obisubset: extract a subset of samples

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

Options to specify input format

Restrict the analysis to a sub-part of the input file

--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.

Sequence annotated format

--genbank

Input file is in genbank format.

--embl

Input file is in embl format.

Specifying the sequence type

--nuc

Input file contains nucleic sequences.

--prot

Input file contains protein sequences.

Options to specify output format

Standard output format

--fasta-output

Output sequences in OBITools fasta format

--fastq-output

Output sequences in Sanger fastq format

Generating an ecoPCR database

--ecopcrdb-output=<PREFIX_FILENAME>

Creates an ecoPCR database from sequence records results

Miscellaneous option

--uppercase

Print sequences in upper case (default is lower case)

Common options

-h, --help

Shows this help message and exits.

--DEBUG

Sets logging in debug mode.

obisubset modifies sequence attributes

obisubset used sequence attribute