Converting a .biom file to a .txt file.

[benz...@hartwick.edu]

Hello,

I am currently trying to convert my OTU.biom table to a OTU.txt format. When I run the command I obtained from the website I get a error back saying i must specify the table type. Is this "out table". I am not sure what it means by specify table type. Attached is the code I have tried. 

Thank you, 

Todd Benziger

[suman...@gmail.com]

Hi Todd,

The table type should be .txt. I have modified the script you ran, try to run this, you should be fine.

biom convert -i full_otu_table_taxa.biom -o full_otu_table_taxa.txt --to-tsv --header-key taxonomy

Medha.

[Jose Morillo]

Hello all,

I have the same problem. The command (copied from http://biom-format.org/documentation/biom_conversion.html) apparently does not work if the original otu table format is not specified, at least in my system (qiime 1.9.0, VB).

Command: biom convert -i nochimerasfiles/final_otu_table.biom -o final_otu_table.txt --to-tsv --header-key taxonomy

result: (..)
pyqi.core.exception.CommandError: Must specify --table-type!

Could you chek if there is a problem?

Thanks,
jose

[Medha Suman]

Hi,

I use the command mentioned below to convert the biom table and it works fine. Give it a try.

biom convert -i otu_table.biom -o otu_table.txt -b --header-key taxonomy

Medha.

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[Benziger, Peter T.]

Hello,

Thank you for the help but I am still running into the same issue. I have also tried with "-b" but it says it is not an option. 

Todd

[Medha Suman]

Hi Todd,

Can you send me the exact command that you are using and the error message that you are getting?

Medha.

[Miriam]

Hi,

Have you found a solution to this? I have the same problem ie. "biom convert -i otu_qiime.biom -o otu_qiime.txt --to-tsv --header-key taxonomy " returns the error "pyqi.core.exception.CommandError: Must specify --table-type!".

I only get the above error if using a biom table created by pick_closed_reference_otus.py, but the command works fine if using a biom table which was converted from a txt table using "biom convert -i otuup.txt -o otu_up.biom --table-type="OTU table" --to-json". 

I noticed that the formats are slightly different between these 2 biom tables (attached). 

I'm using qiime 1.9.0. on linux2 with python 2.7.5. and biom format 2.1.4. and h5py not installed.

Thanks a lot,

Miriam

[Jai Ram Rideout]

Hi Miriam,

Can you try the following command? I added "--table-type 'OTU table'" to the end of your original command.

biom convert -i otu_qiime.biom -o otu_qiime.txt --to-tsv --header-key taxonomy --table-type 'OTU table'

Best,

Jai

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[Miriam]

Thanks Jai!

I added the "--table-type 'OTU table" and it worked. I've also upgraded to qiime 1.9.1 and tried it with the original command again and it now worked too, so either way, all good.

Thanks,

Miriam

[Jai Ram Rideout]

Glad to hear it worked for you!

[Wessam Elnemr]

Hi, 

I have found that biom convert in my system do the opposite. It converts txt to biom. While I need to convert the biom file into txt. Any ideas???

biom convert -i table.txt -o table.biom --table-type "OTU table" --to-hdf5

[Jose Navas]

Hi Wessam,

See this page for possible ways of using biom convert, including going from biom to txt.

http://biom-format.org/documentation/biom_conversion.html

There are multiple options depending on which information you want to maintain.

Also, if you run biom convert --help you can see all possible parameters that biom convert can take.

Hope this helps!

Jose Navas

[Abby Kimball]

Does anyone know the reverse of this? What the code is to get a txt file to a biom file?

[Colin Brislawn]

That (and more!) is on the official biom-format web site:

http://biom-format.org/documentation/biom_conversion.html

One way may be:

biom convert -i otu_table.txt -o new_otu_table.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy

Colin