From 4b214b8d3f349dc7c4ac4a21ceb63b984639d525 Mon Sep 17 00:00:00 2001
From: Alex Rubinsteyn <alex.rubinsteyn@gmail.com>
Date: Tue, 16 Jan 2024 16:45:56 -0500
Subject: [PATCH] Update README.md

---
 README.md | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 08cff48..cfe8127 100644
--- a/README.md
+++ b/README.md
@@ -78,38 +78,40 @@ os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
 
 ## List installed genomes
 
+To see the genomes for which PyEnsembl has already downloaded and indexed metadata you can run:
+
 ```sh
 pyensembl list
 ```
 
+Or equivalently do this in Python:
+
 ```python
 from pyensembl.shell import collect_all_installed_ensembl_releases
 collect_all_installed_ensembl_releases()
 ```
 
-## Load genome quickly
+## Load genome in Python
+
+Here's an example Python snippet that loads fly genome data from Ensembl release v100:
 
 ```python
 from pyensembl import EnsemblRelease
-from pyensembl.species import find_species_by_name
-data = EnsemblRelease(
-    release=100,
-    species=find_species_by_name('drosophila_melanogaster'),
-    )
+data = EnsemblRelease(release=100, species='drosophila_melanogaster')
 ```
 
-## Data structure
+## Data structures
 
-### Gene object
+### Gene 
 
 ```python
-gene=data.gene_by_id(gene_id='FBgn0011747')
+gene = genome.gene_by_id(gene_id='FBgn0011747')
 ```
 
-### Transcript object
+### Transcript 
 
 ```python
-transcript=gene.transcripts[0]
+transcript = gene.transcripts[0]
 ```
 
 ### Protein information