How to obtain Sequence/Alignment file paths

Mark Miller

Hi, I am trying to locate and use sequence and alignment files to complete a MrBayes API call. I was wondering how can i find the path of the file?

Comments

4 comments

Richard Moir

May 13, 2016 05:17
Can you provide a bit more detail? Where did the files come from?
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Mark Miller

May 17, 2016 07:44
I want to get the file path of the alignment and sequences displayed in Geneious.
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Richard Moir

May 17, 2016 22:54
It's not really possible to get the file location because documents aren't necessarily stored as a file, they may be on a shared SQL server. Even if you could, they are stored in a format that is internal to Geneious and generally cannot be read by other tools.

If you need a file for input to another program then you have to export to a format compatible with that tool first:
```
AnnotatedPluginDocument alignmentDocument;
File nexusInputFile = FileUtilities.createTempFile("input", ".nex", false);
PluginUtilities.exportDocuments(nexusInputFile, alignmentDocument);
// TODO: use nexusInputFile to run MrBayes
```
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Mark Miller

May 18, 2016 17:21
This is very helpful. Thank you Richard.
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