# HG changeset patch
# User sanbi-uwc
# Date 1536360083 14400
# Node ID 4852eb1a75e5aebcc091c21011a573254b2f6bbc
# Parent  a4ee45e7237b725034e2be8c14f8ec641441b197
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae

diff -r a4ee45e7237b -r 4852eb1a75e5 data_manager/fetch_refseq.py
--- a/data_manager/fetch_refseq.py	Fri Sep 07 18:08:23 2018 -0400
+++ b/data_manager/fetch_refseq.py	Fri Sep 07 18:41:23 2018 -0400
@@ -52,9 +52,9 @@
         while input_filename != 'STOP':
             if debug:
                 print('Reading', input_filename, file=sys.stderr)
-            with gzip.open(input_filename) as input_file:
+            with gzip.open(input_filename, 'rb') as input_file:
                 read_chunk = functools.partial(input_file.read, (chunk_size))
-                for data in iter(read_chunk, ''):  # use '' as a sentinel to stop the loop
+                for data in iter(read_chunk, b''):  # use b'' as a sentinel to stop the loop. note '' != b'' in Python 3
                     output_file.write(data)
             os.unlink(input_filename)
             input_filename = conn.get()
diff -r a4ee45e7237b -r 4852eb1a75e5 data_manager/fetch_refseq.xml
--- a/data_manager/fetch_refseq.xml	Fri Sep 07 18:08:23 2018 -0400
+++ b/data_manager/fetch_refseq.xml	Fri Sep 07 18:41:23 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.3" tool_type="manage_data">
+<tool id="data_manager_fetch_refseq" name="RefSeq data manager" version="0.0.4" tool_type="manage_data">
     <description>Fetch FASTA data from NCBI RefSeq and update all_fasta data table</description>
     <requirements>
         <requirement type="package" version="3">python</requirement>