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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?

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

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  • $\begingroup$ 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 $\endgroup$ – M__ May 27 '20 at 10:30
  • $\begingroup$ Thank you for the pointer, @Michael. I've added an excerpt from the manual. $\endgroup$ – Ram RS May 27 '20 at 14:28
  • $\begingroup$ Thanks @RamRS ... much better :-) $\endgroup$ – M__ May 27 '20 at 14:40
  • $\begingroup$ This question was answered on StackOverflow: stackoverflow.com/questions/62012615/… $\endgroup$ – Cody Glickman May 27 '20 at 16:18

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