| Previous changeset 6:e57f0b0bc73b (2019-11-28) Next changeset 8:752439501b04 (2023-02-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" |
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modified:
data_manager/data_manager_snpsift_dbnsfp.py tool_dependencies.xml |
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| diff -r e57f0b0bc73b -r fe8a9ab8daf9 data_manager/data_manager_snpsift_dbnsfp.py --- a/data_manager/data_manager_snpsift_dbnsfp.py Thu Nov 28 15:48:39 2019 -0500 +++ b/data_manager/data_manager_snpsift_dbnsfp.py Sun Nov 22 12:54:01 2020 +0000 |
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| @@ -1,4 +1,5 @@ #!/usr/bin/env python +from __future__ import print_function import gzip import json @@ -46,11 +47,6 @@ dbNSFP_name_pat = r'dbNSFP(v|_light)?(\d*).*?' -def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) - - def get_nsfp_genome_version(name): genome_version = 'hg19' dbNSFP_name_pat = r'(dbscSNV|dbNSFP(v|_light)?)(\d*).*?' @@ -66,23 +62,19 @@ def get_annotations(gzip_path): annotations = None - fh = None try: - fh = gzip.open(gzip_path, 'r') - buf = fh.read(10000) + with gzip.open(gzip_path, 'r') as fh: + buf = fh.read(10000) lines = buf.splitlines() headers = lines[0].split('\t') annotations = ','.join([x.strip() for x in headers[4:]]) except Exception as e: - stop_err('Error Reading annotations %s : %s' % (gzip_path, e)) - finally: - if fh: - fh.close() + sys.exit('Error Reading annotations %s : %s' % (gzip_path, e)) return annotations def tabix_file(input_fname, output_fname): - print >> sys.stdout, "tabix_file: %s -> %s" % (input_fname, output_fname) + print("tabix_file: %s -> %s" % (input_fname, output_fname)) ctabix.tabix_compress(input_fname, output_fname, force=True) # Column indices are 0-based. ctabix.tabix_index(output_fname, seq_col=0, start_col=1, end_col=1) @@ -119,7 +111,7 @@ tfh.close() tempfiles.append(file + "_%d" % len(tempfiles)) tfh = open(tempfiles[-1], 'w') - print >> sys.stderr, "%s [%d] pos: %d < %d" % (file, i, pos, lastpos) + print("%s [%d] pos: %d < %d" % (file, i, pos, lastpos), file=sys.stderr) lastpos = pos tfh.write(line) tfh.close() @@ -156,7 +148,8 @@ (options, args) = parser.parse_args() filename = args[0] - params = json.loads(open(filename).read()) + with open(filename) as fh: + params = json.load(fh) target_directory = params['output_data'][0]['extra_files_path'] if not os.path.exists(target_directory): os.mkdir(target_directory) @@ -182,7 +175,7 @@ bzip_path = os.path.join(target_directory, bgzip_name) db_name = re.sub('(.txt)?.gz$', '', bgzip_name) else: - stop_err('Either --softgenetics or --dbnsfp_tabular required') + sys.exit('Either --softgenetics or --dbnsfp_tabular required') if dbnsfp_tsv: bgzip_name = '%s.txt.gz' % db_name bzip_path = os.path.join(target_directory, bgzip_name) @@ -195,7 +188,8 @@ data_manager_dict['data_tables'][data_table].append(data_table_entry) # save info to json file - open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True)) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__": |
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| diff -r e57f0b0bc73b -r fe8a9ab8daf9 tool_dependencies.xml --- a/tool_dependencies.xml Thu Nov 28 15:48:39 2019 -0500 +++ b/tool_dependencies.xml Sun Nov 22 12:54:01 2020 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0" ?> <tool_dependency> <package name="pysam" version="0.8.3"> - <repository changeset_revision="08db58be052a" name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/> + <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="08db58be052a"/> </package> </tool_dependency> \ No newline at end of file |