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.

SEE ALSO