From ea088e4bd692e8e64d56d8a41429a4046e8b649e Mon Sep 17 00:00:00 2001
From: Michael Steinbaugh <mike@steinbaugh.com>
Date: Wed, 18 Sep 2019 15:32:12 -0400
Subject: [PATCH] Improve arg parsing

---
 bin/ensembl-fasta | 51 +++++++++++++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 19 deletions(-)

diff --git a/bin/ensembl-fasta b/bin/ensembl-fasta
index fd361d30ef..ae301c0bc7 100755
--- a/bin/ensembl-fasta
+++ b/bin/ensembl-fasta
@@ -1,10 +1,11 @@
 #!/usr/bin/env python3
-"""Download Ensembl genome annotations in FASTA format.
 """
+Download Ensembl genome annotations in FASTA format.
 
-# See also:
-# - https://docs.python.org/2/howto/argparse.html
-# - https://stackoverflow.com/questions/24180527
+See also:
+- https://docs.python.org/2/howto/argparse.html
+- https://stackoverflow.com/questions/24180527
+"""
 
 import argparse
 import os
@@ -15,41 +16,52 @@ parser = argparse.ArgumentParser()
 optional = parser._action_groups.pop()
 required = parser.add_argument_group('required arguments')
 required.add_argument( \
-    "--organism", required=True, \
+    "--organism", \
+    required=True, \
+    type=str, \
     help="latin name (e.g. \"Homo sapiens\")" \
 )
 required.add_argument( \
-    "--build", required=True, \
-    help="genome build (e.g. \"GRCh38\")" \
+    "--type", \
+    required=True, \
+    choices=['dna', 'cdna'], \
+    help="\"dna\" (genome) or \"cdna\" (transcriptome)" \
 )
 required.add_argument( \
-    "--type", required=True, \
-    help="\"dna\" (genome) or \"cdna\" (transcriptome)" \
+    "--build", \
+    required=True, \
+    type=str, \
+    help="genome build (e.g. \"GRCh38\")" \
 )
 optional.add_argument( \
     "--release", \
+    type=int, \
     help="release version (e.g. \"96\")" \
 )
+optional.add_argument( \
+    "--decompress", \
+    action='store_true', \
+    # default=False, \
+    help="Decompress (but keep) the original file." \
+)
 parser._action_groups.append(optional)
 args = parser.parse_args()
 
 organism = args.organism.replace(" ", "_")
 build = args.build
 type = args.type
-
 release = args.release
+decompress = args.decompress
+
+# Set the release automatically, if necessary.
 if release is None:
     release = subprocess.check_output( \
-        "_koopa_variable ensembl_release_version", \
+        "koopa variable ensembl_release_version", \
         shell=True, universal_newlines=True \
     )
     release = release.rstrip()
 
-# Inform and exit on legacy "transcriptome" usage.
-if type == "transcriptome":
-    print("Use `cdna` instead of `transcriptome`.")
-    sys.exit(1)
-
+# Set the base URL of FTP server.
 if build == "GRCh37":
     release = "87"
     base_url = "ftp://ftp.ensembl.org/pub/grch37"
@@ -80,6 +92,7 @@ except subprocess.CalledProcessError as e:
     sys.exit(1)
 
 # Decompress, but also keep the original compressed file.
-print("Decompressing " + file + ".")
-unzip_file = os.path.splitext(file)[0]
-os.system("gunzip -c " + file + " > " + unzip_file)
+if decompress is True:
+    print("Decompressing " + file + ".")
+    unzip_file = os.path.splitext(file)[0]
+    os.system("gunzip -c " + file + " > " + unzip_file)