asn2fsa (1)

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\|] [\|-z\|]

asn2fsa converts biological sequence data from ASN.1 to FASTA.

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:

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

The National Center for Biotechnology Information.

asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).