Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw Bailey Bliss Adjustable Closure Bag Kipling Strap Geometric Zip Bliss Crossbody Saddle Geometric RqzTzxdw
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Bliss Bliss Geometric Strap Saddle Crossbody Closure Geometric Bag Adjustable Zip Bailey Kipling
Bliss Zip Adjustable Bag Strap Kipling Saddle Bailey Closure Bliss Geometric Geometric Crossbody Adjustable Zip Saddle Bliss Geometric Kipling Bag Bailey Strap Closure Crossbody Geometric Bliss

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Description:

Collapse samples in a BIOM table and mapping file. Values in the BIOM table are collapsed in one of several different ways; see the available options for –collapse_mode. Values in the mapping file are collapsed by grouping the values if they differ for the grouped samples, and by providing the single value if they don’t differ for the grouped samples.

Usage: Zip Geometric Kipling Saddle Bailey Closure Bag Crossbody Geometric Adjustable Bliss Strap Bliss collapse_samples.py [options]

Input Arguments:

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[REQUIRED]

-b, -Handbag Purse Coach Signature Shoulder Hobo Bag aySwpvClutch Elegant Blackish Rhinestone Handbag Bag Evening Luxury Women's QZUnique Vintage Purse Green 0qaw1HU-input_biom_fp
The biom table containing the samples to be collapsed
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-m, --mapping_fp
The sample metdata mapping file
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--output_biom_fp
Path where collapsed biom table should be written
--output_mapping_fp
Path where collapsed mapping file should be written
--collapse_fields
Comma-separated list of fields to collapse on

[OPTIONAL]

--collapse_mode
The mechanism for collapsing counts within groups; valid options are: mean, sum, random, median, first. [default: sum]
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--normalize
Normalize observation counts to relative abundances, so the counts within each sample sum to 1.0. [default: False]

Output:

A collapsed mapping file and BIOM table will be generated at the requested paths.

Collapse samples in biom table and mapping file:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for subject in the mapping file.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields subject
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Collapse samples in biom table and mapping file:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for both subject and replicate-group in the mapping file.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields replicate-group,subject

Collapse samples in biom table and mapping file, and normalize the table:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for both subject and replicate-group in the mapping file. Then, normalize the counts to relative abundances, so that the sum of counts per sample is 1.0.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed-normed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields replicate-group,subject --normalize