.TH ASN2FSA 1 2016-09-01 NCBI "NCBI Tools User's Manual"
.SH NAME
asn2fsa \- convert biological sequence data from ASN.1 to FASTA
.SH SYNOPSIS
.B asn2fsa
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIacc\fP\|]
[\|\fB\-D\fP\|]
[\|\fB\-E\fP\|]
[\|\fB\-H\fP\|]
[\|\fB\-L\fP\ \fIfilename\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-a\fP\ \fItype\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\ \fIpath\fP\|]
[\|\fB\-e\fP\ \fIN\fP\|]
[\|\fB\-f\fP\ \fIpath\fP\|]
[\|\fB\-g\fP\|]
[\|\fB\-h\fP\ \fIfilename\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-k\fP\|]
[\|\fB\-l\fP\|]
[\|\fB\-m\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIpath\fP\|]
[\|\fB\-q\fP\ \fIfilename\fP\|]
[\|\fB\-r\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-u\fP\|]
[\|\fB\-v\fP\ \fIfilename\fP\|]
[\|\fB\-x\fP\ \fIstr\fP\|]
[\|\fB\-y\fP\|]
[\|\fB\-z\fP\|]
.SH DESCRIPTION
\fBasn2fsa\fP converts biological sequence data from ASN.1 to FASTA.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP\ \fIacc\fP
Accession to fetch
.TP
\fB\-D\fP
Use Dash for Gap
.TP
\fB\-E\fP
Extended Seq-ids
.TP
\fB\-H\fP
HTML spans
.TP
\fB\-L\fP\ \fIfilename\fP
Log file
.TP
\fB\-T\fP
Use Threads
.TP
\fB\-a\fP\ \fItype\fP
Input ASN.1 type:
.RS
.PD 0
.IP a
Automatic (default)
.IP z
Any
.IP e
Seq-entry
.IP b
Bioseq
.IP s
Bioseq-set
.IP m
Seq-submit
.IP t
batch processing (suitable for official releases; autodetects specific type)
.PD
.RE
.TP
\fB\-b\fP
Bioseq-set is Binary
.TP
\fB\-c\fP
Bioseq-set is Compressed
.TP
\fB\-d\fP\ \fIpath\fP
Path to ReadDB Database
.TP
\fB\-e\fP\ \fIN\fP
Line length (70 by default; may range from 10 to 120)
.TP
\fB\-f\fP\ \fIpath\fP
Path to indexed FASTA data
.TP
\fB\-g\fP
Expand delta gaps into \fBN\fPs
.TP
\fB\-h\fP\ \fIfilename\fP
Far component cache output file name
.TP
\fB\-i\fP\ \fIfilename\fP
Single input file (standard input by default)
.TP
\fB\-k\fP
Local fetching
.TP
\fB\-l\fP
Lock components in advance
.TP
\fB\-m\fP
Master style for near segmented sequences
.TP
\fB\-o\fP\ \fIfilename\fP
Nucleotide Output file name
.TP
\fB\-p\fP\ \fIpath\fP
Path to ASN.1 Files
.TP
\fB\-q\fP\ \fIfilename\fP
Quality score output file name
.TP
\fB\-r\fP
Remote fetching from NCBI
.TP
\fB\-s\fP
Far genomic contig for quality scores
.TP
\fB\-u\fP
Recurse
.TP
\fB\-v\fP\ \fIfilename\fP
Protein output file name
.TP
\fB\-x\fP\ \fIstr\fP
File selection substring (\fB.ent\fP by default) [String]
.TP
\fB\-y\fP
Debugging
.TP
\fB\-z\fP
Print quality score gap as \-1
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR asn2all (1),
.BR asn2asn (1),
.BR asn2ff (1),
.BR asn2gb (1),
.BR asn2xml (1),
.BR asndhuff (1).