| TBL2ASN(1) | NCBI Tools User's Manual | TBL2ASN(1) |
NAME¶
tbl2asn - prepare a GenBank submission using an ASCII feature table
SYNOPSIS¶
tbl2asn [-] [-A str] [-C str] [-D filename] [-E] [-F str] [-G str] [-H str] [-J] [-K] [-L] [-M str] [-N n] [-O] [-P] [-Q str] [-R] [-S] [-T] [-U] [-V str] [-W] [-X str] [-Y filename] [-Z filename] [-a str] [-b] [-c str] [-f filename] [-g] [-h] [-i filename] [-j str] [-k str] [-l str] [-m str] [-n str] [-o filename] [-p str] [-q] [-r str] [-s] [-t filename] [-u] [-v] [-w filename] [-x str] [-y str] [-z]
DESCRIPTION¶
tbl2asn reads a template along with sequence and table files, and outputs ASN.1 for submission to GenBank. Thus, the submitter does not need to read each set of table and sequence files into Sequin. Furthermore, the template file can contain the organism and submitter information common to all records, obviating the need to input these data for each sequence/table pair.
OPTIONS¶
A summary of options is included below.
- -
- Print usage message
- -a str
- Accession
- -C str
- Genome Center tag
- -D filename
- Descriptors file
- -E
- Recurse
- -F
- Feature ID links:
- -G str
- Alignment Gap Flags (comma separated fields, e.g., p,-,-,-,?,. ) n Nucleotide or p Protein, Begin, Middle, End Gap Characters, Missing Characters, Match Characters Alignment middle Gap characters
- -H str
- Hold until publication:
- y
- For one year
- mm/dd/yyyy
- Until the specified date
- -J
- Delayed genomic product set
- -K
- Safe Bioseq-set
- -L
- Force Local protein_id/transcript_id
- -M str
- Master genome flags:
- -R
- Remote sequence record fetching from ID
- -S
- Smart feature annotation
- -T
- Remote Taxonomy lookup
- -U
- Remove Unnecessary gene xref
- -V str
- Verification (combine any of the following letters)
- -Y filename
- Read a comment string from filename
- -Z filename
- Write a discrepancy report to filename
- -a str
- File type:
- a
- Any (default)
- r20u
- Runs of 20+ Ns are gaps, 100 Ns are unknown length
- r20k
- Runs of 20+ Ns are gaps, 100 Ns are known length
- r10u
- Runs of 10+ Ns are gaps, 100 Ns are unknown length
- r10k
- Runs of 10+ Ns are gaps, 100 Ns are known length
- s
- FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco, s9 Small-genome)
- d
- FASTA Delta
- di
- FASTA Delta with Implicit Gaps
- l
- FASTA+Gap Alignment (l Batch, l1 Pop, l2 Phy, l3 Mut, l4 Eco, l9 Small-genome)
- z
- FASTA with Gap Lines
- e
- PHRAP/ACE
- b
- ASN.1 (in conjunction with
- -b
- Generate GenBank file (deprecated in favor of -V b)
- -c str
- Cleanup (combine any of the following letters)
- d
- Correct Collection Dates (assume month first)
- D
- Correct Collection Dates (assume day first)
- b
- Append note to coding regions that overlap other coding regions with similar product names and do not contain 'ABC'
- x
- Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends
- p
- Add exception to non-extendable partials
- s
- Add exception to short introns
- f
- Fix product names
- -f filename
- Single table file
- -g
- Input is a genomic product set
- -h
- Convert general ID to note
- -i filename
- Single input file
- -j str
- Source qualifiers
- -k str
- CDS flags (combine any of the following letters)
- -l str
- Add type of evidence used to assert linkage across assembly gaps (only for TSA records). Must be one of the following:
- -m str
- Lineage to use for discrepancy report tests
- -n str
- Organism name
- -o filename
- Single output file
- -p str
- Path to files
- -q
- Set sequence ID from input file name
- -r str
- Path for results
- -s
- Read FASTAs as Set
- -t filename
- Read template from filename
- -u
- Convert GenProdSet to NucProtSet
- -v
- Validate (deprecated in favor of -V v)
- -w filename
- Single structured comment file (overrides the use of -X C)
- -x str
- Suffix (default = .fsa)
- -y str
- -z
- Clean up log file Comment
AUTHOR¶
The National Center for Biotechnology Information.
SEE ALSO¶
Psequin(1), sbtedit(1), /usr/share/doc/ncbi-tools-bin/tbl2asn.txt.gz, <http://www.ncbi.nlm.nih.gov/Sequin/table.html>.
| 2016-09-01 | NCBI |