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


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

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