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

Omkar Marne (Inactive) added a comment - 08/Jun/21 4:35 PM - 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/

Chirag Chandrahas Shetty (Inactive) added a comment - 09/Jun/21 3:46 PM diff: https://bitbucket.org/chirag06/track-hub-converter-webapp/commits/d9970089e5caab7b313d72cf9e26247d67d3241e?at=IGBF-2877

Omkar Marne (Inactive) added a comment - 10/Jun/21 5:53 PM - edited Irvin Naylor Please pull the changes. Pull requests - https://bitbucket.org/Inaylor01/track-hub-converter-webapp/pull-requests/4/igbf-2877

Omkar Marne (Inactive) added a comment - 10/Jun/21 6:30 PM - 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 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

Ann Loraine added a comment - 11/Jun/21 10:29 AM - 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]

Ann Loraine added a comment - 11/Jun/21 10:32 AM - 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.

Ann Loraine added a comment - 11/Jun/21 10:46 AM 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/