NAME

       fastahack - indexing and sequence extraction from FASTA files

SYNOPSIS

       fastahack [options] <fasta reference>

DESCRIPTION

       fastahack  is  a  small application for indexing and extracting sequences and subsequences
       from FASTA files.  The included Fasta.cpp library provides a FASTA reader and indexer that
       can  be  embedded into applications which would benefit from directly reading subsequences
       from FASTA files.  The library automatically handles index file generation and use.

       Features:

              FASTA index (.fai) generation for FASTA files

              Sequence extraction

              Subsequence extraction

              Sequence statistics (currently only entropy is provided)

       Sequence and subsequence extraction use fseek64  to  provide  fastest-possible  extraction
       without  RAM-intensive  file  loading  operations.  This makes fastahack a useful tool for
       bioinformaticists who need to quickly extract many subsequences  from  a  reference  FASTA
       sequence.

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

       This software was written by Erik Garrison <erik.garrison@bc.edu>.

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.