本文整理汇总了Python中qiime.util.MetadataMap.mergeMappingFiles方法的典型用法代码示例。如果您正苦于以下问题：Python MetadataMap.mergeMappingFiles方法的具体用法？Python MetadataMap.mergeMappingFiles怎么用？Python MetadataMap.mergeMappingFiles使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类qiime.util.MetadataMap的用法示例。
在下文中一共展示了MetadataMap.mergeMappingFiles方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: main
# 需要导入模块: from qiime.util import MetadataMap [as 别名]
# 或者: from qiime.util.MetadataMap import mergeMappingFiles [as 别名]
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
output_fp = opts.output_fp
mapping_files = [open(fp, 'U') for fp in opts.mapping_fps]
no_data_value = opts.no_data_value
mapping_data = MetadataMap.mergeMappingFiles(mapping_files,
no_data_value=no_data_value)
with open(output_fp, 'w') as f:
f.write(str(mapping_data))示例2: main
# 需要导入模块: from qiime.util import MetadataMap [as 别名]
# 或者: from qiime.util.MetadataMap import mergeMappingFiles [as 别名]
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if opts.show_indices:
for idx_key in sorted(known_indices):
idx = known_indices[idx_key]
print "%s: %s, %s" % (idx_key, idx['name'], idx['source'])
print '\t', 'increased:'
print '\n'.join(['\t\t%s' % t for t in idx['increased']])
print '\t', 'decreased:'
print '\n'.join(['\t\t%s' % t for t in idx['decreased']])
exit(0)
if opts.index is not None and known_indices.get(opts.index) is None:
option_parser.error("%s is not a known index. Known indices are: %s"
% (opts.index, ','.join(known_indices.keys())))
if opts.index is not None and (opts.increased or opts.decreased):
option_parser.error("Cannot specify both an existing and custom index")
if opts.index is None and opts.increased is None and \
opts.decreased is None:
option_parser.error("Must specify an existing or custom index")
if opts.increased and opts.decreased is None:
option_parser.error("Must specify decreased taxa")
if opts.decreased and opts.increased is None:
option_parser.error("Must specify increased taxa")
if opts.index is not None:
name = opts.name if opts.name is not None else opts.index
increased = known_indices[opts.index]['increased']
decreased = known_indices[opts.index]['decreased']
else:
name = opts.name if opts.name is not None else 'index'
increased = set(opts.increased.split(','))
decreased = set(opts.decreased.split(','))
if opts.input is None:
option_parser.error("Input not specified")
if opts.output is None:
option_parser.error("Output not specified")
table = load_table(opts.input)
if opts.mapping_file:
mapping_file = open(opts.mapping_file, 'U')
output_fp = TemporaryFile()
else:
mapping_file = None
output_fp = open(opts.output, 'w')
output_fp.write("#SampleID\t%s\n" % name)
for id_, value in compute_index(table, increased, decreased, opts.key):
output_fp.write("%s\t%f\n" % (id_, value))
if opts.mapping_file:
output_fp.seek(0)
mapping_data = MetadataMap.mergeMappingFiles([output_fp, mapping_file],
no_data_value=nan)
with open(opts.output, 'w') as fp:
fp.write(str(mapping_data))
output_fp.close()