Provided by: ncbi-tools-bin_6.1.20170106-6_amd64 bug

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:
              o      By Overlap
              p      By Product
              l      By Label and Location
              s      Suppress links forced by -M

       -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:
              n      Normal
              b      Big sequence
              p      Power option
              t      TSA

       -N n   Project version number

       -O     Allow run-on ORFs

       -P     Remote publication lookup

       -Q     mRNA title policy
              s      Special mRNA titles
              r      RefSeq mRNA titles

       -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)
              v      Validate with Normal Stringency
              r      Validate without Country Check
              c      BarCode validation
              b      Generate GenBank Flatfile
              g      Generate Gene Report
              t      Validate with TSA check

       -W     Log progress

       -X str Extra flags (combine any of the following letters)
              A      Automatic definition line generation
              C      Apply Comments in .cmt files to all sequences
              E      Treat like Eukarypota in the discrepancy report

       -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 M
                                                )
       -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)
              c      Annotate Longest ORF
              r      Allow Runon ORFs
              m      Allow Alternative Starts
              k      Set Conflict on Mismatch

       -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
              map
              strobe

       -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>.