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  1. IGB
  2. IGBF-4029

Investigate GFF file from NCBI not loading in IGB

        Details

        • Type: Improvement
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

          Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

          To reproduce the issue:

          1. In a web browser:
          2. Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000328365.1/
          3. Click Download
          4. Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
          5. Click Download
          6. Unzip the ncbi_dataset.zip file
          7. In IGB:
          8. Click File > Open Genome from File...
          9. Select Reference Sequence > Browse...
          10. Select the GCA_000328365.1_Capca1_genomic.fna file in the unzipped ncbi_dataset folder
          11. Click OK
          12. Select File > Open File...
          13. Select the genomic.gff file in the unzipped ncbi_dataset folder
          14. Click Open
          15. Note the errors in the IGB Log

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              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-4002 Fix GFF null pointer exception when FASTA included

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-4028 [ 23324 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-4002 [ IGBF-4002 ]
                nfreese Nowlan Freese made changes -
                Description Situation:

                Task:                 		Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.
                nfreese Nowlan Freese made changes -
                Description Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.
                		Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

                To reproduce the issue:
                In a web browser:
                Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002234675.1/
                Click Download
                Select file source > RefSeq Only
                Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
                Click Download
                Unzip the ncbi_dataset.zip file
                In IGB:
                Click File > Open Genome from File...
                Select Reference Sequence > Browse...
                Select the GCF_002234675.1_ASM223467v1_genomic.fna file in the unzipped ncbi_dataset folder
                nfreese Nowlan Freese made changes -
                Description Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

                To reproduce the issue:
                In a web browser:
                Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002234675.1/
                Click Download
                Select file source > RefSeq Only
                Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
                Click Download
                Unzip the ncbi_dataset.zip file
                In IGB:
                Click File > Open Genome from File...
                Select Reference Sequence > Browse...
                Select the GCF_002234675.1_ASM223467v1_genomic.fna file in the unzipped ncbi_dataset folder
                		Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

                To reproduce the issue:
                In a web browser:
                Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002234675.1/
                Click Download
                Select file source > RefSeq Only
                Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
                Click Download
                Unzip the ncbi_dataset.zip file
                In IGB:
                Click File > Open Genome from File...
                Select Reference Sequence > Browse...
                Select the GCF_002234675.1_ASM223467v1_genomic.fna file in the unzipped ncbi_dataset folder
                Click OK
                Select File > Open File...
                Select the genomic.gff file in the unzipped ncbi_dataset folder
                nfreese Nowlan Freese made changes -
                Description Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

                To reproduce the issue:
                In a web browser:
                Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002234675.1/
                Click Download
                Select file source > RefSeq Only
                Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
                Click Download
                Unzip the ncbi_dataset.zip file
                In IGB:
                Click File > Open Genome from File...
                Select Reference Sequence > Browse...
                Select the GCF_002234675.1_ASM223467v1_genomic.fna file in the unzipped ncbi_dataset folder
                Click OK
                Select File > Open File...
                Select the genomic.gff file in the unzipped ncbi_dataset folder                 		Situation: NCBI has many genomes and annotations that are useful to IGB users. Gene annotations are provided as a GFF or GTF file. The GFF (have not tested GTF) file does not currently load correctly in IGB.

                Task: Investigate why the NCBI GFF/GTF file is not loading correctly in IGB.

                To reproduce the issue:
                # In a web browser:
                # Go to https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000328365.1/
                # Click Download
                # Select file types > Genome sequences (FASTA), Annotation features (GTF), and Annotation features (GFF)
                # Click Download
                # Unzip the ncbi_dataset.zip file
                # In IGB:
                # Click File > Open Genome from File...
                # Select Reference Sequence > Browse...
                # Select the GCA_000328365.1_Capca1_genomic.fna file in the unzipped ncbi_dataset folder
                # Click OK
                # Select File > Open File...
                # Select the genomic.gff file in the unzipped ncbi_dataset folder
                # Click Open
                # Note the errors in the IGB Log
                pkulzer Paige Kulzer made changes -
                Sprint Winter 1 [ 209 ] Spring 1 [ 210 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 1 [ 210 ] Spring 3 [ 212 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 3 [ 212 ] Spring 5 [ 214 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 5 [ 214 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Udaya Chinta [ uchinta ]

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated: