asn2fsa - convert biological sequence data from ASN.1 to FASTA
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]
asn2fsa converts biological sequence data from ASN.1 to FASTA.
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
The National Center for Biotechnology Information.
asn2all(1),
asn2asn(1),
asn2ff(1),
asn2gb(1),
asn2xml(1),
asndhuff(1).