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cleanasn - clean up irregularities in NCBI ASN.1 objects


cleanasn [-] [-A filename] [-C str] [-D str] [-F str] [-K str] [-L filename] [-M filename]
[-N 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]


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


A summary of options is included below.

- Print usage message

-A filename
Accession list file

-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

-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

-F str Clean up features, per the flags in str:
u Remove User-objects
d Remove db_xrefs
e Remove /evidence and /inference
r Remove redundant gene xrefs
f Fuse duplicate features
k Package coding-region or parts features
z Delete or update EC numbers

-K str Perform a general cleanup, per the flags in str:
b BasicSeqEntryCleanup
p C++ BasicCleanup (via an external utility)
s SeriousSeqEntryCleanup
g GpipeSeqEntryCleanup
n Normalize descriptor order
u Remove NcbiCleanup User Objects
c Synchronize genetic Codes
d Resynchronize CDS partials
m Resynchronize mRNA partials
t Resynchronize Peptide partials
a Adjust consensus splice
i Promote to "worst" Seq-ID

-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
r Reassign feature IDs
f Fix missing reciprocal feature IDs
c Clear feature IDs

-P Publication options:
a Remove All publications
s Remove Serial number
f Remove Figure, numbering, and name
r Remove Remark
u Update PMID-only publication
# Replace unpublished with PMID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u Unpublished Pub lookup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
x Custom scan

-R Remote fetching from ID (NCBI sequence databases)

-S str Selective difference filter (capital letters skip)
A Author
p Publication
l Location
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
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
e Pop/Phy/Mut/Eco Set definition line
n Instantiate NC title
m Instantiate NM titles
x Special XM titles
p Instantiate Protein titles
c Create mRNAs for coding sequences
f Fix reciprocal protein_id/transcript_id

-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 Processing [String]

-b Input ASN.1 is Binary

-c Input ASN.1 is Compressed

-d str Source database
a Any (default)
g GenBank
r RefSeq
v Only segmented sequences
w Exclude segmented sequences
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)

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