File Name Extract

Shane Flannelly-king

• January 11, 2018 02:36

Hi,

I need to migrate plasmid sequences from our Geneious database into our new biologics registry system. Part of this process involves matching the exported .gb files with external metadata stored in an Excel file. So, I need to extract the names of the plasmids in Geneious and add them to the Excel file. The names of the plasmid sequences seem to be stored in the table string_search_field_value, but these values are in all caps while the actual file names are mixed case. Are the correct mixed case file names stored in a different table?

Thanks,

Shane

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  Matthew Cheung

  • January 15, 2018 02:07

  Hi Shane,

  The table you found is used for indexing purposes to speed up searching. 

  The mixed-case values aren't stored in a separate column so are only available by parsing an XML fragment.  We don't guarantee the format of this XML won't change between versions, but if you're OK with that then you can get the value from the document_xml column of the annotated_document table.  The element you're looking for is:

  <override_cache_name>current_document_name</override_cache_name>

  Cheers,
  Matthew

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  Rogerb

  • March 05, 2018 22:34

  So is there some other way to simply export the file names (or even other properties) that are in a directory displayed in geneious?  There are many times where I would like a list of filenames and say the number of sequences in each file, etc so I can compute some averages for a publication or check the file names against some external resource of phenotypic data etc.  While I can display everything I want to see in the viewing pane in Geneious, I can't find a way to get that information back out.

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  Rogerb

  • March 05, 2018 22:53

  Never mind - I figured out how to do this on my own.  E.g. I made a quick workflow that makes use of the export function. By hitting the Options button to the right of the "File Format" pulldown, I discovered that I could export any of the properties I was interested in (including name) to a .cvs or tab delimited without actually exporting the data.  The location of the Options button was non intuitive as was the label since I was anticipating it would relate to options for the file format and not for WHAT would be exported.

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  Matthew Cheung

  • March 06, 2018 03:29

  Glad you worked it out.  Sorry that the UI was confusing.

  Cheers,

  Matthew

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