster(s)
cluster_order = iso.return_cluster_order(barcode_cluster_dirs)

# Differential analyses to perform
analyses = ['junction', 'isoform', 'isoform-ratio']

condition1 = 'Diagnosis'
condition2 = 'Relapse'
conditions = [(condition1, condition2)]

comp.compute_differentials(
   sample_dict,
   conditions,
   cluster_order,
   gene_symbol_file,
   analyses=analyses
)