[IGBF-2877] Create annot.xml file from track hub's trackDb.txt file - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
- Beginner

Story Points:
1
Epic Link:
Build Track Hub converter
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

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Issue Links

blocks

IGBF-2878 Implement TrackHub Application 2 which is an endpoint for all the IGB requests.

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Chirag Chandrahas Shetty (Inactive) created issue - 04/Jun/21 12:47 PM

Chirag Chandrahas Shetty (Inactive) made changes - 04/Jun/21 12:48 PM

Field	Original Value	New Value
Epic Link		IGBF-2831 [ 19524 ]

Chirag Chandrahas Shetty (Inactive) made changes - 04/Jun/21 12:48 PM

Assignee

Ann Loraine [ aloraine ]

Chirag Chandrahas Shetty (Inactive) made changes - 04/Jun/21 12:49 PM

Description

We just need name parameter from trackDb.txt file. In future we might extract more information from trackDb.txt file like color.

Omkar Marne (Inactive) made changes - 07/Jun/21 10:49 AM

Assignee

Omkar Marne [ omarne ]

Omkar Marne (Inactive) made changes - 07/Jun/21 10:50 AM

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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/

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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/

Omkar Marne (Inactive) made changes - 08/Jun/21 6:20 PM

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In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Omkar Marne (Inactive) made changes - 08/Jun/21 6:21 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Omkar Marne (Inactive) made changes - 08/Jun/21 6:37 PM

Status

First Level Review in Progress [ 10301 ]

Needs 1st Level Review [ 10005 ]

Chirag Chandrahas Shetty (Inactive) made changes - 09/Jun/21 10:22 AM

Link

This issue blocks ~~IGBF-2878~~ [ ~~IGBF-2878~~ ]

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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

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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

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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

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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

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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

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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

Omkar Marne (Inactive) made changes - 10/Jun/21 6:37 PM

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Omkar Marne [ omarne ]

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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]

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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]

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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.

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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.

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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/

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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/

Ann Loraine made changes - 14/Jun/21 9:09 AM

Sprint

Spring 6 2021 May 31 - June 11 [ 122 ]

Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 122, 123 ]

Ann Loraine made changes - 14/Jun/21 9:10 AM

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Ranked higher

Chirag Chandrahas Shetty (Inactive) made changes - 15/Jun/21 10:30 AM

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Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Chirag Chandrahas Shetty (Inactive) made changes - 15/Jun/21 10:31 AM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Chirag Chandrahas Shetty (Inactive) made changes - 16/Jun/21 10:05 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Chirag Chandrahas Shetty (Inactive) made changes - 16/Jun/21 10:06 AM

Assignee

Chirag Chandrahas Shetty [ chirag24 ]

Chirag Chandrahas Shetty (Inactive) made changes - 22/Jun/21 10:04 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Chirag Chandrahas Shetty (Inactive) made changes - 22/Jun/21 10:05 AM

Assignee

Chirag Chandrahas Shetty [ chirag24 ]

Ann Loraine made changes - 28/Jun/21 10:31 AM

Sprint

Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 122, 123 ]

Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9 [ 122, 123, 124 ]

Ann Loraine made changes - 28/Jun/21 10:31 AM

Rank

Ranked higher

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:14 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:15 AM

Assignee

Chirag Chandrahas Shetty [ chirag24 ]

Irvin Naylor (Inactive) made changes - 01/Jul/21 1:17 AM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

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Assignee:

Chirag Chandrahas Shetty (Inactive)

Reporter:

Chirag Chandrahas Shetty (Inactive)

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Dates

Created:

04/Jun/21 12:47 PM

Updated:

01/Jul/21 1:17 AM

Resolved:

01/Jul/21 1:17 AM