Make seq2gfe work without imgt_sqldb (#40)

* Make seq2gfe work without imgt_sqldb
* Bump version: 1.1.4 → 1.1.5

Dockerfile

@@ -8,7 +8,7 @@ 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==1.1.4
+RUN pip install --no-cache-dir py-gfe==1.1.5
 
 RUN touch blank.fasta \
     && seq2gfe -f blank.fasta -l HLA-A \

pygfe/__init__.py

@@ -26,4 +26,4 @@
 
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '1.1.4'
+__version__ = '1.1.5'

scripts/seq2gfe

@@ -6,7 +6,6 @@ import os
 
 from Bio import SeqIO
 from BioSQL import BioSeqDatabase
-from BioSQL.BioSeq import DBSeq
 from seqann import BioSeqAnn, gfe
 from seqann.blast_cmd import get_locus
 
@@ -86,13 +85,9 @@ def main():
         print('{:*^20} {:^20} {:*^20}'.format("", str(seq.description), ""))
         l = 0
         for f in ann.annotation:
-            if isinstance(ann.annotation[f], DBSeq):
-                print(gfe_name, f, ann.method, str(ann.annotation[f]), sep="\t")
-                l += len(ann.annotation[f])
-            else:
-                print(gfe_name, f, ann.method, str(ann.annotation[f].seq), sep="\t")
-                l += len(ann.annotation[f].seq)
-        print("")
+            print(gfe_name, f, ann.method, str(ann.annotation[f]), sep="\t")
+            l += len(ann.annotation[f])
+        print("Total Length:", l)
 
     if serv:
         server.close()

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.4
+current_version = 1.1.5
 commit = True
 tag = True
 

setup.py

@@ -40,7 +40,7 @@
 
 setup(
     name='py-gfe',
-    version='1.1.4',
+    version='1.1.5',
     description="Python package for converting sequence annotations to gene feature enumerations (GFE).",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",