integrate sigP 5.0

[brianjohnhaas]

do it

[LuciaPita]

Dear Brian, dear Trinotate users,

I am using sigP 5.0 on Trinotate v3.2.0. Here some issues I have encountered, in case it can help others. I am not a programmer so probably there are more elegant ways to solve them:

First, I needed to shorten the protein headers of the protein fasta file (transdecoder output; e.g., protein.fasta) to have only the protein ID. Otherwise, there were errors due to invalid characters:

awk -F " " '/^>/ {print $1; next} 1' protein.fasta > sig_v5.input.protein.fasta

Then, I was not able to analyze the whole transcriptome at once, despite trying with different values in the new --batch parameter. The solution was to split the transcriptome with the fasta-splitter script developed by Kirill Kryukov http://kirill-kryukov.com/study/tools/fasta-splitter/. A division into files of 100000 sequences worked for me:

perl fasta-splitter.pl sig_v5.input.protein.fasta --part-size 100000 --measure count

That value, 100000, was the one I used in the --batch parameter for signalP. The results can be easily concatenated later.

[brianjohnhaas]

terrific! thanks for contributing this!

On Fri, Nov 15, 2019 at 4:21 AM LuciaPita notifications@github.com wrote:

Dear Brian, dear Trinotate users,

I am using sigP 5.0 on Trinotate v3.2.0. Here some issues I have encountered, in case it can help others. I am not a programmer so probably there are more elegant ways to solve them:

First, I needed to shorten the protein headers of the protein fasta file (transdecoder output; e.g., protein.fasta) to have only the protein ID. Otherwise, there were errors due to invalid characters:

awk -F " " '/^>/ {print $1; next} 1' protein.fasta > sig_v5.input.protein.fasta

Then, I was not able to analyze the whole transcriptome at once, despite trying with different values in the new --batch parameter. The solution was to split the transcriptome with the fasta-splitter script developed by Kirill Kryukov http://kirill-kryukov.com/study/tools/fasta-splitter/. A division into files of 100000 sequences worked for me:

perl fasta-splitter.pl sig_v5.input.protein.fasta --part-size 100000 --measure count

That value, 100000, was the one I used in the --batch parameter for signalP. The results can be easily concatenated later.

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--

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