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  1. IGB
  2. IGBF-1401

Add Chlorocebus sabaeus ("green monkey") to IGB quickload

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          1
        • Sprint:
          Winter 2018 Sprint 3, Spring 2019 Sprint 1, Spring 2019 Sprint 2, Spring 2019 Sprint 3

          Description

          A user would like us to add green monkey (Chlorocebus sabaeus) to IGB Quickload.

          We should get the sequence data (as usual) from UCSC but get the reference gene models from the GFF available from NCBI as he mentioned below. It would be more convenient to get the gene models from UCSC as usual, but I don't see them listed in the table browser. I think what may have happened is that NCBI has annotated the genome but UCSC has not yet imported the annotations into their database.

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              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-306 New reference genome (Chlorocebus sabaeus)

              • Major - Major loss of function.
              • Closed

              New Feature - A new feature of the product, which has yet to be developed. IGBF-1522 Write program to convert EnsGene table bed12 to bed14

              • Major - Major loss of function.
              • Closed

              New Feature - A new feature of the product, which has yet to be developed. IGBF-1523 Add vervet (green monkey) to IGB species.txt and synonyms.txt files

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. HELP-306 New reference genome (Chlorocebus sabaeus)

              • Major - Major loss of function.
              • Closed

                Activity

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                7 older comments
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                ann.loraine Ann Loraine added a comment -

                Suggestion:

                • Open and read mart file; put data into memory (dictionary where keys are transcript id that matches what's in the bed file)
                • Open bed file, read line by line
                • For each line in the bed file, use field 4 (transcript id) to look up same in mart dictionary
                • Output original line plus two extra fields obtained from the mart file
                Show
                ann.loraine Ann Loraine added a comment - Suggestion: Open and read mart file; put data into memory (dictionary where keys are transcript id that matches what's in the bed file) Open bed file, read line by line For each line in the bed file, use field 4 (transcript id) to look up same in mart dictionary Output original line plus two extra fields obtained from the mart file
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                ann.loraine Ann Loraine added a comment -

                Added tips on how to write the code - hopefully it helps!

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                ann.loraine Ann Loraine added a comment - Added tips on how to write the code - hopefully it helps!
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                Jill Jill Jenkins (Inactive) added a comment -

                There are corresponding ens gene IDs for each ens transcript stable ID; however, not all ens gene IDs are showing in the tool tip. When I check them against the ensGene.bed14 file, they are present. I have re-executed the script and outcome is the same.

                Show
                Jill Jill Jenkins (Inactive) added a comment - There are corresponding ens gene IDs for each ens transcript stable ID; however, not all ens gene IDs are showing in the tool tip. When I check them against the ensGene.bed14 file, they are present. I have re-executed the script and outcome is the same.
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                Jill Jill Jenkins (Inactive) added a comment - - edited

                Inconsistent behavior due to field14 of BED detail not complete - issue on mapping from mart+ensemble merge. Working on resolution now.

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                Jill Jill Jenkins (Inactive) added a comment - - edited Inconsistent behavior due to field14 of BED detail not complete - issue on mapping from mart+ensemble merge. Working on resolution now.
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                Jill Jill Jenkins (Inactive) added a comment -

                Resolved inconsistent behavior, tested in IGB, functions pass.

                Show
                Jill Jill Jenkins (Inactive) added a comment - Resolved inconsistent behavior, tested in IGB, functions pass.

                  People

                  • Assignee:
                    Jill Jill Jenkins (Inactive)
                    Reporter:
                    ieclabau Ivory Blakley (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: