obisort: Sorts sequence records according to the value of a given attribute

obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.

obisort specific options

-k <KEY>, --key=<KEY>
Attribute used to sort the sequence records.

Example:

> obisort -k count seq1.fasta > seq2.fasta

Sorts the sequence records of file seq1.fasta according to their count (numeric order) and prints the results in the seq2.fasta file.

-r, --reverse
Sorts in reverse order.

Example:

> obisort -r -k count seq1.fastq > seq2.fastq

Sorts the sequence records of file seq1.fasta according to their count (reverse numeric order) and prints the results in the seq2.fasta file.

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.

Common options

-h, --help

Shows this help message and exits.

--DEBUG

Sets logging in debug mode.