This is the command cleanasn that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
cleanasn - clean up irregularities in NCBI ASN.1 objects
SYNOPSIS
cleanasn [-] [-A filename] [-C str] [-D str] [-F str] [-K str] [-L filename] [-M filename]
[-N str] [-P str] [-Q str] [-R] [-S str] [-T] [-U str] [-V str] [-X str] [-Z str] [-a str]
[-b] [-c] [-d str] [-f str] [-i filename] [-j filename] [-k filename] [-m str] [-n path]
[-o filename] [-p path] [-q path] [-r path] [-v 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
-A filename
Accession list file
-C str Sequence operations, per the flags in str:
c Compress
d Decompress
v Virtual gaps inside segmented sequence
s Convert segmented set to delta sequence
-D str Clean up descriptors, per the flags in str:
t Remove Title
c Remove Comment
n Remove Nuc-Prot Set title
e Remove Pop/Phy/Mut/Eco Set title
m Remove mRNA title
p Remove Protein title
-F str Clean up features, per the flags in str:
u Remove User-objects
d Remove db_xrefs
e Remove /evidence and /inference
r Remove redundant gene xrefs
f Fuse duplicate features
k Package coding-region or parts features
z Delete or update EC numbers
-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
c Synchronize genetic Codes
d Resynchronize CDS partials
m Resynchronize mRNA partials
t Resynchronize Peptide partials
a Adjust consensus splice
i Promote to "worst" Seq-ID
-L filename
Log file
-M filename
Macro file
-N str Clean up links, per the flags in str:
o Link CDS mRNA by Overlap
p Link CDS mRNA by Product
r Reassign feature IDs
f Fix missing reciprocal feature IDs
c Clear feature IDs
-P Publication options:
a Remove All publications
s Remove Serial number
f Remove Figure, numbering, and name
r Remove Remark
u Update PMID-only publication
# Replace unpublished with PMID
-Q str Report:
c Record count
r ASN.1 BSEC report
s ASN.1 SSEC report
n NORM vs. SSEC report
e PopPhyMutEco AutoDef report
o Overlap report
l Latitude-longitude country diff
d Log SSEC differences
g GenBank SSEC diff
f asn2gb/asn2flat diff
h Seg-to-delta GenBank diff
v Validator SSEC diff
m Modernize Gene/RNA/PCR
u Unpublished Pub lookup
p Published Pub lookup
j Unindexed Journal report
x Custom scan
-R Remote fetching from ID (NCBI sequence databases)
-S str Selective difference filter (capital letters skip)
s SSEC
b BSEC
A Author
p Publication
l Location
r RNA
q Qualifier sort order
g Genbank block
k Package CdRegion or parts features
m Move publication
o Leave duplicate Bioseq publication
d Automatic definition line
e Pop/Phy/Mut/Eco Set definition line
-T Taxonomy Lookup
-U str Modernize, per the flags in str:
g Genes
r RNA
p PCR Primers
-V str Remove features by validator severity:
r Reject
e Error
w Warning
i Info
-X str Miscellaneous options, per str:
d Automatic definition line
e Pop/Phy/Mut/Eco Set definition line
n Instantiate NC title
m Instantiate NM titles
x Special XM titles
p Instantiate Protein titles
c Create mRNAs for coding sequences
f Fix reciprocal protein_id/transcript_id
-Z str Remove indicated User-object
-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
-d str Source database
a Any (default)
g GenBank
e EMBL
d DDBJ
b EMBL or DDBJ
r RefSeq
n NCBI
v Only segmented sequences
w Exclude segmented sequences
x Exclude EMBL/DDBJ
y Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts
-f str Substring filter
-i filename
Single input file (defaults to stdin)
-j filename
First filename
-k filename
Last filename
-m str Flatfile mode:
r Release
e Entrez
s Sequin
d Dump
-n path
asn2flat executable (default is /netopt/ncbi_tools/bin/asn2flat)
-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
-v path
asnval executable (default is /netopt/ncbi_tools/bin/asnval)
-x ext File selection suffix for use with -p (defaults to .ent)
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