Creating locInd file with a curated list of insertions

[emattei]

Hi, I would like to use TElocal with a non-reference list of TE insertions. How can I create my own .locInd file?

Thank you, Eugenio

[olivertam]

Hi Eugenio,

We do have a script that could generate the .locInd file, though it is in alpha. Let me check with the author and see if it can be distributed. Alternatively, if you only have one/two non-reference TE GTF files, we could potentially generate the .locInd file for you.

Thanks for your patience.

[emattei]

Hi, we need to test several individual loci annotations on different organisms so it is not really convenient. I hope you would be able to release the script soon.

Thanks

[olivertam]

Hi Eugenio,

We're still discussing whether the code is stable enough for limited distribution. We'll let you know as soon as possible. Apologies.

Thanks.

[olivertam]

Hi Eugenio,

Here's the link to the TElocal_indexer that should hopefully build the indices for TElocal. It needs to be run in the same environment where you run TElocal, as it depends on the same libraries as that program.

This is the full usage:

usage: TEindexer [-h] --afile annotation-file --itype index-type
                 [--project name] [--verbose verbose] [--version]

Building an index for the genome or transposable element annotations file.

optional arguments:
  -h, --help            show this help message and exit
  --afile annotation-file
                        file for indexing of annotations
  --itype index-type    index type to build for this gtf (gene or TE)
  --project name        Prefix for the index file. Default is empty string
  --verbose verbose     Set verbose level. 0: only show critical message, 1:
                        show additional warning message, 2: show process
                        information, 3: show debug messages. DEFAULT:2
  --version             show program's version number and exit

Example: TEindexer --afile gene_annotation.gtf --itype gene
Example: TEindexer --afile TE_annotation.gtf --itype TE

The example above is typically what we use. It will create a file with the extension .locInd when indexing a TE GTF. Note that this expects a TE GTF in the same style/format as the TEtranscripts GTF file (available here).

As we have previously mentioned, this is in alpha, and there could be portability issues. Please let us know if you encounter issues, and we can try to help.

Thanks, and good luck.

[emattei]

Thank you very much! This is great! Duly noted that is an alpha, I will let you know if there are problems.

[ax-ekk]

Hi,

Is TElocal_indexer no longer available? The link above is not working.

Many thanks! Elin

[olivertam]

Hi Elin,

Thank you for your interest in the software. We have been moving files around, and the TElocal_indexer is now here. Please note that this is still an alpha.

Thanks.

[ax-ekk]

Thank you for the quick reply! I will try it (keeping in mind that it is still alpha)