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.TH CLEANASN 1 2006-05-29 NCBI "NCBI Tools User's Manual"
.SH NAME
cleanasn \- clean up irregularities in NCBI ASN.1 Seq-entry objects
.SH SYNOPSIS
.B cleanasn
[\|\fB\-\fP\|]
[\|\fB\-R\fP\|]
[\|\fB\-c\fP\ \fIstr\fP\|]
[\|\fB\-f\fP\ \fIstr\fP\|]
[\|\fB\-l\fP\ \fIstr\fP\|]
\fB\-p\fP\ \fIpath\fP
[\|\fB\-r\fP\ \fIpath\fP\|]
[\|\fB\-t\fP\|]
.SH DESCRIPTION
\fBcleanasn\fP is a utility program to clean up irregularities in NCBI
ASN.1 Seq-entry or Seq-submit objects.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-R\fP
Enable remote fetching from NCBI's ID database
.TP
\fB\-c\fP\ \fIstr\fP
Perform general clean-ups, per the flags in \fIstr\fP:
.RS
.PD 0
.IP b
BasicSeqEntryCleanup
.IP s
SeriousSeqEntryCleanup
.PD
.RE
.TP
\fB\-f\fP\ \fIstr\fP
Remove extraneous features, per the flags in \fIstr\fP:
.RS
.PD 0
.IP u
Remove User objects
.IP d
Remove Database cross-references
.IP r
Remove Redundant gene cross-references
.PD
.RE
.TP
\fB\-l\fP\ \fIstr\fP
Link related features, per the flags in \fIstr\fP:
.RS
.PD 0
.IP o
LinkCDSmRNAbyOverlap
.IP p
LinkCDSmRNAbyProduct
.IP r
ReassignFeatureIDs
.PD
.RE
.TP
\fB\-p\fP\ \fIpath\fP
Path to input files
.TP
\fB\-r\fP\ \fIpath\fP
Path for Results (changes are otherwise made in place)
.TP
\fB\-t\fP
Enable Taxonomy lookup
.SH AUTHOR
The National Center for Biotechnology Information.
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