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).