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.
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- |
Print usage message |
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-a str |
Accession |
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-C str |
Genome Center tag |
-D filename
Descriptors file
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-E |
Recurse |
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-F |
Feature ID links: |
o
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By Overlap |
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p |
By Product |
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l |
By Label and Location |
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s |
Suppress links forced by -M |
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-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
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-H str |
Hold until publication: |
y
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For one year |
mm/dd/yyyy
Until the specified date
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-J |
Delayed genomic product set |
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-K |
Safe Bioseq-set |
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-L |
Force Local protein_id/transcript_id |
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-M str |
Master genome flags: |
n
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Normal |
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b |
Big sequence |
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p |
Power option |
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t |
TSA |
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-N n |
Project version number
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-O |
Allow run-on ORFs |
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-P |
Remote publication lookup |
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-Q |
mRNA title policy |
s
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Special mRNA titles |
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r |
RefSeq mRNA titles |
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-R |
Remote sequence record fetching from ID
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-S |
Smart feature annotation | ||
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-T |
Remote Taxonomy lookup | ||
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-U |
Remove Unnecessary gene xref | ||
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-V str |
Verification (combine any of the following letters) |
v
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Validate with Normal Stringency |
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r |
Validate without Country Check |
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c |
BarCode validation |
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b |
Generate GenBank Flatfile |
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g |
Generate Gene Report |
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t |
Validate with TSA check |
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-W |
Log progress
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-X str |
Extra flags (combine any of the following letters) |
A
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Automatic definition line generation | |||
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C |
Apply Comments in .cmt files to all sequences | ||
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E |
Treat like Eukarypota in the discrepancy report |
-Y filename
Read a comment string from filename
-Z filename
Write a discrepancy report to filename
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-a str |
File type: |
a
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Any (default) | |||
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r20u |
Runs of 20+ Ns are gaps, 100 Ns are unknown length | ||
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r20k |
Runs of 20+ Ns are gaps, 100 Ns are known length | ||
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r10u |
Runs of 10+ Ns are gaps, 100 Ns are unknown length | ||
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r10k |
Runs of 10+ Ns are gaps, 100 Ns are known length | ||
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s |
FASTA Set (s Batch, s1 Pop, s2 Phy, s3 Mut, s4 Eco, s9 Small-genome) | ||
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d |
FASTA Delta | ||
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di |
FASTA Delta with Implicit Gaps | ||
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l |
FASTA+Gap Alignment (l Batch, l1 Pop, l2 Phy, l3 Mut, l4 Eco, l9 Small-genome) | ||
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z |
FASTA with Gap Lines | ||
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e |
PHRAP/ACE | ||
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b |
-
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ASN.1 (in conjunction with M ) | |||
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-b |
Generate GenBank file (deprecated in favor of -V b) | ||
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-c str |
Cleanup (combine any of the following letters) |
d
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Correct Collection Dates (assume month first) | |||
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D |
Correct Collection Dates (assume day first) | ||
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b |
Append note to coding regions that overlap other coding regions with similar product names and do not contain ’ABC’ | ||
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x |
Extend partial ends of features by one or two nucleotides to abut gaps or sequence ends | ||
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p |
Add exception to non-extendable partials | ||
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s |
Add exception to short introns | ||
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f |
Fix product names |
-f filename
Single table file
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-g |
Input is a genomic product set |
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-h |
Convert general ID to note |
-i filename
Single input file
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-j str |
Source qualifiers |
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-k str |
CDS flags (combine any of the following letters) |
c
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Annotate Longest ORF |
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r |
Allow Runon ORFs |
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m |
Allow Alternative Starts |
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k |
Set Conflict on Mismatch |
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-l str |
Add type of
evidence used to assert linkage across assembly gaps (only
for TSA records). Must be one of the following:
paired-ends
align-genus
align-xgenus
align-trnscpt
within-clone
clone-contig
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map |
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strobe |
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-m str |
Lineage to use for discrepancy report tests
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-n str |
Organism name |
-o filename
Single output file
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-p str |
Path to files |
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-q |
Set sequence ID from input file name |
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-r str |
Path for results |
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-s |
Read FASTAs as Set |
-t filename
Read template from filename
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-u |
Convert GenProdSet to NucProtSet |
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-v |
Validate (deprecated in favor of -V v) |
-w filename
Single structured comment file (overrides the use of -X C)
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-x str |
Suffix (default = .fsa) |
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-y str |
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-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>;.