NAME

       fastahack - fastahack - indexing and extracting sequences and subsequences from FASTA files

DESCRIPTION

       usage: fastahack [options] <fasta reference>

   options:
       -i, --index
              generate fasta index <fasta reference>.fai

       -r, --region REGION
              print the specified region

       -c, --stdin
              read  a  stream  of line-delimited region specifiers on stdin and print the corresponding sequence
              for each on stdout

       -e, --entropy
              print the shannon entropy of the specified region

       -d, --dump
              print the fasta file in the form 'seq_name <tab> sequence'

       REGION is of the form <seq>, <seq>:<start>[sep]<end>, <seq1>:<start>[sep]<seq2>:<end> where start and end
       are 1-based, and the region includes the end position.  [sep] is "-" or ".."

       Specifying  a  sequence  name  alone  will  return the entire sequence, specifying range will return that
       range, and specifying a single coordinate pair, e.g.  <seq>:<start> will return just that base.

       author: Erik Garrison <erik.garrison@bc.edu>