From 44cfd4e97e6d8880b9b3fe4561e948d92f7607fb Mon Sep 17 00:00:00 2001 From: psj1997 <1176894699@qq.com> Date: Sat, 13 Jun 2020 11:53:11 +0800 Subject: [PATCH] fix bug of write --- gmgc_finder/main.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/gmgc_finder/main.py b/gmgc_finder/main.py index aba09cd..e8aa7bf 100644 --- a/gmgc_finder/main.py +++ b/gmgc_finder/main.py @@ -321,7 +321,6 @@ def main(args=None): summary.append(' -{0} ({1:.1%}) had no match in the GMGC' .format(no_match, no_match/num_gene)) - num_genes = hit_table.shape[0] genome_bin = query_genome_bin(hit_table) genome_bin = genome_bin.sort_values('times_gene_hit',ascending=False) @@ -334,22 +333,22 @@ def main(args=None): - with atomic_write(out+'/genome_bin.tsv', 'wt') as ofile: + with atomic_write(out+'/genome_bin.tsv', overwrite=True) as ofile: ofile.write('# Genome_bin from GMGC-Finder v{}\n'.format(__version__)) genome_bin.to_csv(ofile, sep='\t', index=False) - with atomic_write(out+'/hit_table.tsv', 'wt') as ofile: + with atomic_write(out+'/hit_table.tsv', overwrite=True) as ofile: ofile.write('# Results from GMGC-Finder v{}\n'.format(__version__)) hit_table.to_csv(ofile, sep='\t', index=False) - with atomic_write(out+'/summary.txt', 'wt') as ofile: + with atomic_write(out+'/summary.txt', overwrite=True) as ofile: for s in summary: print(s) ofile.write(s+'\n') output_content = resource_string(__name__, 'output.md') - with atomic_write(out+'/README.md', 'wt') as ofile: + with atomic_write(out+'/README.md', overwrite=True) as ofile: ofile.write(bytes.decode(output_content)) end = datetime.datetime.now() @@ -373,7 +372,7 @@ def main(args=None): run_metadata['Inputs'].append( {'aa_input': input_metadata(args.aa_input)}) - with atomic_write(out+'/runlog.yaml', 'wt') as ofile: + with atomic_write(out+'/runlog.yaml',overwrite=True) as ofile: yaml.dump(run_metadata, ofile, default_flow_style=False)