Naming issue for the transcriptome file when running `./simpleaf index`

[naity2]

Dear Authors,

I'm having the follow issue when running ./simpleaf index:
The file [custome_index/ref//transcriptome_splici_fl86.fa] provided for the transcriptome does not appear to exist.

The cause seems to be that the default value for the filename_prefix parameter of the make_splici_txome function is "splici", whereas the line cmd="$salmon index -t $outref/transcriptome_splici_fl$fl.fa -i $outidx -p $threads $sparse_flag" in the usefulaf/bash/simpleaf file has an extra prefix of "transcriptome". Moreoever, ./simpleaf index doesn't provide a --filename-prefix parameter to get around this. Additionally, since outref="$output/ref/", there is an extra "/" in the path.

Could you please help look into this?

Thanks very much!

[rob-p]

Cc @DongzeHE --- also, can you please do a full run through to ensure everything works as expected end-to-end? We'd done this but something must have changed. We need a regression test for this.

[DongzeHE]

sure! will test it now.

[DongzeHE]

Hi @naity2,

I have fixed the bug and given it an end-to-end run using a real dataset. Please do git pull to pull my latest changes.

I am sorry for the inconvenience and thank you so much for bringing this issue up.

-Dongze

[naity2]

Thank you, @DongzeHE, for the prompt response!

Would you please kindly update the docker image as well? Thanks a lot!

[DongzeHE]

The docker image is updated. Enjoy. 😉

[naity2]

The docker image is updated. Enjoy. 😉

Awesome, thank you so much!

[rob-p]

Hi @naity2,

I just wanted to mention that we just released pyroe 0.6.0. This version adds some new commands including id-to-name that can convert a gene_id to gene_name mapping from a GTF or GFF3 file, as well as a convert command that can convert an alevin-fry quantification directory to e.g. an AnnData or loom file. The convert command can take an id to name mapping and apply the renaming during conversion. In general, we've greatly improved the documentation for pyroe, which you can find here. Let us know if you have any questions.

Best,
Rob

[naity2]

Hi @naity2,

I just wanted to mention that we just released pyroe 0.6.0. This version adds some new commands including id-to-name that can convert a gene_id to gene_name mapping from a GTF or GFF3 file, as well as a convert command that can convert an alevin-fry quantification directory to e.g. an AnnData or loom file. The convert command can take an id to name mapping and apply the renaming during conversion. In general, we've greatly improved the documentation for pyroe, which you can find here. Let us know if you have any questions.

Best, Rob

Awesome, thank you so much for the very useful updates!