Q: The gff3_fix program fails with KeyError: ‘ID’.¶
Note that the gff3_fix program requires that all features contain an ID attribute. You can use lib/gff3_ID_generator.py to generate IDs if your gff3 file does not have them for every feature.
Q: When installing, the program fails with following message:
ImportError: No module named wheel.bdist_wheel.¶
Q: When running one of the GFF3-toolkit programs, the program fails with a stack trace error.¶
Usually, this means that there is a problem with the input file. We are working on having each program output error messages with the input file line number. In the meantime, send us your input file and we can help figure out what the problem is.
Q: What are the licensing terms for this project?¶
This software/database is a “United States Government Work” under the terms of the United States Copyright Act. It was written as part of the author’s official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Agriculture Library and the U.S. Government have not placed any restriction on its use or reproduction. (Please see LICENSE.md)
Q: What kind of errors can be detected by gff3_QC.py? (Detection of GFF3 format errors: gff3_QC.py)¶
Currently, ~50 types of formatting errors can be detected. Errors are detected by reviewing three types of feature sets in a GFF3 file, and thus are grouped into three categories (Error category – feature type):
- Intra-model errors (Ema) – multiple features within a model
- Inter-model errors (Emr) – multiple features across models
- Single feature errors (Esf) – each single feature.
Please view the full documentation of gff3_QC.py for the full list of detected error types.
Q: Why is gff3_QC.py taking so long to run? (Detection of GFF3 format errors: gff3_QC.py)¶
gff3_QC.py can take a while if your gff3 file is large - please be patient!
Q: Why does the sorted gff3 file have a different number of lines than the input file? (Sort a GFF3 file: gff3_sort.py)¶
The program gff3_sort.py automatically ignores the hash tag lines other than ##gff-version 3 and ### while sorting a GFF3 file. After sorting, the program puts one line of ### between every gene model in the output GFF3. Therefore, the total lines of the output file might be different from the input. To check the consistency of the lines, please use the following command,
grep -v “#” input.gff |wc -l
grep -v “#” sorted.gff |wc -l
In addition, if your input gff file contains a feature that has two or more parent IDs, the program replicates the feature and lists it under each parent. Thus, the output file would have more lines than the input file.