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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/

        Attachments

          Activity

          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
          Hide
          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 ]
          Hide
          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 ]
          Hide
          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.

          Show
          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 ]
          Hide
          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: