.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH FASTAHACK "1" "December 2020" "fastahack 1.0.0+dfsg-7" "User Commands"
.SH NAME
fastahack \- fastahack - indexing and extracting sequences and subsequences from FASTA files
.SH DESCRIPTION
usage: fastahack [options] <fasta reference>
.SS "options:"
.TP
\fB\-i\fR, \fB\-\-index\fR
generate fasta index <fasta reference>.fai
.TP
\fB\-r\fR, \fB\-\-region\fR REGION
print the specified region
.TP
\fB\-c\fR, \fB\-\-stdin\fR
read a stream of line\-delimited region specifiers on stdin
and print the corresponding sequence for each on stdout
.TP
\fB\-e\fR, \fB\-\-entropy\fR
print the shannon entropy of the specified region
.TP
\fB\-d\fR, \fB\-\-dump\fR
print the fasta file in the form 'seq_name <tab> sequence'
.PP
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 ".."
.PP
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.
.PP
author: Erik Garrison <erik.garrison@bc.edu>