path: root/doc/man/cleanasn.1

.TH CLEANASN 1 2016-09-01 NCBI "NCBI Tools User's Manual"
.SH NAME
cleanasn \- clean up irregularities in NCBI ASN.1 objects
.SH SYNOPSIS
.B cleanasn
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIfilename\fP\|]
[\|\fB\-B\fP\ \fIstr\fP\|]
[\|\fB\-C\fP\ \fIstr\fP\|]
[\|\fB\-D\fP\ \fIstr\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-K\fP\ \fIstr\fP\|]
[\|\fB\-L\fP\ \fIfilename\fP\|]
[\|\fB\-M\fP\ \fIfilename\fP\|]
[\|\fB\-N\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIstr\fP\|]
[\|\fB\-P\fP\ \fIstr\fP\|]
[\|\fB\-Q\fP\ \fIstr\fP\|]
[\|\fB\-R\fP\|]
[\|\fB\-S\fP\ \fIstr\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\ \fIstr\fP\|]
[\|\fB\-V\fP\ \fIstr\fP\|]
[\|\fB\-X\fP\ \fIstr\fP\|]
[\|\fB\-Z\fP\ \fIstr\fP\|]
[\|\fB\-a\fP\ \fIstr\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-f\fP\ \fIstr\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-j\fP\ \fIfilename\fP\|]
[\|\fB\-k\fP\ \fIfilename\fP\|]
[\|\fB\-m\fP\ \fIstr\fP\|]
[\|\fB\-n\fP\ \fIpath\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIpath\fP\|]
[\|\fB\-q\fP\ \fIpath\fP\|]
[\|\fB\-r\fP\ \fIpath\fP\|]
[\|\fB\-v\fP\ \fIpath\fP\|]
[\|\fB\-x\fP\ \fIext\fP\|]
.SH DESCRIPTION
\fBcleanasn\fP is a utility program to clean up irregularities in NCBI
ASN.1 objects.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP\ \fIfilename\fP
Accession list file
.TP
\fB\-B\fP\ \fIstr\fP
Branch, per the flags in str:
.RS
.PD 0
.IP c
Has coding regions
.IP d
No coding regions
.IP p
Passes validation
.IP q
Validator errors or rejects
.IP r
Only pop/phy/mut/eco/WGS sets
.IP s
Exclude pop/phy/mut/eco/WGS sets
.IP t
Only nuc\-prot sets
.IP u
Exclude nuc\-prot sets
.IP v
Only segmented sequences
.IP w
Exclude segmented sequences
.PD
.RE
.TP
\fB\-C\fP\ \fIstr\fP
Sequence operations, per the flags in str:
.RS
.PD 0
.IP c
Compress
.IP d
Decompress
.IP v
Virtual gaps inside segmented sequence
.IP s
Convert segmented set to delta sequence
.IP t
Non\-NucProt segmented set to delta sequence
.IP u
Improved non\-NucProt segmented set to delta sequence
.IP g
Raw to delta by assembly gap
.IP m
Merge assembly gap features
.PD
.RE
.TP
\fB\-D\fP\ \fIstr\fP
Clean up descriptors, per the flags in str:
.RS
.PD 0
.IP t
Remove Title
.IP c
Remove Comment
.IP n
Remove Nuc-Prot Set title
.IP e
Remove Pop/Phy/Mut/Eco Set title
.IP m
Remove mRNA title
.IP p
Remove Protein title
.IP a
Title to name
.IP b
AutoDef title or name
.IP x
Prefix title with organism name
.PD
.RE
.TP
\fB\-F\fP\ \fIstr\fP
Clean up features, per the flags in str:
.RS
.PD 0
.IP u
Remove User-objects
.IP d
Remove db_xrefs
.IP e
Remove \fB/evidence\fP and \fB/inference\fP
