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  1. Bug Repository
  2. BUG-583

Allow bed detail for saving annotations

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • Labels:
      None

      Description

      Allow BED detail as another option for saving selected annotations.

      If gene name and description values are missing, insert "NA" in missing fields.

      To test: open TAIR10, save track as bed, then as bed detail - ensure that the bed detail file has 'gene name' as an option in Annotations>label. Select a subset of genes, repeat above as "Save selected annotations"

      Open Bos Taurus, repeat all of the above. The bed detail files should have "N/A" displayed when label is set to gene name.

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            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            If source sym is of type bed detail then it would output bed detail other wise it would output bed.

            Do you want it to force output bed detail all time?

            Note: Bed detail might be used in other places like Galaxy.

            Show
            hiralv Hiral Vora (Inactive) added a comment - If source sym is of type bed detail then it would output bed detail other wise it would output bed. Do you want it to force output bed detail all time? Note: Bed detail might be used in other places like Galaxy.
            Hide
            ann.loraine Ann Loraine added a comment -

            When users click "Save Track" (formerly "Save Selected") a new window opens that gives "bed" as the only option for the format to use.

            Can you add "bed detail" as a new option?

            If a user chooses this option but is trying to save a track where annotations do not have "gene name" or "description" attributes, then save as BED detail but include the string "NA" (for not available) in the 13th and 14th columns.

            Ideally, if annotations within the track have "gene name" and "description" attributes, then "BED Detail" should be selected as the default option. If the annotations do not have those attributes, then "BED" should be the default option.

            Show
            ann.loraine Ann Loraine added a comment - When users click "Save Track" (formerly "Save Selected") a new window opens that gives "bed" as the only option for the format to use. Can you add "bed detail" as a new option? If a user chooses this option but is trying to save a track where annotations do not have "gene name" or "description" attributes, then save as BED detail but include the string "NA" (for not available) in the 13th and 14th columns. Ideally, if annotations within the track have "gene name" and "description" attributes, then "BED Detail" should be selected as the default option. If the annotations do not have those attributes, then "BED" should be the default option.
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Done in r13227.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Done in r13227.
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            Is the TAIR10 mRNA track a bed detail track? Cause it's offering the BED as default, not bed detail.

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - Is the TAIR10 mRNA track a bed detail track? Cause it's offering the BED as default, not bed detail.
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            It's always going to offer bed. At this point export cannot differentiate between bed file and bed detail file.

            Show
            hiralv Hiral Vora (Inactive) added a comment - It's always going to offer bed. At this point export cannot differentiate between bed file and bed detail file.
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            Currently if a file is a bed detail and you chose to save as a bed, it saves as bed detail - is this the correct behavior? Or is it supposed to actually save as a bed when you ask it to, and a bed detail when you ask it to? Or will it always default to bed detail?

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - Currently if a file is a bed detail and you chose to save as a bed, it saves as bed detail - is this the correct behavior? Or is it supposed to actually save as a bed when you ask it to, and a bed detail when you ask it to? Or will it always default to bed detail?
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            Fixed in r13276.

            It would always output the selected format.

            Show
            hiralv Hiral Vora (Inactive) added a comment - Fixed in r13276. It would always output the selected format.
            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            bed detail is not saving properly for a bed detail file... (no data in it)

            open TAIR10 and the LL juncs. Select 1or 2 annot, and chose save selected. For LL Jun file, save as bed or save as bed detail works. But for TAIR10, bed works fine, but bed detail does not.

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - bed detail is not saving properly for a bed detail file... (no data in it) open TAIR10 and the LL juncs. Select 1or 2 annot, and chose save selected. For LL Jun file, save as bed or save as bed detail works. But for TAIR10, bed works fine, but bed detail does not.
            Hide
            ann.loraine Ann Loraine added a comment -

            If user selects "bed detail" and the annotations have no "gene name" or "description" fields, values "NA" (not available) should be inserted in fields 13 and 14.

            Show
            ann.loraine Ann Loraine added a comment - If user selects "bed detail" and the annotations have no "gene name" or "description" fields, values "NA" (not available) should be inserted in fields 13 and 14.
            Hide
            hiralv Hiral Vora (Inactive) added a comment -

            A typo creeped in. Fixed in r13287.

            Show
            hiralv Hiral Vora (Inactive) added a comment - A typo creeped in. Fixed in r13287.

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              • Assignee:
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                Reporter:
                ann.loraine Ann Loraine
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                  Updated:
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