本文整理汇总了Python中biom.Table.from_hdf5方法的典型用法代码示例。如果您正苦于以下问题：Python Table.from_hdf5方法的具体用法？Python Table.from_hdf5怎么用？Python Table.from_hdf5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biom.Table的用法示例。
在下文中一共展示了Table.from_hdf5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: pick_subsampled_open_reference_otus
# 需要导入模块: from biom import Table [as 别名]
# 或者: from biom.Table import from_hdf5 [as 别名]
#.........这里部分代码省略.........
_index_headers['otu_tables']))
elif run_assign_tax:
tax_input_otu_table_fp = otu_table_fp
otu_table_w_tax_fp = \
'%s/otu_table_mc%d_w_tax.biom' % (output_dir, min_otu_size)
index_links.append(
('OTU table exluding OTUs with fewer than %d sequences and including OTU '
'taxonomy assignments' % min_otu_size,
otu_table_w_tax_fp,
_index_headers['otu_tables']))
elif run_align_and_tree:
align_and_tree_input_otu_table = otu_table_fp
pynast_failure_filtered_otu_table_fp = \
'%s/otu_table_mc%d_no_pynast_failures.biom' % (output_dir,
min_otu_size)
index_links.append(
('OTU table exluding OTUs with fewer than %d sequences and sequences that '
'fail to align with PyNAST' % min_otu_size,
pynast_failure_filtered_otu_table_fp,
_index_headers['otu_tables']))
if run_assign_tax:
if exists(otu_table_w_tax_fp) and getsize(otu_table_w_tax_fp) > 0:
logger.write(
"Final output file exists (%s). Will not rebuild." %
otu_table_w_tax_fp)
else:
# remove files from partially completed runs
remove_files([otu_table_w_tax_fp], error_on_missing=False)
taxonomy_fp = assign_tax(
repset_fasta_fp=final_repset_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
logger=logger,
status_update_callback=status_update_callback)
# Add taxa to otu table
add_metadata_cmd = 'biom add-metadata -i %s --observation-metadata-fp %s -o %s --sc-separated taxonomy --observation-header OTUID,taxonomy' %\
(tax_input_otu_table_fp, taxonomy_fp, otu_table_w_tax_fp)
commands.append([("Add taxa to OTU table", add_metadata_cmd)])
command_handler(commands,
status_update_callback,
logger=logger,
close_logger_on_success=False)
commands = []
if run_align_and_tree:
rep_set_tree_fp = join(output_dir, 'rep_set.tre')
index_links.append(
('OTU phylogenetic tree',
rep_set_tree_fp,
_index_headers['trees']))
if exists(pynast_failure_filtered_otu_table_fp) and\
getsize(pynast_failure_filtered_otu_table_fp) > 0:
logger.write("Final output file exists (%s). Will not rebuild." %
pynast_failure_filtered_otu_table_fp)
else:
# remove files from partially completed runs
remove_files([pynast_failure_filtered_otu_table_fp],
error_on_missing=False)
pynast_failures_fp = align_and_tree(
repset_fasta_fp=final_repset_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
logger=logger,
status_update_callback=status_update_callback)
# Build OTU table without PyNAST failures
with biom_open(align_and_tree_input_otu_table) as biom_file:
table = Table.from_hdf5(biom_file)
filtered_otu_table = filter_otus_from_otu_table(table,
get_seq_ids_from_fasta_file(open(pynast_failures_fp, 'U')),
0, inf, 0, inf, negate_ids_to_keep=True)
write_biom_table(filtered_otu_table,
pynast_failure_filtered_otu_table_fp)
command_handler(commands,
status_update_callback,
logger=logger,
close_logger_on_success=False)
commands = []
if close_logger_on_success:
logger.close()
if not suppress_index_page:
index_fp = '%s/index.html' % output_dir
generate_index_page(index_links, index_fp)示例2: iterative_pick_subsampled_open_reference_otus
# 需要导入模块: from biom import Table [as 别名]
# 或者: from biom.Table import from_hdf5 [as 别名]
#.........这里部分代码省略.........