.IP g
Fuse multi\-interval genes
.IP i
Fuse adjacent\-interval imported features
.IP r
Remove redundant gene xrefs
.IP f
Fuse duplicate features
.IP s
Package features on referenced Bioseq
.IP k
Package coding-region or parts features
.IP z
Delete or update EC numbers
.IP b
Set Best coding\-region reading frame
.IP x
Retranslate coding regions
.IP a
Adjust for missing stop codon
.PD
.RE
.TP
\fB\-K\fP\ \fIstr\fP
Perform a general cleanup, per the flags in str:
.RS
.PD 0
.IP b
BasicSeqEntryCleanup
.IP p
C++ BasicCleanup (via an external utility)
.IP v
AdvancedSeqEntryCleanup
.IP s
SeriousSeqEntryCleanup
.IP x
ExtendedSeqEntryCleanup
.IP g
GpipeSeqEntryCleanup
.IP n
Normalize descriptor order
.IP u
Remove NcbiCleanup User Objects
.IP c
Synchronize genetic Codes
.IP f
CDS partial from translation
.IP e
Impose CDS partials
.IP d
Resynchronize CDS partials
.IP m
Resynchronize mRNA partials
.IP t
Resynchronize Peptide partials
.IP a
Adjust consensus splice
.IP i
Promote to "worst" Seq-ID
.IP r
Reassign local IDs
.IP l
Remove locus
.PD
.RE
.TP
\fB\-L\fP\ \fIfilename\fP
Log file
.TP
\fB\-M\fP\ \fIfilename\fP
Macro file
.TP
\fB\-N\fP\ \fIstr\fP
Clean up links, per the flags in str:
.RS
.PD 0
.IP o
Link CDS mRNA by Overlap
.IP p
Link CDS mRNA by Product
.IP l
Link CDS mRNA by Label and Location
.IP r
Reassign feature IDs
.IP m
Merge colliding feature IDs
.IP f
Fix missing reciprocal feature IDs
.IP c
Clear feature IDs
.PD
.RE
.TP
\fB\-O\fP\ \fIstr\fP
Missing prot\-ref name
.TP
\fB\-P\fP\ \fIstr\fP
Publication options:
.RS
.PD 0
.IP a
Remove All publications
.IP s
Remove Serial number
.IP f
Remove Figure, numbering, and name
.IP r
Remove Remark
.IP u
Update PMID-only publication
.IP j
Lookup ISO Journal title abbreviation
.IP m
Merge identical publication features
.IP #
Replace unpublished with PMID
.PD
.RE
.TP
\fB\-Q\fP\ \fIstr\fP
Report:
.RS
.PD 0
.IP c
Record count
.IP r
ASN.1 BSEC report
.IP s
ASN.1 SSEC report
.IP n
NORM vs. SSEC report
.IP e
PopPhyMutEco AutoDef report
.IP o
Overlap report
.IP l
Latitude-longitude country diff
.IP d
Log SSEC differences
.IP g
GenBank SSEC diff
.IP f
asn2gb/asn2flat diff
.IP h
Seg-to-delta GenBank diff
.IP v
Validator SSEC diff
.IP m
Modernize Gene/RNA/PCR
.IP u
Unpublished Pub lookup
.IP p
Published Pub lookup
.IP j
Unindexed Journal report
.IP t
tRNA anticodon report
.IP w
Component offset report
.IP x
Custom scan
.PD
.RE
.TP
\fB\-R\fP
Remote fetching from ID (NCBI sequence databases)
.TP
\fB\-S\fP\ \fIstr\fP
Selective difference filter (capital letters skip)
.RS
.PD 0
.IP s
SSEC
.IP b
BSEC
.IP A
Author
.IP p
Publication
.IP l
Location
.IP r
RNA
.IP q
Qualifier sort order
