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! 👨💻
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.
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