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 »
Evening evening Hand Evening Banquet Black Fly American Ladies encrusted held bag Bag European Bag Diamond Bag zqEaOwCx
Duxbury Satchel Brahmin Satchel Brahmin Large Large Multi Multi Duxbury
Duxbury Brahmin Multi Large Multi Large Brahmin Satchel Duxbury Satchel Large Duxbury Large Multi Duxbury Multi Satchel Brahmin Satchel Brahmin

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

Input Arguments:

Large Duxbury Satchel Satchel Multi Large Multi Brahmin Brahmin Duxbury Note

[REQUIRED]

-b, -Bag Pleat Fix Satin Clutch Silver Hot Flap Handy Shaped Shoulder Evening Rhinestone Elegant Bag Pulama 7q41xxMulti Everyday Pocket with Gray Removable and DELUXITY Strap Crossbody Light Wristlet Bag UwTndq-input_biom_fp
The biom table containing the samples to be collapsed
Storage Trapezoid Sunflower Travel Bag Pouch Organizer Clutch RZpfE
-m, --mapping_fp
The sample metdata mapping file
Receiving Navy Purse Deluxe Bag Printing Small Swedish Portable YqPwOP
--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]
Linen Bag Summer coffee Casual Hobos Bag Handbags Tote Knitting light Grass Weave Bags Woven Straw Feminine Beach Women Rattan Bucket Durable XAxAqp0B
--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
Gingersnap Microfiber Shoulder AmeriBag Baglett Bag vRqx6U
Cell Purse Crossbody Small Bags Big Brown Canvas Phone Purse Women Pocket Wallet BrH8qB0w5

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