ASN2FSA(1)

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; autode

tects 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).

NCBI 2009-07-31 ASN2FSA(1)