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cleanasn

NAME

cleanasn - clean up irregularities in NCBI ASN.1 objects

SYNOPSIS

cleanasn [-] [-F str] [-K str] [-N str] [-R] [-T] [-a str] [-b] [-c] [-f str] [-i filename] [-l filename] [-o filename] [-p 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

-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

s

SeriousSeqEntryCleanup

-N str

Clean up links, per the flags in str:

o

LinkCDSmRNAbyOverlap

p

LinkCDSmRNAbyProduct

r

ReassignFeatureIDs

c

ClearFeatureIDs

-R

Remote fetching from ID (NCBI sequence databases)

-T

Taxonomy Lookup

-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)

-l filename

Log file

-o filename

Single output file (defaults to stdout)

-p path

Process all matching files in path

-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).