cleanasn

Langue: en

Version: 337583 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

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).