Man page - asn2fsa(1)

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Manual

ASN2FSA

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO

NAME

asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS

asn2fsa [ - ] [ -A acc ] [ -D ] [ -E ] [ -H ] [ -L filename ] [ -T ] [ -a type ] [ -b ] [ -c ] [ -d path ] [ -e N ] [ -f path ] [ -g ] [ -h filename ] [ -i filename ] [ -k ] [ -l ] [ -m ] [ -o filename ] [ -p path ] [ -q filename ] [ -r ] [ -s ] [ -u ] [ -v filename ] [ -x str ] [ -y ] [ -z ]

DESCRIPTION

asn2fsa converts biological sequence data from ASN.1 to FASTA.

OPTIONS

A summary of options is included below.

	-		Print usage message
	-A acc		Accession to fetch
	-D		Use Dash for Gap
	-E		Extended Seq-ids
	-H		HTML spans

-L filename

Log file

-T

Use Threads

-a type

Input ASN.1 type:

	a		Automatic (default)
	z		Any
	e		Seq-entry
	b		Bioseq
	s		Bioseq-set
	m		Seq-submit
	t		batch processing (suitable for official releases; autodetects specific type)
	-b

Bioseq-set is Binary

-c

Bioseq-set is Compressed

-d path

Path to ReadDB Database

-e N

Line length (70 by default; may range from 10 to 120)

-f path

Path to indexed FASTA data

-g

Expand delta gaps into N s

-h filename

Far component cache output file name

-i filename

Single input file (standard input by default)

	-k		Local fetching
	-l		Lock components in advance
	-m		Master style for near segmented sequences

-o filename

Nucleotide Output file name

-p path

Path to ASN.1 Files

-q filename

Quality score output file name

	-r		Remote fetching from NCBI
	-s		Far genomic contig for quality scores
	-u		Recurse

-v filename

Protein output file name

	-x str		File selection substring ( .ent by default) [String]
	-y		Debugging
	-z		Print quality score gap as -1

AUTHOR

The National Center for Biotechnology Information.