cleanasn(1)

clean up irregularities in NCBI ASN.1 objects

Section 1 ncbi-tools-bin bookworm source

Description

CLEANASN

NAME

cleanasn - clean up irregularities in NCBI ASN.1 objects

SYNOPSIS

cleanasn [-] [-A filename] [-B str] [-C str] [-D str] [-F str] [-K str] [-L filename] [-M filename] [-N str] [-O str] [-P str] [-Q str] [-R] [-S str] [-T] [-U str] [-V str] [-X str] [-Z str] [-a str] [-b] [-c] [-d str] [-f str] [-i filename] [-j filename] [-k filename] [-m str] [-n path] [-o filename] [-p path] [-q path] [-r path] [-v path] [-x ext]

DESCRIPTION

cleanasn is a utility program to clean up irregularities in NCBI ASN.1 objects.

OPTIONS

A summary of options is included below.

Print usage message

-A filename

Accession list file

-B str

Branch, per the flags in str:

	c		Has coding regions
	d		No coding regions
	p		Passes validation
	q		Validator errors or rejects
	r		Only pop/phy/mut/eco/WGS sets
	s		Exclude pop/phy/mut/eco/WGS sets
	t		Only nuc-prot sets
	u		Exclude nuc-prot sets
	v		Only segmented sequences
	w		Exclude segmented sequences
	x		Only segmented proteins
	y		Exclude segmented proteins

-C str

Sequence operations, per the flags in str:

	c		Compress
	d		Decompress
	l		Recalculated segmented sequence length
	v		Virtual gaps inside segmented sequence
	s		Convert segmented set to delta sequence
	t		Non-NucProt segmented set to delta sequence
	u		Improved non-NucProt segmented set to delta sequence
	g		Raw to delta by assembly gap
	m		Merge assembly gap features

-D str

Clean up descriptors, per the flags in str:

	t		Remove Title
	c		Remove Comment
	n		Remove Nuc-Prot Set title
	e		Remove Pop/Phy/Mut/Eco Set title
	m		Remove mRNA title
	p		Remove Protein title
	a		Title to name
	b		AutoDef title or name
	x		Prefix title with organism name

-F str

Clean up features, per the flags in str:

	u		Remove User-objects
	d		Remove db_xrefs
	e		Remove /evidence and /inference
	g		Fuse multi-interval genes
	i		Fuse adjacent-interval imported features
	r		Remove redundant gene xrefs
	f		Fuse duplicate features
	s		Package features on referenced Bioseq
	k		Package coding-region or parts features
	z		Delete or update EC numbers
	b		Set Best coding-region reading frame
	x		Retranslate coding regions
	a		Adjust for missing stop codon

-K str

Perform a general cleanup, per the flags in str:

	b		BasicSeqEntryCleanup
	p		C++ BasicCleanup (via an external utility)
	v		AdvancedSeqEntryCleanup
	s		SeriousSeqEntryCleanup
	x		ExtendedSeqEntryCleanup
	g		GpipeSeqEntryCleanup
	n		Normalize descriptor order
	u		Remove NcbiCleanup User Objects
	c		Synchronize genetic Codes
	f		CDS partial from translation
	e		Impose CDS partials
	d		Resynchronize CDS partials
	m		Resynchronize mRNA partials
	t		Resynchronize Peptide partials
	a		Adjust consensus splice
	i		Promote to "worst" Seq-ID
	r		Reassign local IDs
	l		Remove locus

-L filename

Log file

-M filename

Macro file

-N str

Clean up links, per the flags in str:

	o		Link CDS mRNA by Overlap
	p		Link CDS mRNA by Product
	l		Link CDS mRNA by Label and Location
	r		Reassign feature IDs
	m		Merge colliding feature IDs
	f		Fix missing reciprocal feature IDs
	c		Clear feature IDs

-O str

Missing prot-ref name

-P str

Publication options:

	a		Remove All publications
	s		Remove Serial number
	f		Remove Figure, numbering, and name
	r		Remove Remark
	u		Update PMID-only publication
	j		Lookup ISO Journal title abbreviation
	m		Merge identical publication features
	#		Replace unpublished with PMID

-Q str

Report:

	c		Record count
	r		ASN.1 BSEC report
	s		ASN.1 SSEC report
	n		NORM vs. SSEC report
	e		PopPhyMutEco AutoDef report
	o		Overlap report
	l		Latitude-longitude country diff
	d		Log SSEC differences
	g		GenBank SSEC diff
	f		asn2gb/asn2flat diff
	h		Seg-to-delta GenBank diff
	v		Validator SSEC diff
	m		Modernize Gene/RNA/PCR
	u		Unpublished Pub lookup
	p		Published Pub lookup
	j		Unindexed Journal report
	t		tRNA anticodon report
	w		Component offset report
	x		Custom scan
	-R

Remote fetching from ID (NCBI sequence databases)

-S str

Selective difference filter (capital letters skip)

	s		SSEC
	b		BSEC
	A		Author
	p		Publication
	l		Location
	r		RNA
	q		Qualifier sort order
	g		Genbank block
	k		Package CdRegion or parts features
	m		Move publication
	o		Leave duplicate Bioseq publication
	d		Automatic definition line
	e		Pop/Phy/Mut/Eco Set definition line
	-T

Taxonomy Lookup

-U str

Modernize, per the flags in str:

	g		Genes
	r		RNA
	p		PCR Primers

-V str

Remove features by validator severity:

	r		Reject
	e		Error
	w		Warning
	i		Info

-X str

Miscellaneous options, per str:

	d		Automatic definition line
	s		Automatic definition line with Source qualifiers
	e		Pop/Phy/Mut/Eco Set definition line
	n		Instantiate NC title
	m		Instantiate NM titles
	x		Special XM titles
	p		Instantiate Protein titles
	g		GPipe instantiate titles
	c		Create mRNAs for coding sequences
	f		Fix reciprocal protein_id/transcript_id
	v		Revert preRNA or ncRNA transcript_id
	t		Parse anticodon from Sequence
	b		Batch cleanup of multireader output
	z		Wrap SegSet with NucProt set
	w		GFF/WGS genome cleanup

-Z str

Remove indicated User-object

-a str

ASN.1 type

	a		Any (default)
	e		Seq-entry
	b		Bioseq
	s		Bioseq-set
	m		Seq-submit
	t		Batch Bioseq-set
	u		Batch Seq-submit
	-b

Input ASN.1 is Binary

-c

Input ASN.1 is Compressed

-d str

Source database

	a		Any (default)
	g		GenBank
	e		EMBL
	d		DDBJ
	b		EMBL or DDBJ
	i		INSD
	r		RefSeq
	n		NCBI
	x		Exclude EMBL/DDBJ
	y		Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts

-f str

Substring filter

-i filename

Single input file (defaults to stdin)

-j filename

First filename

-k filename

Last filename

-m str

Flatfile mode:

	r		Release
	e		Entrez
	s		Sequin
	d		Dump

-n path

asn2flat executable (default is /netopt/ncbi_tools/bin/asn2flat)

-o filename

Single output file (defaults to stdout)

-p path

Process all matching files in path

-q path

ffdiff executable (default is /netopt/genbank/subtool/bin/ffdiff)

-r path

Path for results

-v path

asnval executable (default is /netopt/ncbi_tools/bin/asnval)

-x ext

File selection suffix for use with -p (defaults to .ent)

AUTHOR

The National Center for Biotechnology Information.