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  1. IGB
  2. IGBF-2348

Add new parameter to NCBI Primer App

    Details

    • Type: New Feature
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      NCBI primer site has added a new parameter. To ensure IGB users have access to the newly available options, we should add this new option to NCBI Primer App.

      See: https://ncbiinsights.ncbi.nlm.nih.gov/2020/04/24/primer-blast-3-match/

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            pooja.nikhare Pooja Nikhare (Inactive) added a comment - - edited

            Observations:
            Following features are working fine:

            • Exon/ Intron options are set to default options (as in NCBI site) and properly sent while sending a request to NCBI set.
            • Options are set default by "Reset Default" Option.

            Observed the following issues:

            • When Exon Junction span is set to default "No Preference". Primer blast for all seq and organism works fine.
              But when it is set to other 2 options - "Primer must span an exon-exon junction", "Primer may not span an exon-exon junction" for few of the sym exception is being thrown. As for these options, NCBI Site redirects to an Info page , the Info page details are to be handled.
              Can be reproduced by testing with Rat genome - Taar7a .
            • According to the NCBI site A refseq mRNA seq is required for exon/intron selection. Can we send default options of exon/intron option as "No Preference" if the database type selected is other than "refseq mRNA" ?
              Because other combination ends up in info page, which user has to see in console.
            • Few parameters have been added in NCBI site like Max target size, Allow splice variants under Primer Pair Specificity Checking Parameters. And Post processing option is removed.

            If required test cases for different options of Exon Junction span can be added. Test case exists for default options "No preference".

            Show
            pooja.nikhare Pooja Nikhare (Inactive) added a comment - - edited Observations: Following features are working fine: Exon/ Intron options are set to default options (as in NCBI site) and properly sent while sending a request to NCBI set. Options are set default by "Reset Default" Option. Observed the following issues: When Exon Junction span is set to default "No Preference". Primer blast for all seq and organism works fine. But when it is set to other 2 options - "Primer must span an exon-exon junction", "Primer may not span an exon-exon junction" for few of the sym exception is being thrown. As for these options, NCBI Site redirects to an Info page , the Info page details are to be handled. Can be reproduced by testing with Rat genome - Taar7a . According to the NCBI site A refseq mRNA seq is required for exon/intron selection. Can we send default options of exon/intron option as "No Preference" if the database type selected is other than "refseq mRNA" ? Because other combination ends up in info page, which user has to see in console. Few parameters have been added in NCBI site like Max target size, Allow splice variants under Primer Pair Specificity Checking Parameters. And Post processing option is removed. If required test cases for different options of Exon Junction span can be added. Test case exists for default options "No preference".
            Show
            noor91zahara Noor Zahara (Inactive) added a comment - For this ticket. kindly use branch IGBF-2320 . https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2320#diff
            Hide
            pooja.nikhare Pooja Nikhare (Inactive) added a comment -

            Tested branch: https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2320

            • Cloned the repo. Ran "mvn install", builds the NCBI app properly without exception.
            • Added https://bitbucket.org/noorzahara/ncbi-primer-local/downloads/ as a repository.
              Install the app. NCBI App got installed and the Primer option tab can be seen in bottom tab.
            • Select a genome. To test default options of Exon junction span options ("No preference")
              select syms, right click on primer blast option. It opens the NCBI primer blast site.
              -Tested different param values for exon/intron selection panel, database, and other genomes. If the parameters are valid NCBI Primer site opens else Error or Info page is captured in console without exception.
            • Click on "Reset Default". All options are set to default.
            Show
            pooja.nikhare Pooja Nikhare (Inactive) added a comment - Tested branch: https://bitbucket.org/noorzahara/ncbi-primer-local/branch/IGBF-2320 Cloned the repo. Ran "mvn install", builds the NCBI app properly without exception. Added https://bitbucket.org/noorzahara/ncbi-primer-local/downloads/ as a repository. Install the app. NCBI App got installed and the Primer option tab can be seen in bottom tab. Select a genome. To test default options of Exon junction span options ("No preference") select syms, right click on primer blast option. It opens the NCBI primer blast site. -Tested different param values for exon/intron selection panel, database, and other genomes. If the parameters are valid NCBI Primer site opens else Error or Info page is captured in console without exception. Click on "Reset Default". All options are set to default.
            Show
            noor91zahara Noor Zahara (Inactive) added a comment - PR submitted https://bitbucket.org/lorainelab/ncbi-primer/pull-requests/1/igbf-2320/diff
            Hide
            pooja.nikhare Pooja Nikhare (Inactive) added a comment -
            Show
            pooja.nikhare Pooja Nikhare (Inactive) added a comment - Added https://bitbucket.org/lorainelab/ncbi-primer/downloads/ (team repos downloads) as a repository in IGB. New parameters can be seen in Exon/intron selection panel under primer options tab. Tested for different parameter values. Moving the ticket to Done.

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              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                  Updated:
                  Resolved: