4.3. jsa.seq.extract: Extract subsequences from a genome¶

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

4.3.1. Synopsis¶

jsa.seq.extract: Extract subsequences

4.3.2. Usage¶

jsa.seq.extract [options] <chr:start-end> <chr:start-end> ...

4.3.3. 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’)

--reverse Reverse complement the subsequence (default=’false’)

--format=s format of the output file (jsa and fasta) (default=’fasta’)

--help Display this usage and exit (default=’false’)