CLEANASN(1)
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).