bionic (1) fastahack.1.gz

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.