findRestSites

Identifies the genomic locations of restriction sites.

usage: findRestSite --fasta mm10.fa --searchPattern AAGCTT -o rest_site_positions.bed
optional arguments
--fasta, -f Path to fasta file for the organism genome.
--searchPattern, -p
 Search pattern. For example, for HindIII this pattern is “AAGCTT”. Both, forward and reverse strand are searched for a match. The pattern is a regexp and can contain regexp specif syntax (see https://docs.python.org/2/library/re.html). For example the patternCG..GC will find all occurrence of CG followed by any two bases and then GC.
--outFile, -o Name for the resulting bed file.