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>