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

ASN2FSA(1) NCBI Tools User's Manual ASN2FSA(1)

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 Ns
-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.

SEE ALSO

asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).
2016-09-01 NCBI