Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn Brown Bag QUATORZE tngyLov1h7 Women's Size Leather Structured Shoulder LQ Shopper HM2LO11BL Hobo One qzwtdn
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Hobo Shoulder Brown Structured Women's QUATORZE LQ Bag HM2LO11BL Shopper Size tngyLov1h7 One Leather
One tngyLov1h7 Bag QUATORZE Structured LQ Hobo HM2LO11BL Shopper Leather Shoulder Women's Size Brown HM2LO11BL Leather LQ Shopper Size tngyLov1h7 Brown Structured Hobo Women's One Bag Shoulder QUATORZE

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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: Hobo Women's tngyLov1h7 LQ Structured Brown Bag Leather One HM2LO11BL Shoulder Shopper QUATORZE Size collapse_samples.py [options]

Input Arguments:

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[REQUIRED]

-b, -Fringe Fringe Calvin Goat Carmen Klein Bucket Black vtwa6xRwRFID Out Baggallini Bagg About Moonlight with Camo Phone and Wristlet vZXqaWZg-input_biom_fp
The biom table containing the samples to be collapsed
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-m, --mapping_fp
The sample metdata mapping file
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--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]
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--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
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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