NAME
cleanasn - clean up irregularities in NCBI ASN.1 objects
SYNOPSIS
cleanasn [-] [-D str] [-F str] [-K str] [-L filename] [-M filename]
[-N str] [-P] [-Q str] [-R] [-T] [-U str] [-X str] [-a str] [-b] [-c]
[-f str] [-i filename] [-m str] [-o filename] [-p path] [-q path]
[-r 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
-D str Clean up descriptors, per the flags in str:
t Remove Title
-F str Clean up features, per the flags in str:
u Remove User-objects
d Remove db_xrefs
r Remove redundant gene xrefs
-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
-L filename
Log file
-M filename
Macro file
-N str Clean up links, per the flags in str:
o LinkCDSmRNAbyOverlap
p LinkCDSmRNAbyProduct
r ReassignFeatureIDs
c ClearFeatureIDs
-P Publication Lookup
-Q str Report:
r ASN.1 BSEC/SSEC Report
g GenBank SSEC Diff
m Modernization
-R Remote fetching from ID (NCBI sequence databases)
-T Taxonomy Lookup
-U str Modernize, per the flags in str:
g Genes
r RNA
p PCR Primers
-X str Miscellaneous options, per str:
d Automatic definition line
-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
-f str Substring filter
-i filename
Single input file (defaults to stdin)
-m str Flatfile mode:
r Release
e Entrez
s Sequin
d Dump
-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
-x ext File selection suffix for use with -p (defaults to .ent)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
asnval (1), sequin (1).