line.split() in silva_blast, tab separated input

[Shellfishgene]

Hi!
I'm just trying this pipline, and always got errors from eukref_gbretrieve.py. On closer inspection they are caused by various instances of line.split() in the silva_blast routine. I'm not a Python guy, but it seems without arguments this splits on any whitespace, however the input file from usearch with the blast6out option is tab separated. If I change line.split() to line.split("\t") throughout silva_blast it works as expected.
I'm puzzled as to why this is, obviously it should never have worked without this change, but I guess it does for others?

[kolecko007]

Hi, thanks for the info, we will look into it. From the sound of it it might be incompatibility between usearch versions. Usearch changes (or at leasrt changed) output formatting, which broke the pipeline. What usearch version do you have installed? Cheers Martin On 1 Apr 2020, at 22:05, Shellfishgene <notifications@github.com<mailto:notifications@github.com>> wrote: Hi! I'm just trying this pipline, and always got errors from eukref_gbretrieve.py. On closer inspection they are caused by various instances of line.split() in the silva_blast routine. I'm not a Python guy, but it seems without arugments this splits on any whitespace, however the input file from usearch with the blast6out option is tab separated. If I change line.split() to line.split("\t") throughout silva_blast it works as expected. I'm puzzled as to why this is, obviously it should never have worked without this change, but I guess it does for others? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#11>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACSDHFI2AFLS3CDVVJYGDGDRKOM7VANCNFSM4LZQNLJA>.