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.
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- |
Print usage message |
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-A acc |
Accession to fetch |
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-D |
Use Dash for Gap |
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-E |
Extended Seq-ids |
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-H |
HTML spans |
-L filename
Log file
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-T |
Use Threads |
-a type
Input ASN.1 type:
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a |
Automatic (default) | ||
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z |
Any | ||
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e |
Seq-entry | ||
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b |
Bioseq | ||
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s |
Bioseq-set | ||
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m |
Seq-submit | ||
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t |
batch processing (suitable for official releases; autodetects specific type) | ||
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-b |
Bioseq-set is Binary
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-c |
Bioseq-set is Compressed |
-d path
Path to ReadDB Database
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-e N |
Line length (70 by default; may range from 10 to 120) |
-f path
Path to indexed FASTA data
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-g |
Expand delta gaps into Ns |
-h filename
Far component cache output file name
-i filename
Single input file (standard input by default)
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-k |
Local fetching |
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-l |
Lock components in advance |
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-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
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-r |
Remote fetching from NCBI |
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-s |
Far genomic contig for quality scores |
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-u |
Recurse |
-v filename
Protein output file name
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-x str |
File selection substring (.ent by default) [String] | ||
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-y |
Debugging | ||
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-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).