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ASN2FSA

ASN2FSA

Section: NCBI Tools User's Manual (1) Updated: 2009-07-31
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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
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]
-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).


 

Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO

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Time: 21:09:27 GMT, April 16, 2011