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  1. IGB
  2. IGBF-510

Preserve Custom Genomes between IGB Sessions

    Details

    • Story Points:
      3
    • Sprint:
      Fall 6 Nov 30 - Dec 11, Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22

      Description

      IGB makes it possible for users to visualize "custom genomes," which are genomes where they have used their own reference genome and visualized their own data files.

      Please see this User's Guide page for guidance on how this features works from the user's perspective:

      https://wiki.transvar.org/pages/viewpage.action?pageId=23200542

      Unfortunately, each time a user needs to use their "custom genome," they have to repeat the entire process described in the wiki.

      Instead of making them do this every time, let's implement a way for them to save their custom genome between sessions.

      How this could work:

      • Users will do the same thing as now when opening their custom genome.
      • We will create a new submenu option under the "File" menu that says "Save Custom Genome to Local Quickload Site"
      • When they choose that option, a popup will appear that asks the user to select a folder in the file system
      • Once they do that, IGB creates a quickload site consisting of meta-data files only - contents.txt, genome.txt, annots.xml
      • The annots.xml file tag "file" attribute will point to the local (or remote) files the user has loaded into IGB

      Note that thanks to the new "reference" file tag implemented in IGB 9.1.6, the reference sequence no longer has to reside in the same folder as the Quickload site, as was previously the case.

        Issue Links

          Activity

          Hide
          aloraine Ann Loraine added a comment -

          Excellent question. "load_hint" when saved to annots.xml should only take the value "Whole Sequence."

          So if a dataset / data file (in IGB) has "load_hint" equal to any other value, then when you create the annots.xml "file" element for it, the element's "load_hint" attribute should not be specified at all. In other words, it should be absent for that particular file.

          Show
          aloraine Ann Loraine added a comment - Excellent question. "load_hint" when saved to annots.xml should only take the value "Whole Sequence." So if a dataset / data file (in IGB) has "load_hint" equal to any other value, then when you create the annots.xml "file" element for it, the element's "load_hint" attribute should not be specified at all. In other words, it should be absent for that particular file.
          Show
          noor91zahara Noor Zahara added a comment - Code diff - https://bitbucket.org/noorzahara/save_customegenome/commits/13e00fc7989171ac992ca4d1dd4f90ac60c0aecc
          Hide
          aloraine Ann Loraine added a comment -

          The load_hint if present in an annots.xml file should always be "Whole Sequence." But it should only be included if the load hint in the data set / file within IGB is set in this way. This "load hint" is what ensures that a reference gene model track loads as soon as the user selects a genome version.

          Show
          aloraine Ann Loraine added a comment - The load_hint if present in an annots.xml file should always be "Whole Sequence." But it should only be included if the load hint in the data set / file within IGB is set in this way. This "load hint" is what ensures that a reference gene model track loads as soon as the user selects a genome version.
          Hide
          aloraine Ann Loraine added a comment -

          Nowlan Freese - if you have time today, please try out the new version of the app. It requires latest 9.1.8 to be installed.

          Show
          aloraine Ann Loraine added a comment - Nowlan Freese - if you have time today, please try out the new version of the app. It requires latest 9.1.8 to be installed.
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Testing on Mac on master branch Jar (my laptop would not allow master dmg to be opened).

          1) Created a quickload while in the 2013 human genome. I then removed all other quickloads. Loading the human genome appears correctly, various data sources are working.

          2) I created a custom genome with 2bit sequence and bed annotation. I then created a quickload. Loading the custom quickload mostly appears correctly. The color of the annotation track appeared correclty, but the load_hint (Whole Sequence) was not set. When I created the custom genome I entered:
          Genome Version: E_unicornis_Apr_2017
          Species: Equus unicornis
          When I loaded the quickload the Species appeared as E_unicornis (not Equus unicornis) and the Genome Version was E_unicornis_Apr_2017.

          Overall appears to be working correctly.
          Ann Loraine - I'm unclear if the load_hint should be set and if the custom genome Species can be saved.

          Show
          nfreese Nowlan Freese added a comment - - edited Testing on Mac on master branch Jar (my laptop would not allow master dmg to be opened). 1) Created a quickload while in the 2013 human genome. I then removed all other quickloads. Loading the human genome appears correctly, various data sources are working. 2) I created a custom genome with 2bit sequence and bed annotation. I then created a quickload. Loading the custom quickload mostly appears correctly. The color of the annotation track appeared correclty, but the load_hint (Whole Sequence) was not set. When I created the custom genome I entered: Genome Version: E_unicornis_Apr_2017 Species: Equus unicornis When I loaded the quickload the Species appeared as E_unicornis (not Equus unicornis) and the Genome Version was E_unicornis_Apr_2017. Overall appears to be working correctly. Ann Loraine - I'm unclear if the load_hint should be set and if the custom genome Species can be saved.

            People

            • Assignee:
              Unassigned
              Reporter:
              mason Mason Meyer
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              Dates

              • Created:
                Updated:

                Agile