bump version; fix for gzip writing output

Author: Jon Palmer

gfftk/__version__.py

@@ -1,3 +1,3 @@
-VERSION = (0, 1, 6)
+VERSION = (0, 1, 7)
 
 __version__ = ".".join(map(str, VERSION))

gfftk/genbank.py

@@ -6,6 +6,7 @@
 from .go import go_term_dict
 from .interlap import InterLap
 import io
+import gzip
 
 
 def tbl2dict(input, fasta, annotation=False, table=1, debug=False):
@@ -434,7 +435,13 @@ def _goFormat(id, goDict=goDict):
             return False
 
     if output:
-        tbl = zopen(output, mode="w")
+        if output.endswith(".gz"):
+            copen = gzip.open
+            mopen = "wt"
+        else:
+            copen = open
+            mopen = "w"
+        tbl = copen(output, mopen)
     else:
         tbl = sys.stdout
     # now convert to tbl format

gfftk/gff.py

@@ -8,6 +8,7 @@
 from urllib.parse import unquote
 import uuid
 import io
+import gzip
 
 
 def start_end_gap(seq, coords):
@@ -1275,7 +1276,13 @@ def _sortDict(d):
     sortedGenes = OrderedDict(sGenes)
     # then loop through and write GFF3 format
     if output:
-        gffout = zopen(output, mode="w")
+        if output.endswith(".gz"):
+            copen = gzip.open
+            mopen = "wt"
+        else:
+            copen = open
+            mopen = "w"
+        gffout = copen(output, mopen)
     else:
         gffout = sys.stdout
     gffout.write("##gff-version 3\n")
@@ -1522,7 +1529,13 @@ def _sortDict(d):
     sGenes = natsorted(iter(input.items()), key=_sortDict)
     sortedGenes = OrderedDict(sGenes)
     if output:
-        gtfout = zopen(output, mode="w")
+        if output.endswith(".gz"):
+            copen = gzip.open
+            mopen = "wt"
+        else:
+            copen = open
+            mopen = "w"
+        gtfout = copen(output, mopen)
     else:
         gtfout = sys.stdout
     for k, v in list(sortedGenes.items()):