Will ORForise work for multi-fasta genome file?

[yazhinia]

Hi,
I wanted to use this tool to compare results of multiple ORF prediction tools for genome sequence having multiple fasta sequence entries. Will it be applied to this case?

Thank you.

[NickJD]

Hi.
ORForise does handle multi-contig genomes.
Each contig gets its own output directory with sequence data, metrics and summary files.
Then a final combined summary is produced.

I have just made some adjustments to ORForise release 1.5.1 to make it easier to use and get more informative outputs.

The pip version has also been updated to 1.5.1

At some point I will update the GitHub README.
Let me know how it goes and whether you have any suggestions.

Thanks.

[yazhinia]

Dear Nick,
I want to compare and combine results of a few different tools that are not tested in ORForise. I get the following errors,

Code:
Annotation-Compare -ref Prodigal.gff -dna 12718_7#34.assembly.fa -t Bakta,smORFinder -tp bakta.gff,smorfinder.gff

Error:
Tool not available - Did you get the name right?

With Aggregate-compare
Code:
Aggregate-Compare -ref Prodigal.gff -dna 12718_7#34.assembly.fa -t Bakta,smORFinder -tp bakta.gff,smorfinder.gff

Error:
Bakta Tool not available

I wanted to Keep Prodigal as a base at top priority and aggregate ORF predictions from other tools in the regions not covered by Prodigal or covered in different frames and shorter than Prodigal prediction.

Any help is much appreciated.

Thank you.

[NickJD]

I am not aware of the output format of smORFinder, but if it outputs in 'standard' GFF format, you should be able to use -t GFF as ORForise has 'general-purpose' GFF compatibility.
If that doesn't work, send me an example output file, and I can add it to the tool list pretty quickly.

For Bakta, its format should be about the same as Prokka, so for the -t tool part, just provide -t Prokka and it should work.

I will add to the next version a Bakta->Prokka pseudoname in the code so it works automatically.

[yazhinia]

As long as input files are in gff format, is it possible to run the comparison without checking the tool names?

[NickJD]

The GFF specification is unfortunately interpreted differently by each tool and there can be minor differences between their outputs.
The '-t GFF' option should work on most tools that provide a GFF so yes, if you have a GFF file, you could try to just provide the GFF option for it and hopefully ORForise will be able to understand the file.
If not, let me know with an example file and I can make some modifications.