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

-C str: Sequence operations, per the flags in str:

c: Compress
d: Decompress
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.

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

AUTHOR

SEE ALSO