→ OTU (Operational taxonomic unit)
print_biom_table_summary.py # old command
raw sequence counts
# Get number of OTU's per sample (not normalized OTU table)
biom summarize-table -i otu_table_mc2_w_tax.biom --qualitative -o stats_OTUs_per_sample.txt
# Get number of reads per sample (not normalized OTU table)
biom summarize-table -i otu_table_mc2_w_tax.biom -o stats_reads_per_sample.txt
head -20 stats_reads_per_samples.txt # print top 20 lines
Num samples: 40
Num observations: 113869 (total number of OTU cluster)
Total count: 1436372 (total number of sequences)
Table density (fraction of non-zero values): 0.041
Counts/sample summary:
Min: 5123.0
Max: 51423.0
Median: 22415.0
Mean: 27632.043
Std. dev.: 5203.534
Sample Metadata Categories: None provided
Observation Metadata Categories: taxonomy
Counts/sample detail:
SampleA: 5123.0
SampleB: 5634.0
SampleC: 6192.0
°°°
http://biom-format.org/documentation/summarizing_biom_tables.html
# Convert .biom into .tsv text file (including taxa labels)
biom convert -i otu_table.biom -o otu_table.csv --to-tsv --header-key taxonomy
# Convert tab-separated .csv text file into .biom file
type "OTU table" requires last (empty) column "taxonomy"
biom convert -i otu_table.csv -o otu_table.biom --table-type="OTU table" --process-obs-metadata taxonomy --to-hdf5
View biom-file on command line
biom head -i otu_table.biom
QIIME - filtering, splitting, and merging biom files
# example: remove all control samples from biom file (keep all '*' , but not '!' Control)
filter_samples_from_otu_table.py -i otu_table.biom -o otu_table_without_Control.biom -m mapfile.txt -s 'Treatment:*,!Control'
Python package
http://biom-format.org/documentation/generated/biom.table.Table.head.html
read more
Biom file format
http://biom-format.org/documentation/biom_format.html
http://biom-format.org/documentation/biom_conversion.html
OTU table and .biom format