我使用R 包 biomformat 版本 1.2.0的函数make_biom和函数创建了一个 BIOM 文件 yyy.biom 。write_biom
yyy.biom 看起来像：
"id":{},
"format":["Biological Observation Matrix 1.0.0-dev"],
"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],
"type":["OTU table"],
"generated_by":["biomformat 1.2.0"],
"date":["2017-09-21 14:36:28"],
"matrix_type":["dense"],
"matrix_element_type":["int"],
"shape":[5,6],
"rows":[
{"id":["GG_OTU_1"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]},
{"id":["GG_OTU_2"],"metadata":["k__Bacteria","p__Cyanobacteria","c__Nostocophycideae","o__Nostocales","f__Nostocaceae","g__Dolichospermum","s__"]},
{"id":["GG_OTU_3"],"metadata":["k__Archaea","p__Euryarchaeota","c__Methanomicrobia","o__Methanosarcinales","f__Methanosarcinaceae","g__Methanosarcina","s__"]},
{"id":["GG_OTU_4"],"metadata":["k__Bacteria","p__Firmicutes","c__Clostridia","o__Halanaerobiales","f__Halanaerobiaceae","g__Halanaerobium","s__Halanaerobiumsaccharolyticum"]},
{"id":["GG_OTU_5"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]}
],
"columns":[
{"id":["Sample1"],"metadata":["CGCTTATCGAGA","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample2"],"metadata":["CATACCAGTAGC","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample3"],"metadata":["CTCTCTACCTGT","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample4"],"metadata":["CTCTCGGCCTGT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample5"],"metadata":["CTCTCTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample6"],"metadata":["CTAACTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]}
],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
BIOM 验证返回错误：
$ biom validate-table -i yyy.biom
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/biom", line 6, in <module>
sys.exit(biom.cli.cli())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 49, in validate_table
valid, report = _validate_table(input_fp, format_version, detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 62, in _validate_table
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 113, in __call__
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 97, in run
return self._validate_json(**kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 305, in _validate_json
status_msg = method(table_json)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 496, in _valid_type
if value.lower() not in self.TableTypes:
AttributeError: 'list' object has no attribute 'lower'
我尝试导入 QIIME 2 并收到此错误：
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
view_type=source_format)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 192, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
result = transformation(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in transformation
new_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 207, in wrapped
file_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 128, in _8
data = _parse_biom_table_v100(ff)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/table.py", line 3672, in from_json
dtype = MATRIX_ELEMENT_TYPE[json_table['matrix_element_type']]
TypeError: unhashable type: 'list'
QIIME 2 支持建议格式 1.0.0-dev 可能导致问题。会是这样吗？如果是这样有没有办法改变格式？
谢谢！