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  1. IGB
  2. IGBF-1226

IGB doesn't read gzipped fasta file

        Details

        • Story Points:
          2
        • Sprint:
          B - Summer 2018

          Description

          Users tried to use a fasta.gz file as the sequence for a custom genome.
          This didn't work. IGB will work with fasta, but not fasta.gz.

          This was brought to our attention through this biostars post:
          https://biostar.usegalaxy.org/p/27494/

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              ieclabau Ivory Blakley (Inactive) created issue -
              ieclabau Ivory Blakley (Inactive) made changes -
              Field Original Value New Value
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Sprint A - Spring 2018 [ 48 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked lower
              ann.loraine Ann Loraine made changes -
              Labels Beginner
              kkorey Kiran Korey (Inactive) made changes -
              Assignee Ann Loraine [ aloraine ] Kiran Korey [ kkorey ]
              kkorey Kiran Korey (Inactive) made changes -
              Status Open [ 1 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Story Points 2
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              ann.loraine Ann Loraine added a comment - - edited

              Created using shell commands:

              wget http://igbquickload.org/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011.2bit

              twoBitToFa S_cerevisiae_Apr_2011.2bit S_cerevisiae_Apr_2011.fa

              gzip S_cerevisiae_Apr_2011.fa

              twoBitToFa is from Jim Kent code. Google to find it.

              Show
              ann.loraine Ann Loraine added a comment - - edited Created using shell commands: wget http://igbquickload.org/S_cerevisiae_Apr_2011/S_cerevisiae_Apr_2011.2bit twoBitToFa S_cerevisiae_Apr_2011.2bit S_cerevisiae_Apr_2011.fa gzip S_cerevisiae_Apr_2011.fa twoBitToFa is from Jim Kent code. Google to find it.
              ann.loraine Ann Loraine made changes -
              Attachment S_cerevisiae_Apr_2011.fa.gz [ 14066 ]
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              kkorey Kiran Korey (Inactive) added a comment -

              Needs First level review, please refer to the branch in the link below

              https://bitbucket.org/kkorey/kkorey-igb/branch/IGB-1226-GZIP

              Show
              kkorey Kiran Korey (Inactive) added a comment - Needs First level review, please refer to the branch in the link below https://bitbucket.org/kkorey/kkorey-igb/branch/IGB-1226-GZIP
              kkorey Kiran Korey (Inactive) made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              ann.loraine Ann Loraine made changes -
              Status Needs 1st Level Review [ 10005 ] Reviewing [ 10301 ]
              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ] Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing [ 10301 ] Ready for Pull Request [ 10304 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ] Kiran Korey [ kkorey ]
              kkorey Kiran Korey (Inactive) made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Assignee Kiran Korey [ kkorey ] Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Needs Testing [ 10002 ]
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              ann.loraine Ann Loraine added a comment -

              This addresses a user-reported bug.

              I will likely include this in the release.

              Please make a note to notify the person who reported this when the new version comes out so that they can update their IGB.

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              ann.loraine Ann Loraine added a comment - This addresses a user-reported bug. I will likely include this in the release. Please make a note to notify the person who reported this when the new version comes out so that they can update their IGB.
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ] Mason Meyer [ mason ]
              mason Mason Meyer (Inactive) made changes -
              Status Needs Testing [ 10002 ] Testing In Progress [ 10003 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Assignee Mason Meyer [ mason ] Ivory Blakley [ ieclabau ]
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              ieclabau Ivory Blakley (Inactive) added a comment -

              Testing...

              using A_thaliana_Jun_2009.fa
              $ gzip A_thaliana_Jun_2009.fa
              > A_thaliana_Jun_2009.fa.gz

              IGB was able to read the fa.gz file just like the fa. If I drag/drop it into IGB, it lads a single long sequence feature representing each chromosome. If I select it as a custom genome it loads the genome sequence.

              Note that gzip is not the same bgzip.

              Show
              ieclabau Ivory Blakley (Inactive) added a comment - Testing... using A_thaliana_Jun_2009.fa $ gzip A_thaliana_Jun_2009.fa > A_thaliana_Jun_2009.fa.gz IGB was able to read the fa.gz file just like the fa. If I drag/drop it into IGB, it lads a single long sequence feature representing each chromosome. If I select it as a custom genome it loads the genome sequence. Note that gzip is not the same bgzip.
              ieclabau Ivory Blakley (Inactive) made changes -
              Fix Version/s 9.0.1 Minor Release [ 10500 ]
              ieclabau Ivory Blakley (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Testing In Progress [ 10003 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Workflow Loraine Lab Workflow [ 17914 ] Fall 2019 Workflow Update [ 19846 ]
              ann.loraine Ann Loraine made changes -
              Workflow Fall 2019 Workflow Update [ 19846 ] Revised Fall 2019 Workflow Update [ 21965 ]

                People

                • Assignee:
                  ieclabau Ivory Blakley (Inactive)
                  Reporter:
                  ieclabau Ivory Blakley (Inactive)
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                  Dates

                  • Created:
                    Updated:
                    Resolved: