Man page - fastahack(1)

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Package:  fastahack
apt-get install fastahack

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• fastahack(1)
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• fastahack

Manual

FASTAHACK

NAME
DESCRIPTION
options:

---

NAME

fastahack - fastahack - indexing and extracting sequences and subsequences from FASTA files

DESCRIPTION

usage: fastahack [options] <fasta reference>

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: Erik Garrison <erik.garrison@bc.edu>

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