NPS2GPS(1) General Commands Manual NPS2GPS(1)NAME
nps2gps - convert nucleotide-protein sets to ASN.1 genomic product sets
SYNOPSIS
nps2gps [-] [-D] [-F] [-G str] [-L] [-N] [-P] [-Q] [-R] [-T] [-U] [-f str] [-i filename] [-o filename] [-p path] [-r path] [-x str]
DESCRIPTION
nps2gps converts NCBI Bioseq-sets from simple nucleotide-protein sets to full genomic product sets complete with mRNA transcripts, which it
outputs as text ASN.1.
OPTIONS
A summary of options is included below.
- Print usage message
-D RefSeq mRNA Titles
-F Map by Feature ID
-G str General ID database name
-L Lock components in advance
-N Promote Non-coding RNAs
-P mRNA ID from Protein
-Q Special mRNA titles
-R Enable Remote fetching from ID
-T Map by Transcript ID
-U Remove Unnecessary gene cross-references
-f str Substring filter
-i filename
Single input file (default = stdin)
-o filename
Single output file (default = stdout)
-p path
Path to files for batch conversion
-r path
Path for results of batch conversion
-x str File selection suffix for batch conversion (default = .ent)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).
NCBI Tools User's Manual 2012-06-24 NPS2GPS(1)
Check Out this Related Man Page
ASN2ALL(1) NCBI Tools User's Manual ASN2ALL(1)NAME
asn2all - generate reports from ASN.1 biological data
SYNOPSIS
asn2all [-] [-A acc] [-F filename] [-G] [-J n] [-K n] [-M] [-T] [-X] [-a type] [-b] [-c] [-d path] [-f format] [-h] [-i filename] [-k] [-l]
[-n policy] [-o filename] [-p path] [-r] [-v filename] [-x ext]
DESCRIPTION
asn2all is primarily intended for generating reports from the binary ASN.1 Bioseq-set release files downloaded from the NCBI ftp site
(ncbi-asn1 directory). It can produce GenBank and GenPept flatfiles, FASTA sequence files, INSDSet structured XML, TinySeq XML, and
Sequin-style 5-column feature tables.
The release files (which have the extension .aso.gz) should be uncompressed with gunzip(1), resulting in files with the extension .aso.
For example, gbpri1.aso is the first file in the primate division, and the command
gunzip gbpri1.aso.gz
will result in gbpri1.aso being created. The original gbpri1.aso.gz file is removed after successful decompression.
In asn2all, the name of the file to be processed is specified by the -i command line argument. Use -a t to indicate that it is a release
file and -b to indicate that it is binary ASN.1. A text ASN.1 file obtained from Entrez can be processed by using -a a instead of -a t -b.
Nucleotide and protein records can be processed simultaneously. Use the -o argument to indicate the nucleotide output file, and the -v
argument for the protein output file.
The -f argument determines the format to be generated, and is documented in more detail (along with other options) in the following sec-
tion.
OPTIONS
A summary of options is included below.
- Print usage message
-A accession
Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1
enables fetching of external features
-F filename
Accession Filter file
-G Relaxed Genome Mapping
-J n Seq-loc from
-K n Seq-loc to
-M Seq-loc Minus strand
-T Use Threads
-X EXtended qualifier output
-a type
Input ASN.1 type:
a Automatic (default)
c Catenated
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 indexed binary ASN.1 Data
-f format
Output Format:
g GenBank/GenPept (default)
m GenBank Master Style
f FASTA
d CDS FASTA
e Gene FASTA
t Sequin-style 5-column feature table
y TinySet XML (akin to FASTA)
s INSDSet XML (akin to GenBank/GenPept)
a structurally equivalent text ASN.1
x structurally equivalent XML
c cache components
-h Display extra Help message
-i filename
Input file name (standard input by default)
-k Enable local fetching
-l Lock components in advance
-n policy
Near FASTA policy:
a All
n Near only (default)
f Far only
-o filename
Nucleotide Output file name
-p path
Path to files
-r Enable Remote fetching
-v filename
Protein output file name
-x ext File selection suffix when working with entire directories. (default is .aso)
EXAMPLES
The command
asn2all -i gbpri1.aso -a t -b -f g -o gbpri1.nuc -v gbpri1.prt
will generate GenBank and GenPept reports from gbpri1.aso.
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1), asndhuff(1), gene2xml(1), gunzip(1).
NCBI 2012-06-24 ASN2ALL(1)