Example GFFs

Author: davmlaw

README.md

@@ -48,12 +48,22 @@ This takes less than 4 seconds to load via a network drive on my machine.
 
     sudo pip install pyreference
 
-Pre-process your GFF3 or GTF files to create genes.gtf.json.gz (~1/20th the size of the input GTF file)
+Choose your annotation:
+
+    # Latest Ensembl GRCh37
+    wget ftp://ftp.ensembl.org/pub/grch37/release-87/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz
+
+    # Latest Ensembl GRCh38
+    wget ftp://ftp.ensembl.org/pub/release-104/gff3/homo_sapiens/Homo_sapiens.GRCh38.104.gff3.gz
 
-    pyreference_gff_to_json.py --gtf genes.gtf
+    # Latest RefSeq GRCh37
+    wget http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/105.20201022/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_genomic.gff.gz
 
-or
+    # Latest RefSeq GRCh38
+    http://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/annotation_releases/109.20210514/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz
 
+Pre-process your GFF3 or GTF files to create genes.gtf.json.gz (~1/20th the size of the input GTF file)
+    
     pyreference_gff_to_json.py --gff3 genes.gff.gz
 
 Create a ~/pyreference.cfg file pointing to your references.
@@ -78,7 +88,6 @@ Substitute ArgumentParser with pyreference.ReferenceArgumentParser to add a --bu
 
 args.reference is now initialised to the correct build/annotation.
 
-
 	from pyreference import ReferenceArgumentParser
 
 	parser = ReferenceArgumentParser()

setup.py

@@ -4,7 +4,7 @@
 setup(name='pyreference',
       packages=find_packages(),
       version='0.6',
-      description='Library for working with reference genomes',
+      description='Library for working with reference genomes and gene GTF/GFFs',
       author='David Lawrence',
       author_email='davmlaw@gmail.com',
       url='https://github.com/SACGF/pyreference',