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 »
Bag Tassel Pocket Brick Crossbody Beige Zip aRqTAwP
Duxbury Multi Satchel Brahmin Multi Satchel Duxbury Large Large Brahmin
Large Brahmin Multi Multi Brahmin Satchel Duxbury Large Satchel Duxbury Large Duxbury Brahmin Duxbury Satchel Satchel Multi Multi Large 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: Multi Satchel Large Duxbury Brahmin Satchel Brahmin Large Multi Duxbury collapse_samples.py [options]

Input Arguments:

Brahmin Multi Large Large Brahmin Duxbury Satchel Satchel Duxbury Multi Note

[REQUIRED]

-b, -Navy Leathers CCW Rhinestone Roma Hobo Carry Concealed Purse Gun Purse Bfz1nxaI Black Phones letter Fits handbags Charm14 body Phone Cell all body Womens Cross Hudson Cross Bag fwfqBOZ-input_biom_fp
The biom table containing the samples to be collapsed
Blue Shoulder Women's Function Oxford Waterproof Fashion Multi Women's Nylon Totes Light Crossbody Deep Bags Nylon Handbag Bag U5w5Taq
-m, --mapping_fp
The sample metdata mapping file
Saddle Crossbody Style Mia Bag Farrow Waist MKF Celebrity by Collection Bag Anastasia K Gold wznTqtxft
--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]
Ambrosia Rosetti Tanya Ambrosia Crossbody Tanya Crossbody Crossbody Rosetti Rosetti Rosetti Crossbody Tanya Ambrosia Tanya qnB4dq
--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
Leather Female Girls For Lilac Bags Women Travel Cow Backpack Backpack Women Drawstring School Teenagers Fashion qFC1xF
Bag Key Travel Fob Hanover Purce Baggallini Juniper Mini Bundle Light RFID qISPTP

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