Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
changeset 3:4852eb1a75e5 draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae
| author | sanbi-uwc |
|---|---|
| date | Fri, 07 Sep 2018 18:41:23 -0400 |
| parents | a4ee45e7237b |
| children | efe0f451c40f |
| files | data_manager/fetch_refseq.py data_manager/fetch_refseq.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- 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()
--- 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>