problems with taxonomy when converting regular otu-table.txt into biom

[yata]

Hi

I am trying to convert traditional out-table.txt with taxonomy into otu-table.biom, but this new biom table doesn't have exactly same taxonomy format as a regular biom table, and creates errors in summarize taxa. Below are the examples, where I highlighted the differences in the format:

Biom table #1 created from the traditional otu-table.txt using convert_biom.py -i otu_table.txt -o otu_table.biom --biom_table_type="otu table"

{"id": "348374", "metadata": {"taxonomy": "Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides"}}, {"id": "348377", "metadata": {"taxonomy": "Firmicutes; Clostridia; Clostridiales"}}, 

Biom table #2:

 {"id": "174809", "metadata": {"taxonomy": ["Bacteroidetes", "Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Bacteroides"]}},

Result of summarize_taxa.py when using biomtable #1:

A;c;t;i;n;o 0.000129074450143 0.019326221432

C;h;l;a;m;y 0.0 0.0 0.0

Here's the version of qiime I'm using:

System information

==================

         Platform: linux2

   Python version: 2.7.1 (r271:86832, Dec  5 2011, 19:57:28)  [GCC 4.4.3]

Python executable: /srv/cgs/local/qiime/shared_libraries/Python-2.7.1/bin/python2.7

Dependency versions

===================

                     PyCogent version: 1.5.1

                        NumPy version: 1.5.1

                   matplotlib version: 1.0.1

                  biom-format version: 0.9.3-dev

                QIIME library version: 1.4.0-dev

                 QIIME script version: 1.4.0-dev

        PyNAST version (if installed): 1.1

RDP Classifier version (if installed): rdp_classifier-2.2.jar

QIIME config values

===================

                     blastmat_dir: None

      topiaryexplorer_project_dir: None

     pynast_template_alignment_fp: /srv/cgs/local/qiime/shared_libraries/greengenes/core_set_aligned.fasta.imputed

                  cluster_jobs_fp: /srv/cgs/local/denoiser/latest/Denoiser/make_sge_cluster_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: None

                     torque_queue: friendlyq

              qiime_test_data_dir: None

   template_alignment_lanemask_fp: /srv/cgs/local/qiime/shared_libraries/greengenes/lanemask_in_1s_and_0s

                    jobs_to_start: 1

                cloud_environment: False

                qiime_scripts_dir: /srv/cgs/local/qiime/Qiime_1.4/bin

            denoiser_min_per_core: 50

                      working_dir: /srv/cgs/local/qiime/tmp

                    python_exe_fp: python

                         temp_dir: /srv/cgs/local/qiime/tmp

                      blastall_fp: blastall

                 seconds_to_sleep: 60

assign_taxonomy_id_to_taxonomy_fp: None

Any advice is appreciated.

Thanks,

Tanya

[Sathish]

hey i had the same issue a few days ago and posted on the forum:

convert_biom.py -i testwithtaxhead.txt --biom_table_type="otu table" -o testwithtax.biom --process_obs_metadata=taxonomy

[Sathish]

https://groups.google.com/forum/?fromgroups#!topic/qiime-forum/q-bitBwOJOM

You need to include the process_obs_metadata flag as described in the last example here:

http://biom-format.org/documentation/biom_conversion.html#special-case-usage-examples

convert_biom.py --biom_table_type="otu table" -i merged_otu_table.txt -o test.biom --process_obs_metadata=taxonomy

That flag should work now since the updated biom version.

Sathish

On Friday, May 11, 2012 8:11:56 PM UTC-5, yata wrote:

[Tanya Yatsunenko]

Cool! That worked. Thanks!

Tanya