NAME¶

asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS¶

asn2fsa [-] [-A acc] [-D] [-E] [-H] [-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] [-y] [-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

-E

Extended Seq-ids

-H

HTML spans

-L filename

Log file

-T

Use Threads

-a type

Input ASN.1 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]

-y

Debugging

-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).