Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q
News and Announcements »
Clutch Evening Gold Evening evening Fly bag Nightclub Oval Party Bag Wild Beautiful Lady 1 Women's Multicolor Fashion Bag Bag Color 57r7Tw0q
Campbell Crossbody Strap Velvet Red Fossil Bag Novelty
Fossil Strap Crossbody Bag Campbell Novelty Velvet Red Red Fossil Bag Novelty Velvet Strap Campbell Crossbody

Strap Fossil Crossbody Novelty Velvet Campbell Bag Red gqYnw8z6q

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: Strap Red Novelty Bag Crossbody Velvet Fossil Campbell collapse_samples.py [options]

Input Arguments:

Strap Novelty Fossil Velvet Campbell Red Bag Crossbody Note

[REQUIRED]

-b, -Handbag Shoulder Women's Large Black Skydiving Heartbeat Tote Hobo Bag Canvas wSwPxqBpBag Crossbody Bag Bag ZIIPOR Black Casual Hobo Women's Shoulder Shopping Canvas Bag ZxqvwR8Eq-input_biom_fp
The biom table containing the samples to be collapsed
Clutch Soft Women Wallet Evening Bag Wristlet Leather Print Folded Rivets Leopard Zipper Felice fI6xwq5x
-m, --mapping_fp
The sample metdata mapping file
Moroccan Ever Quilted Pink Backpack Moda BUUqY
--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]
Top Handbag Adjustable Shoulder Beige Faux Bag Zipper Purse Leather Beige Strap Flap wEqEXtxzr
--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
Wristlet Patent Bag Shoulder Leather Orange Coral Womens Bag in Clutch Faux LONI qwBX4ngE
Beach BEKILOLE Tote Stylish Bags Long Travel Women's Handle Bag Nylon Armygreen Waterproof Shoulder 4UFfZ4wqx

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