Body: <p>How can I import a biom file?</p>
  <p>When I run the following code:</p>
  <pre><code>library(phyloseq)
  import_biom(
      &quot;/Users/name/Dropbox/*****.biom&quot;, 
      parseFunction=parse_taxonomy_greengenes, 
      parallel=F)
  </code></pre>
  <p>I get the following error message:</p>
  <blockquote>
  <p>biom either as JSON (BIOM-v1) or HDF5 (BIOM-v2). Check file path, file
  name, file itself, then try agai</p>
  </blockquote>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T08:43:44.047Z
Comments.Text: what happens when you do ``file.exists("/Users/name/Dropbox/*****.bio")``
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T09:37:59.173Z
Comments.Text: you can check with `file *****.biom` as well, to check if your biom file is text or HDF5-like file, to distinguish between versions 1 and 2.
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T12:20:42.427Z
Comments.Text: The relevant package for `import_biom` should be added to your code (e.g. `library(phyloseq)`).
Comments.UserDisplayName: Greg
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T13:11:34.207Z
Comments.Text: Thank you.    file.exists("/Users/name/Dropbox/*****.bio")  [1] TRUE
Comments.UserDisplayName: user224050
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T13:12:54.930Z
Comments.Text: > to check if your biom file is text or HDF5-like file, to distinguish between versions 1 and 2.
  How can I check? If it is version 1, what should I do and if it is version 2, what should I do?
Comments.UserDisplayName: user224050
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-10T17:03:14.787Z
Comments.Text: Biological Observation Matrix 1.0.0, so I think this is JSON file.
Comments.UserDisplayName: user224050
Tags: <r>
Title: Help importing a biom file into R
ThreadText: # Help importing a biom file into R
  
  (Asked by: username_0 on 2020-09-10)
  
  How can I import a biom file?
  
  When I run the following code:
  
  ```
  library(phyloseq)
  import_biom(
      "/Users/name/Dropbox/*****.biom", 
      parseFunction=parse_taxonomy_greengenes, 
      parallel=F)
  
  ```
  
  I get the following error message:
  
  > biom either as JSON (BIOM-v1) or HDF5 (BIOM-v2). Check file path, file
  > name, file itself, then try agai
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: what happens when you do ``file.exists("/Users/name/Dropbox/*****.bio")``  
  > **username_2**: you can check with `file *****.biom` as well, to check if your biom file is text or HDF5-like file, to distinguish between versions 1 and 2.  
  > **username_3**: The relevant package for `import_biom` should be added to your code (e.g. `library(phyloseq)`).  
  > **username_0**: Thank you.    file.exists("/Users/name/Dropbox/*****.bio")  [1] TRUE  
  > **username_0**: > to check if your biom file is text or HDF5-like file, to distinguish between versions 1 and 2. How can I check? If it is version 1, what should I do and if it is version 2, what should I do?  
  > **username_0**: Biological Observation Matrix 1.0.0, so I think this is JSON file.  
  
  ---
  
  ## 0 answers
  
  