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  1. IGB
  2. IGBF-598

Fix select and selectfeature commands, and update loadmode documentation to reflect actual options available

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      Description

      It seems there are a few non-functioning scripts that should be removed from the IGB Scripting language, such as the "Select" script.

      These non-functioning scripts should be removed from the IGB command language as it may add confusion to users.

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            dcnorris David Norris (Inactive) added a comment -

            Add specifics to the description on what should be removed.

            Show
            dcnorris David Norris (Inactive) added a comment - Add specifics to the description on what should be removed.
            Hide
            mason Mason Meyer (Inactive) added a comment - - edited

            After testing I can confirm that all of the scripts listed on this page (https://wiki.transvar.org/display/igbman/IGB+Script+List) are working except for:

            1) select
            2) selectfeature
            3) the loadmode command parameters "REGION_IN_VIEW" and "CHROMOSOME" (the command works as expected with the other parameters)

            Reassigning to David for fixes.

            Show
            mason Mason Meyer (Inactive) added a comment - - edited After testing I can confirm that all of the scripts listed on this page ( https://wiki.transvar.org/display/igbman/IGB+Script+List ) are working except for: 1) select 2) selectfeature 3) the loadmode command parameters "REGION_IN_VIEW" and "CHROMOSOME" (the command works as expected with the other parameters) Reassigning to David for fixes.
            Hide
            dcnorris David Norris (Inactive) added a comment -

            loadmode only accepts the following options

            1. no_load
            2. region_in_view / visible (they are synonyms in the scripting engine)
            3. genome

            region_in_view/visible doesn't really load the region in view, but results in the load mode of "Manual". This is actually not a bug, but a case of very poor naming by the original developers.

            There is not chromosome load mode, it was removed a few years ago.

            Show
            dcnorris David Norris (Inactive) added a comment - loadmode only accepts the following options 1. no_load 2. region_in_view / visible (they are synonyms in the scripting engine) 3. genome region_in_view/visible doesn't really load the region in view, but results in the load mode of "Manual". This is actually not a bug, but a case of very poor naming by the original developers. There is not chromosome load mode, it was removed a few years ago.
            Hide
            dcnorris David Norris (Inactive) added a comment -

            select and selectfeature work as expected on the development branch, but required a fix related to case sensitivity to work as expected.

            e.g. to test go to the latest Arabidopsis Genome Version and run the following script

            select AT1G36940.1

            note the selection occurs and the viewer is "jump zoomed" to the position.

            Now, load another script with this command instead.

            selectfeature AT1G36940.1

            The main viewer is not jump zoomed, but is now centered on this selection. To confirm this, simply operate the zoom slider and zoom into a level where you can see the selection of the gene model.

            Show
            dcnorris David Norris (Inactive) added a comment - select and selectfeature work as expected on the development branch, but required a fix related to case sensitivity to work as expected. e.g. to test go to the latest Arabidopsis Genome Version and run the following script select AT1G36940.1 note the selection occurs and the viewer is "jump zoomed" to the position. Now, load another script with this command instead. selectfeature AT1G36940.1 The main viewer is not jump zoomed, but is now centered on this selection. To confirm this, simply operate the zoom slider and zoom into a level where you can see the selection of the gene model.
            Hide
            dcnorris David Norris (Inactive) added a comment -

            merged fix to master branch for minor release 8.3.4

            Show
            dcnorris David Norris (Inactive) added a comment - merged fix to master branch for minor release 8.3.4
            Hide
            tmall Tarun Mall (Inactive) added a comment -

            My testing verified that these commands are functioning and we updated the document based on the functioning.
            Since the story is resolved, I'll close it.

            Show
            tmall Tarun Mall (Inactive) added a comment - My testing verified that these commands are functioning and we updated the document based on the functioning. Since the story is resolved, I'll close it.

              People

              • Assignee:
                dcnorris David Norris (Inactive)
                Reporter:
                mason Mason Meyer (Inactive)
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                • Created:
                  Updated:
                  Resolved: