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josuebarrera / GenEra

genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
GNU General Public License v3.0
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JGI like ID symbols fix #21

Closed RocesV closed 11 months ago

RocesV commented 11 months ago

Dear @josuebarrera,

This small change should fix the weird behaviour of FASTSTEP3R with JGI like GeneIDs (which usually contain "|" symbols).

ISSUE

https://github.com/josuebarrera/GenEra/issues/18

PROBLEM:

Data.table as default sep try to maximize the number of lines so the package uses a bunch of different symbols which include |.

SOLUTION:

Now in the the modified FASTSTEP3R "\t" sep is specified for reading $DIAMONDOUT and tmp_genelist. I have tested this with 5 proteomes in JGI and it seems that it is working fine.

I hope that this small change could be helpful and if you find any issues, i will be completely available so let me know! 👨‍💻

Cheers,

Víctor

josuebarrera commented 11 months ago

Hello @RocesV!

Thank you very much for the changes, I think this will be enough to make the pipeline work for any fasta header. I'll go ahead and merge the pull request.

Cheers, Josué.