1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
|
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2013, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2011-2013, The BIOM Format Development Team"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso", "Daniel McDonald"]
__license__ = "BSD"
__url__ = "http://biom-format.org"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
from pyqi.core.interfaces.optparse import (OptparseUsageExample,
OptparseOption, OptparseResult)
from pyqi.core.command import (make_command_in_collection_lookup_f,
make_command_out_collection_lookup_f)
from biom.interfaces.optparse.input_handler import (load_biom_table,
load_metadata)
from biom.interfaces.optparse.output_handler import write_biom_table
from biom.commands.table_converter import CommandConstructor
cmd_in_lookup = make_command_in_collection_lookup_f(CommandConstructor)
cmd_out_lookup = make_command_out_collection_lookup_f(CommandConstructor)
usage_examples = [
OptparseUsageExample(ShortDesc="Converting from classic to BIOM format",
LongDesc="Convert the classic file table.txt to a "
"HDF5 BIOM format OTU table",
Ex='%prog -i table.txt -o table.biom '
'--table-type "OTU table" --to-hdf5')
]
inputs = [
OptparseOption(Parameter=cmd_in_lookup('table'),
Type='existing_filepath',
Handler=load_biom_table,
ShortName='i', Name='input-fp',
Help='the input table filepath, either in BIOM or classic '
'format'),
OptparseOption(Parameter=cmd_in_lookup('sample_metadata'),
Type='existing_filepath',
Handler=load_metadata,
ShortName='m',
Name='sample-metadata-fp'),
OptparseOption(Parameter=cmd_in_lookup('observation_metadata'),
Type='existing_filepath',
Handler=load_metadata, Name='observation-metadata-fp'),
OptparseOption(Parameter=cmd_in_lookup('header_key')),
OptparseOption(Parameter=cmd_in_lookup('output_metadata_id')),
OptparseOption(Parameter=cmd_in_lookup('process_obs_metadata')),
OptparseOption(Parameter=cmd_in_lookup('table_type')),
OptparseOption(Parameter=cmd_in_lookup('tsv_metadata_formatter')),
OptparseOption(Parameter=cmd_in_lookup('to_json'),
Action='store_true'),
OptparseOption(Parameter=cmd_in_lookup('to_tsv'),
Action='store_true'),
OptparseOption(Parameter=cmd_in_lookup('to_hdf5'),
Action='store_true'),
OptparseOption(Parameter=cmd_in_lookup('collapsed_samples'),
Action='store_true'),
OptparseOption(Parameter=cmd_in_lookup('collapsed_observations'),
Action='store_true'),
OptparseOption(Parameter=None,
Type='new_filepath',
ShortName='o',
Name='output-fp',
Required=True,
Help='the output filepath')
]
outputs = [
OptparseResult(Parameter=cmd_out_lookup('table'),
Handler=write_biom_table,
InputName='output-fp')
]
|
