Importing metagenome_contrib.tsv.gz to qiime2 format

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Sreevatshan Srinivasan

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Apr 14, 2021, 10:50:45 AM4/14/21
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Hello Gavin,

  Hope you are doing good. I had generated the EC and KO files in standalone version. I would like to import metegenome contribution of both files to qiime2 format (.qza). I had tried to import the file thru biom format but it show an error like this,

File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 5025, in _extract_data_from_tsv
    values = list(map(dtype, fields[1:-1]))
ValueError: could not convert string to float: 'EC:1.1.1.1'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 672, in load_table
    table = parse_biom_table(fp)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 416, in parse_biom_table
    t = Table.from_tsv(file_obj, None, None, lambda x: x)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 4875, in from_tsv
    t_md_name) = Table._extract_data_from_tsv(lines, **kwargs)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/table.py", line 5029, in _extract_data_from_tsv
    raise TypeError(msg % (lineno, badidx+1, badval))
TypeError: Invalid value on line 1, column 1, value EC:1.1.1.1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/picrust2/miniconda3/bin/biom", line 8, in <module>
    sys.exit(cli())
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/cli/table_converter.py", line 114, in convert
    table = load_table(input_fp)
  File "/home/picrust2/miniconda3/lib/python3.8/site-packages/biom/parse.py", line 674, in load_table
    raise TypeError("%s does not appear to be a BIOM file!" % f)
TypeError: EC_pred/pred_metagenome_contrib.tsv.gz does not appear to be a BIOM file!

Biom version is 2.1.10. Hope to hear from you soon..!

Best,

Sreevatshan

Gavin Douglas

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Apr 14, 2021, 1:05:04 PM4/14/21
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Hey Sreevatshan,


That table actually isn't a BIOM table and as far as I know there's no way to import it to QIIME 2 currently unfortunately. You would need to use a software like R to analyze that table.


Cheers,

Gavin

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Sreevatshan Srinivasan

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Apr 14, 2021, 1:19:27 PM4/14/21
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Hello Gavin,

thank you for the quick reply could you recommend any R package for analysis of the contribution file.?

Best,

Sreevatshan

Gavin Douglas

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Apr 15, 2021, 9:38:22 AM4/15/21
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Hey Sreevatshan,

There aren’t any R packages specifically to analyze this format, sorry! You would need to use custom code.

One thing is that because the table is in “long-format” (i.e., each abundance  value is on a separate line) it is amenable to being plotted with ggplot2. But you would need to first subset the table first to a relatively small number of values you would want to plot, because those tables can be massive. Similarly, with a subsetted table you could also view the data on BURITTO, which is on a standalone website.


All the best,

Gavin

kunle Raimi

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May 14, 2021, 9:43:17 AM5/14/21
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Dear Gavin 

Thanks for your time always.

Kindly assist me. Am running the picrusts2 script : "picrust2_pipeline.py -s clustered-sequences.fasta -i feature-table.biom -o picrust2_out_pipeline -p 1 --metagenome_contrib" to generate the metagenome contribution but its returning error

Error: error: unrecognized arguments: --metagenome_contrib

Hope to receive a solution soon.

Kunle

Gavin Douglas

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May 14, 2021, 11:07:06 AM5/14/21
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Hi there,

That command has been obsolete for a few versions - that functionality is performed by “—stratified” by default now. You can see the latest command syntax in the latest version of the tutorial on the wiki.


Cheers,

Gavin

Kilaza Samson

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May 14, 2021, 11:54:03 AM5/14/21
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Hi, i think STAMP can analyse such data output.

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