Provided by: libfastahack0_0.0+git20160702.bbc645f+dfsg-6_amd64
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. 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.
-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 <email@example.com>. This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.