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
|
.. _compute_core_microbiome:
.. index:: compute_core_microbiome.py
*compute_core_microbiome.py* -- Identify the core microbiome.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
**Usage:** :file:`compute_core_microbiome.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fp
The input otu table in BIOM format
-o, `-`-output_dir
Directory to store output data
**[OPTIONAL]**
`-`-max_fraction_for_core
The max fractions of samples that an OTU must be observed in to be considered part of the core as a number in the range [0,1] [default: 1.0]
`-`-min_fraction_for_core
The min fractions of samples that an OTU must be observed in to be considered part of the core as a number in the range [0,1] [default: 0.5]
`-`-num_fraction_for_core_steps
The number of evenly sizes steps to take between min_fraction_for_core and max_fraction_for_core [default: 11]
`-`-otu_md
The otu metadata category to write to the output file [defualt: taxonomy]
`-`-mapping_fp
Mapping file path (for use with --valid_states) [default: None]
`-`-valid_states
Description of sample ids to retain (for use with --mapping_fp) [default: None]
**Output:**
Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in at least 50% of the samples. Write the list of core OTUs to a text file, and a new BIOM file containing only the core OTUs.
::
compute_core_microbiome.py -i otu_table.biom -o otu_table_core
Identify the core OTUs in otu_table.biom, defined as the OTUs that are present in all of the samples in the 'Fast' treatment (as specified in the mapping file). Write the list of core OTUs to a text file.
::
compute_core_microbiome.py -i otu_table.biom -o otu_table_core_fast --mapping_fp map.txt --valid_states "Treatment:Fast"
|
