asn2fsa1
Convert biological sequence data from asn.1 to fasta
Usage
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]
Overview
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 (
.entby default) [String]
-
-y -
Debugging
-
-z -
Print quality score gap as -1
Releases
10 releases since Debian 4.0 (Etch); the text changed 4 times.
-E since Debian 7 (Wheezy);
-H since Debian 7 (Wheezy);
-y since Debian 9 (Stretch).