NAME
asn2fsa - convert biological sequence data from ASN.1 to FASTA
SYNOPSIS
asn2fsa [-] [-A acc] [-D] [-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] [-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
-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]
-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).