<p><a href="http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf" rel="nofollow noreferrer">The manual</a> says fields in a tabular output file are space-delimited. It should be fairly straightforward to load a space-delimited file in pandas.</p>

<p>From the manual:</p>

<blockquote>
  <p><code>--tblout &lt;f&gt;</code> Save a simple tabular (space-delimited) file summarizing the per-target output, with one data line per homologous target model found.</p>
</blockquote>

CC BY-SA 4.0
2020-05-27T10:30:37.843Z
While this link may answer the question, it is better to include the essential parts of the answer here and provide the link for reference.  Link-only answers can become invalid if the linked page changes. - [From Review](/review/low-quality-posts/4581)
M__
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2020-05-27T14:28:17.253Z
Thank you for the pointer, @Michael. I've added an excerpt from the manual.
Ram RS
CC BY-SA 4.0
2020-05-27T14:40:46.413Z
Thanks @RamRS ... much better :-)
M__
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2020-05-27T16:18:00.147Z
This question was answered on StackOverflow:  https://stackoverflow.com/questions/62012615/convert-a-hmmer-tblout-output-to-a-pandas-dataframe/62021471#62021471
Cody Glickman
CC BY-SA 4.0
2020-05-26T21:28:25.397Z
2020-05-27T14:27:57.570Z
2020-05-27T14:27:57.570Z
Ram RS
<p>Is there a way to convert a hmmer output to a pandas dataframe? I am also unsure how to load a hmmer tblout table into python via the Bio module. I believe you can call a hmmer format with SeqIO.parse or SeqIO.search. How can you convert the table to a pandas dataframe?</p>

CC BY-SA 4.0
2020-05-27T16:18:44.413Z
This question was answered on Stack Overflow: https://stackoverflow.com/questions/62012615/convert-a-hmmer-tblout-output-to-a-pandas-dataframe/62021471#62021471
Cody Glickman
CC BY-SA 4.0
2020-05-27T18:02:57.940Z
It is rude to cross-post on multiple forums.
Ram RS
<hmmer><pandas><dataframe>
Converting hmmer --tblout to pandas dataframe
# Converting hmmer --tblout to pandas dataframe

(Asked by: username_0 on 2020-05-25)

Is there a way to convert a hmmer output to a pandas dataframe? I am also unsure how to load a hmmer tblout table into python via the Bio module. I believe you can call a hmmer format with SeqIO.parse or SeqIO.search. How can you convert the table to a pandas dataframe?

**Tags:** hmmer, pandas, dataframe
> **Comments:**
> **username_0**: This question was answered on Stack Overflow: https://stackoverflow.com/questions/62012615/convert-a-hmmer-tblout-output-to-a-pandas-dataframe/62021471#62021471  
> **username_1**: It is rude to cross-post on multiple forums.  

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## 1 answers

### Answer by username_1 on 2020-05-26. Score: 2 | Accepted answer

[The manual](http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf) says fields in a tabular output file are space-delimited. It should be fairly straightforward to load a space-delimited file in pandas.

From the manual:

> `--tblout`  Save a simple tabular (space-delimited) file summarizing the per-target output, with one data line per homologous target model found.

> **Comments:**
> **username_2**: While this link may answer the question, it is better to include the essential parts of the answer here and provide the link for reference.  Link-only answers can become invalid if the linked page changes. - [From Review](/review/low-quality-posts/4581)  
> **username_1**: Thank you for the pointer, @Michael. I've added an excerpt from the manual.  
> **username_2**: Thanks @RamRS ... much better :-)  
> **username_0**: This question was answered on StackOverflow:  https://stackoverflow.com/questions/62012615/convert-a-hmmer-tblout-output-to-a-pandas-dataframe/62021471#62021471  

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