Provided by: libfastahack0_0.0+git20160702.bbc645f+dfsg-6_amd64 bug


       fastahack - indexing and sequence extraction from FASTA files


       fastahack [options] <fasta reference>


       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.


              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


       -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.


       This software was written by Erik Garrison <>.

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