Provided by: ncbi-tools-bin_6.1.20170106+dfsg1-9_amd64 
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.
SEE ALSO
asndisc(1), asnval(1), sequin(1).