.IP g
Genbank block
.IP k
Package CdRegion or parts features
.IP m
Move publication
.IP o
Leave duplicate Bioseq publication
.IP d
Automatic definition line
.IP e
Pop/Phy/Mut/Eco Set definition line
.PD
.RE
.TP
\fB\-T\fP
Taxonomy Lookup
.TP
\fB\-U\fP\ \fIstr\fP
Modernize, per the flags in str:
.RS
.PD 0
.IP g
Genes
.IP r
RNA
.IP p
PCR Primers
.PD
.RE
.TP
\fB\-V\fP\ \fIstr\fP
Remove features by validator severity:
.RS
.PD 0
.IP r
Reject
.IP e
Error
.IP w
Warning
.IP i
Info
.PD
.RE
.TP
\fB\-X\fP\ \fIstr\fP
Miscellaneous options, per str:
.RS
.PD 0
.IP d
Automatic definition line
.IP s
Automatic definition line with Source qualifiers
.IP e
Pop/Phy/Mut/Eco Set definition line
.IP n
Instantiate NC title
.IP m
Instantiate NM titles
.IP x
Special XM titles
.IP p
Instantiate Protein titles
.IP g
GPipe instantiate titles
.IP c
Create mRNAs for coding sequences
.IP f
Fix reciprocal protein_id/transcript_id
.IP v
Revert preRNA or ncRNA transcript_id
.IP t
Parse anticodon from Sequence
.IP b
Batch cleanup of multireader output
.IP z
Wrap SegSet with NucProt set
.IP w
GFF/WGS genome cleanup
.PD
.RE
.TP
\fB\-Z\fP\ \fIstr\fP
Remove indicated User-object
.TP
\fB\-a\fP\ \fIstr\fP
ASN.1 type
.RS
.PD 0
.IP a
Any (default)
.IP e
Seq-entry
.IP b
Bioseq
.IP s
Bioseq-set
.IP m
Seq-submit
.IP t
Batch Bioseq-set
.IP u
Batch Seq-submit
.PD
.RE
.TP
\fB\-b\fP
Input ASN.1 is Binary
.TP
\fB\-c\fP
Input ASN.1 is Compressed
.TP
\fB\-d\fP\ \fIstr\fP
Source database
.RS
.PD 0
.IP a
Any (default)
.IP g
GenBank
.IP e
EMBL
.IP d
DDBJ
.IP b
EMBL or DDBJ
.IP i
INSD
.IP r
RefSeq
.IP n
NCBI
.IP x
Exclude EMBL/DDBJ
.IP y
Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts
.PD
.RE
.TP
\fB\-f\fP\ \fIstr\fP
Substring filter
.TP
\fB\-i\fP\ \fIfilename\fP
Single input file (defaults to stdin)
.TP
\fB\-j\fP\ \fIfilename\fP
First filename
.TP
\fB\-k\fP\ \fIfilename\fP
Last filename
.TP
\fB\-m\fP\ \fIstr\fP
Flatfile mode:
.RS
.PD 0
.IP r
Release
.IP e
Entrez
.IP s
Sequin
.IP d
Dump
.PD
.RE
.TP
\fB\-n\fP\ \fIpath\fP
\fBasn2flat\fP executable (default is \fB/netopt/ncbi_tools/bin/asn2flat\fP)
.TP
\fB\-o\fP\ \fIfilename\fP
Single output file (defaults to stdout)
.TP
\fB\-p\fP\ \fIpath\fP
Process all matching files in \fIpath\fP
.TP
\fB\-q\fP\ \fIpath\fP
\fBffdiff\fP executable (default is \fB/netopt/genbank/subtool/bin/ffdiff\fP)
.TP
\fB\-r\fP\ \fIpath\fP
Path for results
.TP
\fB\-v\fP\ \fIpath\fP
\fBasnval\fP executable (default is \fB/netopt/ncbi_tools/bin/asnval\fP)
.TP
\fB\-x\fP\ \fIext\fP
File selection suffix for use with \fB\-p\fP (defaults to \fB.ent\fP)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR asndisc (1),
.BR asnval (1),
.BR sequin (1).