trim.seqs, only one group file from allfiles

mothur bugs
1

Hello everyone,

Under 1.16, trim.seqs with allfiles=T would generate one groups file per sample, as is documented in the manual. However, the behavior has changed in 1.17 (affecting both 1.17.0 and 1.17.2) to only output a single groups file, regardless of the value of allfiles.

I suspect this is a bug, as there appears to have been major refactoring of trimseqscommand.cpp between 1.16 and 1.17, but please let me know if I’m misunderstanding what I should expect from allfiles.

Thank you very much!
Jared

2

Jared - thanks for bringing this to our attention - we’re on it. There was a big change between 1.16 and 1.17 in trim.seqs and I managed to screw up a few things (this is what happens when a PI starts mucking with stuff).

Pat

3

We are working on this, but here’s a workaround that will get you the group files you want.

list.seqs(fasta=yourFasta.groupName.fasta)
get.seqs(group=yourGroupfile, accnos=yourFasta.groupName.accnos)

This will ouput a yourGroupFile.pick.groups file which you will want to rename so that you know which fasta file it relates to.

example:
list.seqs(fasta=f5m.700015283.v13.rep3.wu.fasta)
get.seqs(group=f5m.groups, accnos=f5m.700015283.v13.rep3.wu.accnos)

creates f5m.pick.groups which I would rename to f5m.700015283.v13.rep3.wu.groups.

I hope this helps,

Sarah

4

Thank you both!

– jared