From bb6910b7a15b29f6aaca7f62684a712c36f1bfaa Mon Sep 17 00:00:00 2001
From: Pradeep Bashyal <pbashyal@nmdp.org>
Date: Wed, 31 Mar 2021 10:34:23 -0500
Subject: [PATCH] Make seq2gfe work with imgt_sqldb (#39)
MIME-Version: 1.0
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* Make seq2gfe work with imgt_sqldb
* Bump version: 1.1.3 → 1.1.4
---
 Dockerfile        |  8 ++++++--
 pygfe/__init__.py |  2 +-
 scripts/seq2gfe   | 19 ++++++++++---------
 setup.cfg         |  2 +-
 setup.py          |  2 +-
 5 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c0bd609..e752ba4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -8,11 +8,15 @@ RUN apt-get update -q \
     && apt-get clean
 
 RUN pip install --no-cache-dir seq-ann==1.1.0
-RUN pip install --no-cache-dir py-gfe==1.1.3
+RUN pip install --no-cache-dir py-gfe==1.1.4
 
 RUN touch blank.fasta \
     && seq2gfe -f blank.fasta -l HLA-A \
 	  && seq2gfe -f blank.fasta -l KIR3DL2 -k
 
-ENV BIOSQLHOST=imgt_biosqldb 
+
+ENV BIOSQLHOST=imgt_biosqldb
 ENV BIOSQLPORT=3306
+ENV BIOSQLDB=bioseqdb
+ENV BIOSQLUSER=root
+ENV BIOSQLPASS=my-secret-pw
diff --git a/pygfe/__init__.py b/pygfe/__init__.py
index 79cffe4..24d80bc 100644
--- a/pygfe/__init__.py
+++ b/pygfe/__init__.py
@@ -26,4 +26,4 @@
 
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '1.1.3'
+__version__ = '1.1.4'
diff --git a/scripts/seq2gfe b/scripts/seq2gfe
index 2300b30..f50c57b 100755
--- a/scripts/seq2gfe
+++ b/scripts/seq2gfe
@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import argparse
+import os
 
 from Bio import SeqIO
 from BioSQL import BioSeqDatabase
@@ -42,7 +43,7 @@ def main():
                         action='store_true')
 
     args = parser.parse_args()
-    fastafile = args.file
+    fasta_file = args.file
     loc = args.locus
     serv = args.server
 
@@ -56,21 +57,21 @@ def main():
 
     server = None
     if serv:
-        import os
-        biosqldb_host = os.getenv('BIOSQLPORT', 'localhost')
-        biosqldb_port = os.getenv('BIOSQLPORT', '3306')
+        biosqldb_host = os.getenv('BIOSQLHOST', 'localhost')
+        biosqldb_port = int(os.getenv('BIOSQLPORT', 3306))
         biosqldb_user = os.getenv('BIOSQLUSER', 'root')
-        biosqldb_pass = os.getenv('BIOSQLPASSWORD', '')
+        biosqldb_pass = os.getenv('BIOSQLPASS', '')
+        biosqldb_name = os.getenv("BIOSQLDB", "bioseqdb")
 
         server = BioSeqDatabase.open_database(driver="pymysql",
-                                            user=biosqldb_user, passwd=biosqldb_pass,
-                                            host=biosqldb_host, port=biosqldb_port,
-                                            db="bioseqdb")
+                                              user=biosqldb_user, passwd=biosqldb_pass,
+                                              host=biosqldb_host, port=biosqldb_port,
+                                              db=biosqldb_name)
 
     seqann = BioSeqAnn(verbose=verbose, server=server, kir=kir)
 
     gfe_maker = gfe.GFE()
-    for seq in SeqIO.parse(fastafile, "fasta"):
+    for seq in SeqIO.parse(fasta_file, "fasta"):
         if not loc:
             loc = get_locus(seq, kir=kir, verbose=verbose,
                             refdata=seqann.refdata)
diff --git a/setup.cfg b/setup.cfg
index 03ae76b..aa9acdf 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.3
+current_version = 1.1.4
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index eabc258..86ad08a 100644
--- a/setup.py
+++ b/setup.py
@@ -40,7 +40,7 @@
 
 setup(
     name='py-gfe',
-    version='1.1.3',
+    version='1.1.4',
     description="Python package for converting sequence annotations to gene feature enumerations (GFE).",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",