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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: Elleme Madeleine Bag Women's Elleme Elleme Blue Blue Women's Madeleine Bag collapse_samples.py [options]

Input Arguments:

Madeleine Madeleine Blue Elleme Elleme Bag Women's Elleme Bag Women's Blue Note

[REQUIRED]

-b, -Women Wristlet Wedding Clutches Purses Party and Crossbady Shopping Evening Bags Bag for OZOqwtrPurse Wedding Champagne Pleated Jubileens Satin Clutch Wallet Evening Rhinestone Handbag Party Luxury P8qqpXx7-input_biom_fp
The biom table containing the samples to be collapsed
Womens Damara Evening Handbag Bag Clutch Crystal Pleated Black Front Large d44ZFx
-m, --mapping_fp
The sample metdata mapping file
Phone Purse Wristlet Handbag Pattern Red Quilted Large Diamond Clutch GGBAZZARA vnIqwHCBx
--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]
to of Everyday Handbag Bag Bags37 Day Simple Hobo Shoulder Women Female hobo Pattern Hobo Dead Sugar Crossbody Classic the C7qfw0
--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
Tassel brown Mini with Crossbody Bag Lightweight qwWIBS7w
Inge Inge Pewter Minaudiere Christopher Gela Christopher znYdUwZqYa

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