4.2. jsa.seq.sort: Sort the sequences in a file

jsa.seq.sort sort the sequences from a file or from a standard input into some order.

jsa.seq.sort is included in the Japsa package. Please see check the installation page for instructions.

4.2.1. Synopsis

jsa.seq.sort: Sort sequences based on their lengths

4.2.2. Usage

jsa.seq.sort [options]

4.2.3. Options

--input=s	Name of the input file, - for standard input (REQUIRED)
--output=s	Name of the output file, - for standard output (REQUIRED)
--alphabet=s	Alphabet of the input file. Options: DNA (DNA=DNA16), DNA4 (ACGT), DNA5(ACGTN), DNA16 and Protein (default=’DNA’)
--number	Add the order number to the beginning of contig name (default=’false’)
--pad	Pad – this only applied for number (default=’false’)
--reverse	Reverse sort order (default=’false’)
--sortKey=s	Sort key (default=’length’)
--help	Display this usage and exit (default=’false’)