pasilla

This module is a port of the R Bioconductor pasilla package, version 1.31.0.

This module provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in [Brooks2011]. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The R package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.

We describe below how to load the data to build an :class:`AnnData` object (NB: the snippet below is wrapped in the :func:`pasilla` function for convenience):

import importlib.resources
import pandas as pd
import anndata as ad

data_dir = importlib.resources.files("inmoose.data.pasilla")
cts = pd.read_csv(data_dir.joinpath("pasilla_gene_counts.tsv"), sep='\t', index_col=0)
anno = pd.read_csv(data_dir.joinpath("pasilla_sample_annotation.csv"), index_col=0)

# The columns of `cts` and the rows of `anno` use different labels and are
# not in the same order. We first need to harmonize them before building the
# AnnData object.

# first get rid of the "fb" suffix
anno.index = [i[:-2] for i in anno.index]

# second reorder the index
anno = anno.reindex(cts.columns)

# we are now ready to build the AnnData object
adata = ad.AnnData(cts.T, anno)
adata