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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Add option to take NCBI template file for tbl2asn #120

Open tseemann opened 9 years ago

tseemann commented 9 years ago

Email from Yu Wan:

3. Would it be possible to make Prokka to take an option for the NCBI template file?
wanyuac commented 9 years ago

Hi Torsten, thanks for your consideration of this issue. I am still trying to submit an annotation file to GenBank and I found the problem would be more complicated. Would you wait for me to give you a detailed summary of those issues after I made the submission successful?

wanyuac commented 9 years ago

Hi Torsten,

A template is necessary for generating an SQN file for submitting to GenBank because the reference information is required, according to the email from NCBI:

"[1] Your .sqn file is not formatted correctly. You need to include a template file when you run tbl2asn. You can create a template here: http://www.ncbi.nlm.nih.gov/WebSub/template.cgi."

I used this command to run tbl2asn, which works properly: tbl2asn -V b -a r10k -M n -y 'Annotated using prokka 1.11 from http://www.vicbioinformatics.com' -t AH0650_Sm1.sbt -i AH0650_Sm1.fsa -Z AH0650_Sm1.err 2> tbl2asn.log

Furthermore, I think the option "-l paired-ends" that Prokka uses to run tbl2asn is redundant because the "-l" option does not appear in the tbl2asn's manual.

tseemann commented 9 years ago

@wanyuac What version of tbl2asn are you using? The -l option has been around for quite a while. Which manual do you mean? Is the manual up to date with the tool?

  -l  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
tseemann commented 9 years ago

The Prokka manual says that the .sqn file the Prokka produces is for loading into Sequin to combine with your other submitter information. You can then use Sequin to save the final "Seq-Submit" record.

I will consider adding the option. Could you please send me your .SBT file for testing?

wanyuac commented 9 years ago

Hi Torsten

I am using tbl2asn/24.2, whose manual does not contail an option of "-l" (http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/).

I have sent you my template file already.