merge_cmd = 'merge_otu_tables.py -i %s -o %s' %\
(','.join(otu_table_fps), otu_table_fp)
commands.append([("Merge OTU tables", merge_cmd)])
# Build master rep set
final_repset_fp = '%s/rep_set.fna' % output_dir
final_repset_from_iteration_repsets_fps(repset_fasta_fps, final_repset_fp)
command_handler(commands,
status_update_callback,
logger=logger,
close_logger_on_success=False)
commands = []
# initialize output file names - these differ based on what combination of
# taxonomy assignment and alignment/tree building is happening.
if run_assign_tax and run_align_and_tree:
tax_input_otu_table_fp = otu_table_fp
otu_table_w_tax_fp = \
'%s/otu_table_mc%d_w_tax.biom' % (output_dir, min_otu_size)
align_and_tree_input_otu_table = otu_table_w_tax_fp
pynast_failure_filtered_otu_table_fp = \
'%s/otu_table_mc%d_w_tax_no_pynast_failures.biom' % (output_dir,
min_otu_size)
elif run_assign_tax:
tax_input_otu_table_fp = otu_table_fp
otu_table_w_tax_fp = \
'%s/otu_table_mc%d_w_tax.biom' % (output_dir, min_otu_size)
elif run_align_and_tree:
align_and_tree_input_otu_table = otu_table_fp
pynast_failure_filtered_otu_table_fp = \
'%s/otu_table_mc%d_no_pynast_failures.biom' % (output_dir,
min_otu_size)
if run_assign_tax:
if exists(otu_table_w_tax_fp) and getsize(otu_table_w_tax_fp) > 0:
logger.write(
"Final output file exists (%s). Will not rebuild." %
otu_table_w_tax_fp)
else:
# remove files from partially completed runs
remove_files([otu_table_w_tax_fp], error_on_missing=False)
taxonomy_fp = assign_tax(
repset_fasta_fp=final_repset_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
logger=logger,
status_update_callback=status_update_callback)
# Add taxa to otu table
add_metadata_cmd = 'biom add-metadata -i %s --observation-metadata-fp %s -o %s --sc-separated taxonomy --observation-header OTUID,taxonomy' %\
(tax_input_otu_table_fp, taxonomy_fp, otu_table_w_tax_fp)
commands.append([("Add taxa to OTU table", add_metadata_cmd)])
command_handler(commands,
status_update_callback,
logger=logger,
close_logger_on_success=False)
commands = []
if run_align_and_tree:
if exists(pynast_failure_filtered_otu_table_fp) and\
getsize(pynast_failure_filtered_otu_table_fp) > 0:
logger.write("Final output file exists (%s). Will not rebuild." %
pynast_failure_filtered_otu_table_fp)
else:
# remove files from partially completed runs
remove_files([pynast_failure_filtered_otu_table_fp],
error_on_missing=False)
pynast_failures_fp = align_and_tree(
repset_fasta_fp=final_repset_fp,
output_dir=output_dir,
command_handler=command_handler,
params=params,
qiime_config=qiime_config,
parallel=parallel,
logger=logger,
status_update_callback=status_update_callback)
# Build OTU table without PyNAST failures
with biom_open(align_and_tree_input_otu_table) as biom_file:
table = Table.from_hdf5(biom_file)
filtered_otu_table = filter_otus_from_otu_table(table,
get_seq_ids_from_fasta_file(open(pynast_failures_fp, 'U')),
0, inf, 0, inf, negate_ids_to_keep=True)
write_biom_table(filtered_otu_table,
pynast_failure_filtered_otu_table_fp)
command_handler(commands,
status_update_callback,
logger=logger,
close_logger_on_success=False)
commands = []
logger.close()