GFF3toolkit
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NAL-i5K
Python programs for processing GFF3 files
Thank you for your development of the great gff3 tools. While I use "gff3_to_fasta -st user_defined -u mRNA CDS" to get fasta file, it seems to get child (this is...
Hello, I would like to use the GFF3toolkit to remove some gene models (all with one isoform, from an external list) from a gff3 file. I first run `gff3_QC -g...
When I run gff3_merge I get the following error Traceback (most recent call last): File "/tools/python/3.6.3/bin/gff3_merge", line 8, in sys.exit(script_main()) File "/tools/python/3.6.3/lib/python3.6/site-packages/gff3tool/bin/gff3_merge.py", line 229, in script_main main(args.gff_file1, args.gff_file2, args.fasta, report_fh,...
When using gff3_merge, I had to use the user-defined file option. The sequence extraction and blast seemed to run fine, but the replacement still didn't work. I tried the same...
run `pip install gff3tool` Stopped `Building wheel for gff3tool (setup.py) ... -`
Hi, I installed gff3toolkit by pip install, using python 3.5. My code is ``` /work/LAS/mash-lab/jing/bin/Anaconda3/envs/mypy3.5/bin/gff3_merge -g1 transdecoder_final.gff3 -g2 Zm_B73.gff3 -f Zm-B73-REFERENCE-NAM-5.0.fa -og merged_final+anno.gff3 -r merged_fina_anno_report.txt ``` It's failed when identify...
https://github.com/NAL-i5K/GFF3toolkit/issues/78 python gff3tool/lib/gff3_ID_generator.py -g merged.gff -og id.gff -uuid -r report.txt -t CDS
I cannot install gff3tool in a freshly created conda env (including python=2.7 and perl): (gff3tool_env) [user@XXX]$ pip install gff3tool DEPRECATION: Python 2.7 will reach the end of its life on...
At least gff3-py will continue to be maintained, we should switch back to it: https://github.com/hotdogee/gff3-py/releases/tag/1.0.0 rather than including another copy inside the repo.
I ran gff3_merge program, and I got the error ``` Traceback (most recent call last): File "/home/meiyang/anaconda3/bin/gff3_merge", line 33, in sys.exit(load_entry_point('gff3tool==2.1.0', 'console_scripts', 'gff3_merge')()) File "/home/meiyang/anaconda3/lib/python3.9/site-packages/gff3tool-2.1.0-py3.9.egg/gff3tool/bin/gff3_merge.py", line 229, in script_main main(args.gff_file1,...
