How can taxonomy assignment be done during pick_open_reference_otus.py

[Hiunvun Chin]

Hi,
I think taxonomy assignment can be done if run pick_open_reference_otus.py?
But there is no the option "-t" to pass the id_to_taxonomy.txt file. I wonder how the assignment can be conducted?
My result is with all "unassigned".

Thank you.
Chin

[Stefan Janssen]

I reached out to my co-workers with your problem. Stay tuned.

[Hiunvun Chin]

Hi,
Thanks.
It seems it could be done if a parameters file is passed together with the scripts. But would you please see if correct? I run it and it seems no error.
Scripts:

pick_open_reference_otus.py -i seqs.fna -r silva119_97_rep_set_18S.fasta -p para_file.txt -o open_ref_otus/

parameters file:

pick_otus:enable_rev_strand_match True

assign_taxonomy:id_to_taxonomy_fp /Silva119_release/taxonomy_eukaryotes/97/taxonomy_97_all_levels_18S.txt
assign_taxonomy:reference_seqs_fp /Silva_119_rep_set97_18S.fna  #maybe it is repeated in the script using -r?
assign_taxonomy:assignment_method rdp
assign_taxonomy:similarity 0.80
assign_taxonomy:rdp_max_memory 12000

align_seqs:template_fp /Silva119_release/core_alignment/core_Silva119_alignment.fna

filter_alignment:allowed_gap_frac 0.80
filter_alignment:entropy_threshold 0.10

Thank you.
Chin

[Jamie Morton]

Hi Chin,

Yes, that appears to be correct.  Glad that is working!

Best,

Jamie