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Trinotate report omits some columns in .xls? #82

Closed yumi-nakadera closed 2 years ago

yumi-nakadera commented 2 years ago

Dear Brian,

It may not be crucial issue, but would be very useful if it gets solved.. I loaded SQlite with blastx, blastp, pfam, tmhmm, signalp outputs, and made the .xls report. However, the report does not contain some data. For example, signalp is empty in .xls, but it is there in .sqlite.

Screenshot 2022-06-20 at 10 38 55 AM

Screenshot 2022-06-20 at 10 51 49 AM

I attach the whole script below. Could you tell me if I missed out something? Best regards, Yumi

transcripts, pep, gene-trans-map

Trinotate ref.Trinotate.sqlite init --gene_trans_map modified_centroids.fasta.gene_trans_map --transcript_fasta modified_centroids.fasta --transdecoder_pep modified_centroids.fasta.transdecoder_dir/longest_orfs.pep

BLAST homology (protein, transcripts)

Trinotate ref.Trinotate.sqlite LOAD_swissprot_blastp blastp2.outfmt6 Trinotate ref.Trinotate.sqlite LOAD_swissprot_blastx blastx2.outfmt6

hmmer/pfam

Trinotate ref.Trinotate.sqlite LOAD_pfam TrinotatePFAM.out

tmhmm (transmembrane)

Trinotate ref.Trinotate.sqlite LOAD_tmhmm tmhmm.out

SignalP (signal peptide)

Trinotate ref.Trinotate.sqlite LOAD_signalp signalp.out

write out the output in .xls

Trinotate ref.Trinotate.sqlite report > ref.trinotate_annotation_report.xls

yumi-nakadera commented 2 years ago

sorry that was my mistake and solved it.. working perfectly now! Thanks for making such a nice software.

brianjohnhaas commented 2 years ago

Hi,

Are you sure all sigP entries are missing info in the spreadsheet? If you 'grep' for an ID that has it in the sqlite database, does it show up as an empty '.' column in the spreadsheet?

On Mon, Jun 20, 2022 at 4:54 AM Yumi @.***> wrote:

Dear Brian,

It may not be crucial issue, but would be very useful if it gets solved.. I loaded SQlite with blastx, blastp, pfam, tmhmm, signalp outputs, and made the .xls report. However, the report does not contain some data. For example, signalp is empty in .xls, but it is there in .sqlite.

[image: Screenshot 2022-06-20 at 10 38 55 AM] https://user-images.githubusercontent.com/100600260/174561312-824cbdf4-6ad1-4a50-ba38-fc330dc24247.png

[image: Screenshot 2022-06-20 at 10 51 49 AM] https://user-images.githubusercontent.com/100600260/174563811-3e98e8a2-a781-43ab-af27-d7a61124a3f2.png

I attach the whole script below. Could you tell me if I missed out something? Best regards, Yumi

transcripts, pep, gene-trans-map

Trinotate ref.Trinotate.sqlite init --gene_trans_map modified_centroids.fasta.gene_trans_map --transcript_fasta modified_centroids.fasta --transdecoder_pep modified_centroids.fasta.transdecoder_dir/longest_orfs.pep

BLAST homology (protein, transcripts)

Trinotate ref.Trinotate.sqlite LOAD_swissprot_blastp blastp2.outfmt6 Trinotate ref.Trinotate.sqlite LOAD_swissprot_blastx blastx2.outfmt6

hmmer/pfam

Trinotate ref.Trinotate.sqlite LOAD_pfam TrinotatePFAM.out

tmhmm (transmembrane)

Trinotate ref.Trinotate.sqlite LOAD_tmhmm tmhmm.out

SignalP (signal peptide)

Trinotate ref.Trinotate.sqlite LOAD_signalp signalp.out

write out the output in .xls

Trinotate ref.Trinotate.sqlite report > ref.trinotate_annotation_report.xls

— Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate/issues/82, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXZJ32LJMRX6ATVZKSLVQAWVVANCNFSM5ZIEMDUQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

yumi-nakadera commented 2 years ago

Thanks for asking! It is solved and showing nicely now.