Summarizing BIOM tables¶
If you have an existing BIOM file and want to compile a summary of the information in that table, you can use the biom summarize-table command.
To get help with biom summarize-table you can call:
biom summarize-table -h
This command takes a BIOM file or gzipped BIOM file as input, and will print a summary of the count information on a per-sample basis to the new file specified by the -o parameter. The example file used in the commands below can be found in the biom-format/examples directory.
Summarizing sample data¶
To summarize the per-sample data in a BIOM file, you can run:
biom summarize-table -i rich_sparse_otu_table.biom -o rich_sparse_otu_table_summary.txt
The following information will be written to rich_sparse_otu_table_summary.txt:
Num samples: 6 Num observations: 5 Total count: 27 Table density (fraction of non-zero values): 0.500 Counts/sample summary: Min: 3.0 Max: 7.0 Median: 4.000 Mean: 4.500 Std. dev.: 1.500 Sample Metadata Categories: LinkerPrimerSequence; BarcodeSequence; Description; BODY_SITE Observation Metadata Categories: taxonomy Counts/sample detail: Sample5: 3.0 Sample2: 3.0 Sample6: 4.0 Sample3: 4.0 Sample4: 6.0 Sample1: 7.0
As you can see, general summary information about the table is provided, including the number of samples, the number of observations, the total count (i.e., the sum of all values in the table), and so on, followed by the per-sample counts.
Summarizing sample data qualitatively¶
To summarize the per-sample data in a BIOM file qualitatively, where the number of unique observations per sample (rather than the total count of observations per sample) are provided, you can run:
biom summarize-table -i rich_sparse_otu_table.biom --qualitative -o rich_sparse_otu_table_qual_summary.txt
The following information will be written to rich_sparse_otu_table_qual_summary.txt:
Num samples: 6 Num observations: 5 Observations/sample summary: Min: 1 Max: 4 Median: 2.500 Mean: 2.500 Std. dev.: 0.957 Sample Metadata Categories: LinkerPrimerSequence; BarcodeSequence; Description; BODY_SITE Observation Metadata Categories: taxonomy Observations/sample detail: Sample5: 1 Sample4: 2 Sample1: 2 Sample6: 3 Sample2: 3