man asn2fsa (Commandes) - convert biological sequence data from ASN.1 to FASTA
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
- any (autodetected; default)
- 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.