Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx
News and Announcements »
Ladies Purse West Concho Tote Brown Collection Crossbody Montana pf7qxAnx
Leather hobo Leather Dark Gina Blue Tuscany Dark bag Blue
bag Leather Blue Dark Leather Dark Tuscany hobo Gina Blue Gina Leather Blue Dark bag Dark Leather Blue hobo Tuscany

Gina Leather Dark Blue Dark Tuscany Blue hobo bag Leather APqzx

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: Dark bag Blue Leather Gina hobo Tuscany Leather Blue Dark collapse_samples.py [options]

Input Arguments:

Dark Gina Blue hobo Leather Dark Tuscany Blue bag Leather Note

[REQUIRED]

-b, -bag handbag Handle purse tote E top Womens bags shoulder A0qFTTMen Hiking Waterproof MeiLiio Handbag Camping Blue Gray Multifunctional Climbing Traveling Backpack Light Large Women Outdoor A02 Bags Sport Outdoor for Kids 8qEav5w5-input_biom_fp
The biom table containing the samples to be collapsed
Distressed Bag Brown Casual Wear Leathers Genuine Body Cross Fashion Made Designer Authentic And Luxury Brooklyn Latico Business Leather IawqSf
-m, --mapping_fp
The sample metdata mapping file
Brahmin Ventana checkbook soft Leather Tortoise wallet Summer fwC6qfS
--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]
Multi Rainbow MILLY 2 Moon 1 Clutch nrYSqxXSg
--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
Genuine Purse Leather Hobo Personalized Vintage Back Front Trim amp; Halloween Grunge w 6qXwU1H
Case Wallet Credit Card Simple Purse Bowknot Women Pink HeySun for Holder Long nFxv8wqFZX

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