Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2877

Create annot.xml file from track hub's trackDb.txt file

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      1
    • Sprint:
      Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9

      Description

      We just need name parameter from trackDb.txt file. In future we might extract more information from trackDb.txt file like color. We can get the location of trackhubDB.txt file from the following API https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt

        Attachments

          Issue Links

            Activity

            Show
            omarne Omkar Marne added a comment - - edited https://bitbucket.org/omarne/track-hub-converter-webapp/src/main/ Link for reference code : https://www.geeksforgeeks.org/how-to-convert-lists-to-xml-in-python/
            Show
            chirag24 Chirag Chandrahas Shetty added a comment - diff: https://bitbucket.org/chirag06/track-hub-converter-webapp/commits/d9970089e5caab7b313d72cf9e26247d67d3241e?at=IGBF-2877
            Hide
            omarne Omkar Marne added a comment - - edited
            Show
            omarne Omkar Marne added a comment - - edited Irvin Naylor Please pull the changes. Pull requests - https://bitbucket.org/Inaylor01/track-hub-converter-webapp/pull-requests/4/igbf-2877
            Hide
            omarne Omkar Marne added a comment - - edited

            Dr. Ann Loraine I compared all the trackdb.txt files and all the files have similar parameters ( track, long label, short label and type). So we can use either of the parameters as title.
            Currently, we have used track as 'title' which would be fine I guess.

            Below are the links for all trackdb.txt files.

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632525.1_BALB_cJ_v1//GCA_001632525.1_BALB_cJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624445.1_CAST_EiJ_v1//GCA_001624445.1_CAST_EiJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624185.1_129S1_SvImJ_v1//GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624535.1_FVB_NJ_v1//GCA_001624535.1_FVB_NJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632555.1_C57BL_6NJ_v1//GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624295.1_AKR_J_v1//GCA_001624295.1_AKR_J_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624215.1_A_J_v1//GCA_001624215.1_A_J_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624745.1_NZO_HlLtJ_v1//GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624675.1_NOD_ShiLtJ_v1//GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624865.1_SPRET_EiJ_v1//GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632575.1_C3H_HeJ_v1//GCA_001632575.1_C3H_HeJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624835.1_WSB_EiJ_v1//GCA_001624835.1_WSB_EiJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624475.1_CBA_J_v1//GCA_001624475.1_CBA_J_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624775.1_PWK_PhJ_v1//GCA_001624775.1_PWK_PhJ_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632615.1_LP_J_v1//GCA_001632615.1_LP_J_v1.trackDb.txt

            http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624505.1_DBA_2J_v1//GCA_001624505.1_DBA_2J_v1.trackDb.txt

            https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg19/trackDb.txt

            Show
            omarne Omkar Marne added a comment - - edited Dr. Ann Loraine I compared all the trackdb.txt files and all the files have similar parameters ( track, long label, short label and type). So we can use either of the parameters as title. Currently, we have used track as 'title' which would be fine I guess. Below are the links for all trackdb.txt files. http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632525.1_BALB_cJ_v1//GCA_001632525.1_BALB_cJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624445.1_CAST_EiJ_v1//GCA_001624445.1_CAST_EiJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624185.1_129S1_SvImJ_v1//GCA_001624185.1_129S1_SvImJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624535.1_FVB_NJ_v1//GCA_001624535.1_FVB_NJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632555.1_C57BL_6NJ_v1//GCA_001632555.1_C57BL_6NJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624295.1_AKR_J_v1//GCA_001624295.1_AKR_J_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624215.1_A_J_v1//GCA_001624215.1_A_J_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624745.1_NZO_HlLtJ_v1//GCA_001624745.1_NZO_HlLtJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624675.1_NOD_ShiLtJ_v1//GCA_001624675.1_NOD_ShiLtJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624865.1_SPRET_EiJ_v1//GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632575.1_C3H_HeJ_v1//GCA_001632575.1_C3H_HeJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624835.1_WSB_EiJ_v1//GCA_001624835.1_WSB_EiJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624475.1_CBA_J_v1//GCA_001624475.1_CBA_J_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624775.1_PWK_PhJ_v1//GCA_001624775.1_PWK_PhJ_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001632615.1_LP_J_v1//GCA_001632615.1_LP_J_v1.trackDb.txt http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624505.1_DBA_2J_v1//GCA_001624505.1_DBA_2J_v1.trackDb.txt https://ftp.ncbi.nlm.nih.gov/snp/population_frequency/TrackHub/20200227123210/hg19/trackDb.txt
            Hide
            aloraine Ann Loraine added a comment - - edited

            A trackDb.txt "database" record typically contains:

            • bigDataURL
            • track
            • long label
            • short label

            type to annots.xml fields:

            track hub field -> annots "file" element attributes:

            • bigDataUrl -> name
            • long label -> description (if available)
            • short label -> title

            option for how to construct title field:

            • [track] / [type] / [short label]
            Show
            aloraine Ann Loraine added a comment - - edited A trackDb.txt "database" record typically contains: bigDataURL track long label short label type to annots.xml fields: track hub field -> annots "file" element attributes: bigDataUrl -> name long label -> description (if available) short label -> title option for how to construct title field: [track] / [type] / [short label]
            Hide
            aloraine Ann Loraine added a comment - - edited

            Question:

            Given this trackDb.txt:

            How do I "open" it using the UCSC Genome Browser?

            We need to be able to easily do this so that we can do a proper mapping between trackDb.txt fields and annots.xml fields.

            Show
            aloraine Ann Loraine added a comment - - edited Question: Given this trackDb.txt: http://hgdownload.soe.ucsc.edu//hubs//mouseStrains//GCA_001624835.1_WSB_EiJ_v1//GCA_001624835.1_WSB_EiJ_v1.trackDb.txt How do I "open" it using the UCSC Genome Browser? We need to be able to easily do this so that we can do a proper mapping between trackDb.txt fields and annots.xml fields.
            Hide
            aloraine Ann Loraine added a comment -

            Next step: modify or use your code to literally create a quickload "site" for your local computer (just create all the required files)

            Look at: https://bitbucket.org/lorainelab/igbquickload/src/master/

            Show
            aloraine Ann Loraine added a comment - Next step: modify or use your code to literally create a quickload "site" for your local computer (just create all the required files) Look at: https://bitbucket.org/lorainelab/igbquickload/src/master/

              People

              • Assignee:
                chirag24 Chirag Chandrahas Shetty
                Reporter:
                chirag24 Chirag Chandrahas Shetty
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: