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  1. Bug Repository
  2. BUG-127

Genbank compatibility established

          Details

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

            Description

            Genbank files should work.

            Bacterial files here http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi

            However, also fine a few mammalian genbank files to test.

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                relates to

                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  alyssa Alyssa Gulledge (Inactive) created issue -
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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited

                  my bad - wrong version tested...

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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited my bad - wrong version tested...
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  There are definitely alias issues - the name of the chromosome is very random, and so these files can only be opened as unknown species. Also, the sequence cannot be loaded even though it is in theory exported as well as the annotations are.

                  Attached are 2 genbank files, one is a single gene from apis mellifera, the second is a much larger file from c. elegans.

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                  alyssa Alyssa Gulledge (Inactive) added a comment - There are definitely alias issues - the name of the chromosome is very random, and so these files can only be opened as unknown species. Also, the sequence cannot be loaded even though it is in theory exported as well as the annotations are. Attached are 2 genbank files, one is a single gene from apis mellifera, the second is a much larger file from c. elegans.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment sequence(3).gb [ 10257 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Attachment sequence(4).gb [ 10258 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.6 [ 10021 ] Bug Repository [ 10030 ]
                  Key IGBA-73 BUG-127
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  However, despite the alias issues, this still works just fine

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                  alyssa Alyssa Gulledge (Inactive) added a comment - However, despite the alias issues, this still works just fine
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  david David Norris (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  david David Norris (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  david David Norris (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Katharine Kubiak [ kkubiak ]
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Comment [ Attached files do not load any data ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9845 Windows

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                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9845 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed 6.7.0 (9891) on Mac

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                  anuj Anuj Puram (Inactive) added a comment - Passed 6.7.0 (9891) on Mac
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Vineeth Mylapur [ smylapur ]
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Passed 7.0 (11936) on windows.

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                  smylapur Vineeth Mylapur (Inactive) added a comment - Passed 7.0 (11936) on windows.
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-622 [ BUG-622 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Resolution Fixed [ 1 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: