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  1. IGB
  2. IGBF-1189

Add S. Cerevisiae June 2008 genome to IGB Quickload - User request

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
        • Story Points:
          0.5
        • Sprint:
          Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3

          Description

          A user from HELP-279 has contacted us about the June 2008 S. Cerevisiae genome missing from IGB Quickload.

          To aid in the task of adding this genome, I have attached the:

          1) 2bit reference genome, obtained here:
          http://hgdownload.soe.ucsc.edu/goldenPath/sacCer2/bigZips/

          2) Reference Annotations in BED format, obtained from the UCSC Table Browser using the "SGD Gene" track

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-1414 Check that 2008 yeast genome synonyms are in species.txt and synonyms.txt

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. HELP-279 S. cerevisiae Jun_2008 reference genome not loading

              • Closed

                Activity

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                9 older comments
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                ieclabau Ivory Blakley (Inactive) added a comment - - edited

                The gene descriptions were added following the instructions here:
                https://wiki.transvar.org/display/igbdevelopers/Updating+RefGene+UCSC+data+set+for+an+existing+genome+in+IGB+QuickLoad
                With some modification.

                I encountered a problem with the ucscToBedDetail.py script from the GenomeSource repo:
                https://bitbucket.org/lorainelab/genomesource
                That issue has been resolved.

                The authoritative body for this genome is SDG. UCSC provides a bed table of sdg genes. The identifiers used in this bed file are locus_ids, which is an available field in the gene_info file from ncbi. I modified the ucscToBedDetail.py script to filter by taxID and use the locus id rather than the gene id to get the information from the gene_info table. I copied the modified script (ucscToBedDetail_SacCer_locusID.py) to the test quickload site so Ann and include it as documentation if appropriate.

                Out of 6,717 models in the sdg genes bed file, 698 were not found in the gene_info list (so they have NA for the gene description).

                Show
                ieclabau Ivory Blakley (Inactive) added a comment - - edited The gene descriptions were added following the instructions here: https://wiki.transvar.org/display/igbdevelopers/Updating+RefGene+UCSC+data+set+for+an+existing+genome+in+IGB+QuickLoad With some modification. I encountered a problem with the ucscToBedDetail.py script from the GenomeSource repo: https://bitbucket.org/lorainelab/genomesource That issue has been resolved. The authoritative body for this genome is SDG. UCSC provides a bed table of sdg genes. The identifiers used in this bed file are locus_ids, which is an available field in the gene_info file from ncbi. I modified the ucscToBedDetail.py script to filter by taxID and use the locus id rather than the gene id to get the information from the gene_info table. I copied the modified script (ucscToBedDetail_SacCer_locusID.py) to the test quickload site so Ann and include it as documentation if appropriate. Out of 6,717 models in the sdg genes bed file, 698 were not found in the gene_info list (so they have NA for the gene description).
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                ieclabau Ivory Blakley (Inactive) added a comment -

                This is ready for review.

                Remember, you can access the quicklaod site for the 2008 S.Cerevisiae genome assembly here:
                http://18.222.191.240/Quickload_IGBF-1189_S.Cerevisiae/

                I am assigning this to Ann for review.
                Please see my last comment.
                If this passes review then Ann can take over.

                Show
                ieclabau Ivory Blakley (Inactive) added a comment - This is ready for review. Remember, you can access the quicklaod site for the 2008 S.Cerevisiae genome assembly here: http://18.222.191.240/Quickload_IGBF-1189_S.Cerevisiae/ I am assigning this to Ann for review. Please see my last comment. If this passes review then Ann can take over.
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                ann.loraine Ann Loraine added a comment - - edited
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                ann.loraine Ann Loraine added a comment - - edited Added to new https://svn.bioviz.org/repos/genomes subversion repository. To browse, visit https://svn.bioviz.org/viewvc (visit on non-UNCC network due to issues with internal DNS, to be fixed soon) However, did not add S_cerevisiae_Jun_2008_refGene.bed.gz because it is not mentioned in the annots.xml file.
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                ann.loraine Ann Loraine added a comment - - edited

                Deployed as part of current (newly migrated) quickload site.

                To test:

                • Test using master branch installer for 9.0.2
                • Inspect Species menu of Current Genome tab; check for new yeast genome related menu options (IGB has a bug whereby newly added genomes are shown incorrectly using their UCSC-style or other synonyms)
                • Select Current Genome tab, select Saccharomyces cerevisiae species (this is budding yeast)
                • Check that 2008 genome is listed in genome version menu
                • Select 2008 genome
                • Make sure that reference gene model data set is loaded upon visiting the genome
                • Make sure that sequence data can be loaded
                • Make sure that the menu item in Current Genome lists the species and genome correctly, with correct tooltips

                Report any problems here and if there are problems, return to To-Do column.

                Show
                ann.loraine Ann Loraine added a comment - - edited Deployed as part of current (newly migrated) quickload site. To test: Test using master branch installer for 9.0.2 Inspect Species menu of Current Genome tab; check for new yeast genome related menu options (IGB has a bug whereby newly added genomes are shown incorrectly using their UCSC-style or other synonyms) Select Current Genome tab, select Saccharomyces cerevisiae species (this is budding yeast) Check that 2008 genome is listed in genome version menu Select 2008 genome Make sure that reference gene model data set is loaded upon visiting the genome Make sure that sequence data can be loaded Make sure that the menu item in Current Genome lists the species and genome correctly, with correct tooltips Report any problems here and if there are problems, return to To-Do column.
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                ptambvek Pranav Sanjay Tambvekar (Inactive) added a comment -

                Tested as described, the application behaves as expected.

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                ptambvek Pranav Sanjay Tambvekar (Inactive) added a comment - Tested as described, the application behaves as expected.

                  People

                  • Assignee:
                    ieclabau Ivory Blakley (Inactive)
                    Reporter:
                    mason Mason Meyer (Inactive)
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                    Dates

                    • Created:
                      Updated:
                      Resolved: