asn2gb(1) [debian man page]
ASN2GB(1) NCBI Tools User's Manual ASN2GB(1) NAME
asn2gb - convert ASN.1 biological data to a GenBank-style flat format SYNOPSIS
asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode] [-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N] [-u N] [-y N] DESCRIPTION
asn2gb converts descriptions of biological sequences from NCBI's ASN.1 format to one of several flat-file formats, and is the successor to asn2ff(1). OPTIONS
A summary of options is included below. - Print usage message -A accession Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1 enables fetching of external features (as with the legacy -F option) -F Fetch remote annotations (equivalent to specifying -A accession,0,-1) -a asn-type ASN.1 Type: [Single record] a Any (autodetected; default) e seq-Entry b Bioseq s bioseq-Set m seq-subMit q Catenated [Release file; components individually processed and freed] t baTch bioseq-set u batch seq-sUbmit -b Input file is binary -c Batch file is compressed -d Seq-loc minus strand -f format Format: b GenBank (default) bp or pb GenBank and GenPept e EMBL p GenPept q nucleotide GBSet (XML) r protein GBSet (XML) t Feature table only x nucleotide INSDSet (XML) y tiny seq (XML) Y FASTA z protein INSDSet (XML) -g N Bit flags (all default to off): 1 HTML 2 XML 4 ContigFeats 8 ContigSrcs 16 FarTransl -h N Lock/Lookup Flags (all default to off): 8 LockProd 16 LookupComp 64 LookupProd -i filename Input file name (default = stdin) -j N Start location (default is 0, beginning of sequence) -k N End location (default is 0, end of sequence) -l filename Log file -m mode Mode: r Release e Entrez s Sequin (default) d Dump -n filename Asn2Flat Executable (default = asn2flat) -o filename Output file name (default = stdout) -p Propagate top descriptors -q filename Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff) -r Enable remote fetching -s style Style: n Normal (default) s Segment m Master c Contig -t N Batch: 1 Report 2 Sequin/Release 3 asn2gb SSEC/nocleanup 4 asn2flat BSEC/nocleanup 5 asn2gb/asn2flat 6 asn2gb NEW dbxref/OLD dbxref 7 oldasn2gb/newasn2gb -u N Custom flags (all default to off): 4 Hide features 1792 Hide references 8192 Hide sources 262144 Hide translations -y N Feature itemID AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1), insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz. NCBI
2011-09-02 ASN2GB(1)
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CLEANASN(1) NCBI Tools User's Manual CLEANASN(1) 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) AUTHOR
The National Center for Biotechnology Information. SEE ALSO
asndisc(1), asnval(1), sequin(1). NCBI
2012-06-24 CLEANASN(1)