cleanasn(1)
clean up irregularities in NCBI ASN.1 objects
SYNOPSIS
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]
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
- -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Replace unpublished with PMID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)
-
- 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
- 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
- e
-
EMBL
- d
-
DDBJ
- b
-
EMBL or DDBJ
- r
-
RefSeq
- n
-
NCBI
- 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)
AUTHOR
The National Center for Biotechnology Information.
