NAME

obisubset - description of obisubset

The obisubset command extracts a subset of samples from a sequence file after its dereplication using obiuniq program.

OBISUBSET SPECIFIC OPTIONS

-s <TAGNAME>, --sample=<TAGNAME>,: The option -s allows to specify the tag containing sample descriptions, the default value is set to merged_sample.
Example:

> obiuniq -m sample seq1.fasta > seq2.fasta
> obisubset -s merged_sample -n sample1 seq2.fasta > seq3.fasta

After the dereplication of the sequences using the in the new attribute merged_sample.

-o <TAGNAME>, --other-tag=<TAGNAME>,: Another tag to clean according to the sample subset
Example:

> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta

-l <FILENAME>, --sample-list=<FILENAME>,: File containing the samples names (one sample id per line).
Example:

> obisubset -s merged_sample -o -l ids.txt seq2.fasta > seq3.fasta

-p <REGEX>, --sample-pattern=<REGEX>,: A regular expression pattern matching the sample ids to extract.
Example:

> obisubset -s merged_sample -o -p "negative_.*" seq2.fasta > seq3.fasta

-n <SAMPLEIDS>, --sample-name=<SAMPLEIDS>,: A sample id to extract
Example:

> obisubset -s merged_sample -o -n sample1 seq2.fasta > seq3.fasta

--skip <N>: The N first sequence records of the file are discarded from the analysis and not reported to the output file

--only <N>: Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the –skip option.