ID Conversion

[rmhubley]

Feature Request: While I understand the necessity for ID conversion, the way it's implemented breaks downstream processing of the results. There are two ways to solve this (that I can think of), provide a translation from the old identifiers to the new in an output file, or convert back before outputting the final files.

[oushujun]

Hi Robert,

Sorry for the delayed response. Which ID conversion were you referring to? Can you please provide a little bit more information on the original format, the new format, and the expected format?

Shujun

[oushujun]

Hi Robert,

I am revisitin this issue. The ID conversion code implemented in LTR_retriever was to help users that don't know how to format their sequence IDs before any whole genome annotations. It's always recommended to format seq IDs before analysis. The current ID length allocation is limited to 13 characters because the downstream rmblast restrict ID length to 50 characters (If I remember correctly). The remaining length is reserved to contain coordinate information in intermediate files. Please refer to more discussions in #16 #93. Your proposed translation system may work, but still require users to tidy up sequence IDs before any analysis.

Thanks!
Shujun