-
Notifications
You must be signed in to change notification settings - Fork 7
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'master' of github.com:biocore/mds-approximations into t…
…est_data_file_cleanup
- Loading branch information
Showing
10 changed files
with
198 additions
and
104 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,164 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| import os | ||
|
|
||
| import click | ||
| import numpy as np | ||
| from skbio import DistanceMatrix | ||
| from skbio.stats.distance import randdm | ||
| from bayesian_regression.util.generators import band_table, block_table | ||
| from skbio.diversity import beta_diversity | ||
|
|
||
|
|
||
| @click.command() | ||
| @click.option('--structure', 'structure', type=str, | ||
| help='Optional. Generate structure in the random data that ' | ||
| 'models distributions of microbial communities. ' | ||
| 'Options: "band" or "block". If not specified, then ' | ||
| 'draws from gaussian distribution to generate distance ' | ||
| 'matrices.', default=None) | ||
| @click.option('--structure-distance-metric', 'distance_metric', type=str, | ||
| help='Distance metric to use when generating distance matrix' | ||
| ' using the --structure flag. "braycurtis" by default', | ||
| default='braycurtis') | ||
| @click.option('--dim', 'dimensions', type=int, multiple=True, | ||
| help='Dimension of the input matrix/matrices to generate') | ||
| @click.option('--seed', 'seed', type=int, | ||
| help='Random number generator seed value.') | ||
| @click.option('--sub', 'subsample_dims', type=str, multiple=True, | ||
| help='Generate subsampled distance matrix with given' | ||
| 'dimension (must be smaller than original dimension)' | ||
| ' for each randomly generated distance matrix.' | ||
| ' Can specify as int or percentage') | ||
| @click.option('--overwrite', 'overwrite', type=bool, default=False, | ||
| help='Overwrite output directory if it already exists. Do not ' | ||
| 'overwrite, by default.') | ||
| @click.argument('output_dir', type=click.Path(), default=None) | ||
| def generate(dimensions, output_dir, seed, distance_metric, subsample_dims, | ||
| structure, overwrite): | ||
| """ | ||
| Generate random distance matrix. By default, generates a random distance | ||
| matrix drawing from a gaussian probability distribution. Since realistic | ||
| microbiome OTU tables and distance matrices typically do not follow such | ||
| a probability distribution, as they often contain "structure", i.e. | ||
| discrete block-like patterns or patterns along a gradient, another | ||
| option is provided to generate more realistic microbiome data that mimics | ||
| block or band-like structure, e.g. block-like could represent one grou of | ||
| microbes associated with a diseased state and another set associated with a | ||
| healthy state. | ||
| Parameters | ||
| ---------- | ||
| dimensions : number | ||
| Dimension of the input matrix/matrices to generate. | ||
| output_dir : str | ||
| Path to the directory to output results to. | ||
| seed : number | ||
| Random seed for generating distance matrices. Optional. | ||
| distance_metric : str | ||
| Distance metric to use when generating distance matrix | ||
| using the --structure flag. "braycurtis" by default. | ||
| See skbio.diversity.beta_diversity for all accepted parameters. | ||
| subsample_dims : list of str | ||
| Generate subsampled distance matrix with given dimension | ||
| (must be smaller than original dimension) for each randomly | ||
| generated distance matrix. Can specify as int denoting specific | ||
| dimension or as percentage of, for example '25%', denoting percentage | ||
| of each main dimension specified in the 'dimensions' parameter. | ||
| structure : bool | ||
| Optional. Generate structure in the random data that | ||
| models distributions of microbial communities. | ||
| Options: "band" or "block". If not specified, then | ||
| draws from gaussian distribution to generate distance | ||
| matrices. | ||
| overwrite : bool | ||
| False by default. If True, overwrites output_dir if it already exists. | ||
| """ | ||
|
|
||
| if seed is not None: | ||
| np.random.seed(seed) | ||
|
|
||
| if (not overwrite and os.path.exists(output_dir) and not click.confirm( | ||
| 'The output directory %s exists. ' | ||
| 'Do you want to overwrite?' % output_dir)): | ||
| click.echo('Aborting.') | ||
| return | ||
|
|
||
| if not os.path.exists(output_dir): | ||
| os.makedirs(output_dir) | ||
|
|
||
| for dim in dimensions: | ||
| outpath = os.path.join(output_dir, 'randdm-{}.txt'.format(dim)) | ||
|
|
||
| click.echo('Generating random distance matrix: %s' % outpath) | ||
|
|
||
| # Generate random distance matrix | ||
| if structure is not None: | ||
| click.echo('Generating synthetic OTU table with "{}"-like ' | ||
| 'microbial distribution...'.format(structure)) | ||
| if structure == 'band': | ||
| biom_table = band_table(dim, dim, seed=seed)[0] | ||
| elif structure == 'block': | ||
| biom_table = block_table(dim, dim, seed=seed)[0] | ||
| else: | ||
| raise ValueError('Invalid value for --structure parameter.') | ||
|
|
||
| otu_table = biom_table.matrix_data.todense() | ||
|
|
||
| click.echo('Generating distance matrix from OTU table...') | ||
| distance_matrix = beta_diversity(distance_metric, otu_table, | ||
| validate=False) | ||
|
|
||
| else: | ||
| click.echo('Generating random distance matrix ' | ||
| '(gaussian distribution)') | ||
| distance_matrix = randdm(dim, constructor=DistanceMatrix) | ||
|
|
||
| # Serialize distance matrix | ||
| distance_matrix.write(outpath) | ||
|
|
||
| # Subsampling | ||
| for subsample_dim in subsample_dims: | ||
| # Parse parameter values into integers | ||
| try: | ||
| if '%' in subsample_dim: | ||
| percent = float(subsample_dim[:-1]) / 100 | ||
| subsample_dim = int(percent * dim) | ||
| else: | ||
| subsample_dim = int(subsample_dim) | ||
| except ValueError: | ||
| click.echo('Format for --sub parameter is incorrect. Please ' | ||
| 're-run with --help for instructions on accepted ' | ||
| 'formats for this parameter.') | ||
| return | ||
|
|
||
| if subsample_dim <= 0: | ||
| raise ValueError('Subsample dimension must be greater than 0') | ||
|
|
||
| if subsample_dim >= dim: | ||
| raise ValueError('Subsample dimension %d must be smaller than' | ||
| 'original matrix dimension %d' % ( | ||
| subsample_dim, | ||
| dim)) | ||
| subsampled_outpath = os.path.join(output_dir, | ||
| 'randdm-{}-sub-{}.txt' | ||
| .format(dim, subsample_dim)) | ||
|
|
||
| click.echo( | ||
| 'Subsampling original randomly generated distance matrix ' | ||
| 'with subsample dimension %d: %s' % (subsample_dim, | ||
| subsampled_outpath)) | ||
|
|
||
| ids = distance_matrix.ids | ||
| # Subsample without replacement | ||
| subsampled_ids = np.random.choice(ids, subsample_dim, | ||
| replace=False) | ||
| subsampled_matrix = distance_matrix.filter(subsampled_ids) | ||
| subsampled_matrix.write(subsampled_outpath) | ||
|
|
||
| click.echo('Done.') | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| generate() |
Oops, something went wrong.