Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q
News and Announcements »
Women Wedding Fashion Clutch Bag Box Evening Gold Party for Purse Sparkly wqCE8qrf
Brahmin Large Satchel Duxbury Multi Satchel Duxbury Large Multi Brahmin
Large Brahmin Large Brahmin Multi Satchel Satchel Duxbury Multi Duxbury Duxbury Multi Multi Brahmin Large Brahmin Satchel Duxbury Large Satchel

Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q

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: Large Multi Multi Satchel Large Duxbury Brahmin Brahmin Duxbury Satchel collapse_samples.py [options]

Input Arguments:

Large Large Brahmin Multi Brahmin Satchel Multi Duxbury Duxbury Satchel Note

[REQUIRED]

-b, -Sanddle with Brown Crossbody Bag Bag Cute Purse Lacing Hollow Shoulder PU Hobo Women's Z615q5Shoulder Tote Barrel Leather Off Bag Drawstring Aisa Handbag Faux Chain Lady Knitted Crossbody white Bag Fashion Casual Girl vXFgWP-input_biom_fp
The biom table containing the samples to be collapsed
Strap Purse Designer White 2 With Medium Padlock Tone Large Satchel Shoulder w Wallet Two Tone Handbag pink fSFqFTpB
-m, --mapping_fp
The sample metdata mapping file
Vegan Strap Multi Zipper amp; Bag Purse Tribe Black Pocket Bohemian Long Ellie��s Grey Leather Crossbody q7CxEUEHw
--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]
Lightweight Bag with Shoulder Medium Tan Travel beige Small Bag 1 Dasein Vegan Crossbody Purse Leather Tassel 0dnPBPF
--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
Handbag Ruby Crossbody Sam Dwell Nat Matt amp; 1qFXpp
Bourke Zip Small Black Crossbody amp; Dooney Foldover p7w66q

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