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  1. IGB
  2. IGBF-2836

Get familiar with track hub format

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25

          Description

          None of us is very familiar yet with the Track Hub specification.

          To gain better knowledge of it, we could write some code (e.g., a script) that given a Track Hub URL, produces an IGB Quickload file and folder structure from the Track Hub.

          When a user "opens" this folder in IGB, they should be able to then see files from the Track Hub displayed in the Available Data Sets section of IGB.

          This task will expose potential problems with mapping Track Hub specification aspects onto the IGB Quickload specification.

          If such a script existed, we could automate conversion of all available public Track Hubs.

          Request: Please add any new code to this repository: https://bitbucket.org/lorainelab/igbquickload

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-2833 Find, watch, and curate Track Hub instructional videos and other materials

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2831 [ 19524 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue is blocked by IGBF-2833 [ IGBF-2833 ]
                ann.loraine Ann Loraine made changes -
                Description None of us is very familiar yet with the Track Hub specification.

                To gain better knowledge of it, we should write some code (e.g., a script) that given a Track Hub URL, produces an IGB Quickload file and folder structure from the Track Hub.

                When a user "opens" this folder in IGB, they should be able to then see files from the Track Hub displayed in the Available Data Sets section of IGB.

                This task will expose potential problems with mapping Track Hub specification aspects onto the IGB Quickload specification.

                If such a script existed, we could automate conversion of all available public Track Hubs.
                		None of us is very familiar yet with the Track Hub specification.

                To gain better knowledge of it, we should write some code (e.g., a script) that given a Track Hub URL, produces an IGB Quickload file and folder structure from the Track Hub.

                When a user "opens" this folder in IGB, they should be able to then see files from the Track Hub displayed in the Available Data Sets section of IGB.

                This task will expose potential problems with mapping Track Hub specification aspects onto the IGB Quickload specification.

                If such a script existed, we could automate conversion of all available public Track Hubs.

                Request: Please add the script to this repository: https://bitbucket.org/lorainelab/igbquickload
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2021 Apr 5 - Apr 16 [ 118 ] Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 118, 119 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - - edited

                Quickload website: http://igbquickload.org/quickload

                Show
                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - - edited Quickload website: http://igbquickload.org/quickload
                omarne Omkar Marne (Inactive) made changes -
                Assignee Omkar Marne [ omarne ]
                omarne Omkar Marne (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Summary Get familiar with track hub format by writing a converter Get familiar with track hub format
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30 [ 118, 119 ] Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14 [ 118, 119, 120 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description None of us is very familiar yet with the Track Hub specification.

                To gain better knowledge of it, we should write some code (e.g., a script) that given a Track Hub URL, produces an IGB Quickload file and folder structure from the Track Hub.

                When a user "opens" this folder in IGB, they should be able to then see files from the Track Hub displayed in the Available Data Sets section of IGB.

                This task will expose potential problems with mapping Track Hub specification aspects onto the IGB Quickload specification.

                If such a script existed, we could automate conversion of all available public Track Hubs.

                Request: Please add the script to this repository: https://bitbucket.org/lorainelab/igbquickload
                		None of us is very familiar yet with the Track Hub specification.

                To gain better knowledge of it, we could write some code (e.g., a script) that given a Track Hub URL, produces an IGB Quickload file and folder structure from the Track Hub.

                When a user "opens" this folder in IGB, they should be able to then see files from the Track Hub displayed in the Available Data Sets section of IGB.

                This task will expose potential problems with mapping Track Hub specification aspects onto the IGB Quickload specification.

                If such a script existed, we could automate conversion of all available public Track Hubs.

                Request: Please add any new code to this repository: https://bitbucket.org/lorainelab/igbquickload
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Note that in the UCSC system, there appear to be two types of hubs: Track hubs and assembly hubs.
                Assembly hubs contain reference sequence data information. Track hubs contain data that are mapped onto the reference genomes specified by assembly hubs. ("Assembly" is another name for the collection of sequences that make up a reference genome version.)
                UCSC has a REST API (emits JSON format data) clients can use to get information about track hubs and assembly hubs. I think the converter can probably take advantage of this API in several ways, such as identifying the location of 2bit files needed by IGB to display reference genome sequence data.
                See: http://genome.ucsc.edu/goldenPath/help/api.html

                attn: Chirag Chandrahas Shetty, Irvin Naylor, Logan Weidenhammer, Omkar Marne

                Show
                ann.loraine Ann Loraine added a comment - Note that in the UCSC system, there appear to be two types of hubs: Track hubs and assembly hubs. Assembly hubs contain reference sequence data information. Track hubs contain data that are mapped onto the reference genomes specified by assembly hubs. ("Assembly" is another name for the collection of sequences that make up a reference genome version.) UCSC has a REST API (emits JSON format data) clients can use to get information about track hubs and assembly hubs. I think the converter can probably take advantage of this API in several ways, such as identifying the location of 2bit files needed by IGB to display reference genome sequence data. See: http://genome.ucsc.edu/goldenPath/help/api.html attn: Chirag Chandrahas Shetty , Irvin Naylor , Logan Weidenhammer , Omkar Marne
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14 [ 118, 119, 120 ] Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 118, 119, 120, 121 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                omarne Omkar Marne (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                omarne Omkar Marne (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 118, 119, 120, 121 ] Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 118, 119, 120, 121, 122 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Hide
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                This api might help us create quickload/contents.txt file
                https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt

                Show
                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - This api might help us create quickload/contents.txt file https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt
                Hide
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                Similar to genome.txt

                https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly

                Show
                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - Similar to genome.txt https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly
                Hide
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                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment -

                trackDb.txt is similar annots.xml

                Show
                chirag24 Chirag Chandrahas Shetty (Inactive) added a comment - trackDb.txt is similar annots.xml
                omarne Omkar Marne (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Hide
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                omarne Omkar Marne (Inactive) added a comment -

                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
                omarne Omkar Marne (Inactive) added a comment - 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/
                omarne Omkar Marne (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                omarne Omkar Marne (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                Hide
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                omarne Omkar Marne (Inactive) 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

                Show
                omarne Omkar Marne (Inactive) 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
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                omarne Omkar Marne (Inactive) added a comment - - edited

                Dr. [~aloraine] - 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.

                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 (Inactive) added a comment - - edited Dr. [~aloraine] - 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. 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
                omarne Omkar Marne (Inactive) made changes -
                Assignee Omkar Marne [ omarne ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11 [ 118, 119, 120, 121, 122 ] Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30, Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 118, 119, 120, 121, 122, 123 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                omarne Omkar Marne (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                omarne Omkar Marne (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                omarne Omkar Marne (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                omarne Omkar Marne (Inactive) made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                omarne Omkar Marne (Inactive) made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                omarne Omkar Marne (Inactive) made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                omarne Omkar Marne (Inactive) made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                omarne Omkar Marne (Inactive) made changes -
                Assignee Omkar Marne [ omarne ]

                  People

                  • Assignee:
                    omarne Omkar Marne (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: