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NAL-i5K / GFF3toolkit

Python programs for processing GFF3 files
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gff3_fix error #107

Closed yemao701 closed 4 years ago

yemao701 commented 4 years ago

Thanks you for your wonderful tool kit! When I run gff3_fix follow your instruction, I encountered a error: QQ截图20200804004653 This is the error report generated by gff3_QC: QQ截图20200804004741 This is my gff file:

Finalv2.rep.genename.v2.nored.zip

Can you help me fix this problem?

mpoelchau commented 4 years ago

@yemao701 sorry about the issues. gff3_fix expects ID attributes for all features. I'll update the FAQ and readme with this information. You can use the gff3_ID_generator.py script in the lib directory to generate IDs.

python lib/gff3_ID_generator.py -g in.gff3 -og out.gff -uuid -r report.txt

yemao701 commented 4 years ago

@yemao701 sorry about the issues. gff3_fix expects ID attributes for all features. I'll update the FAQ and readme with this information. You can use the gff3_ID_generator.py script in the lib directory to generate IDs.

python lib/gff3_ID_generator.py -g in.gff3 -og out.gff -uuid -r report.txt

Thank you for your timely response.

yemao701 commented 4 years ago

@mpoelchau Sorry to bother you again, when I ran lib/gff3_ID_generator.py I got this error. QQ截图20200805144408 I install gfftools through pip3 install.

hsiaoyi0504 commented 4 years ago

@yemao701 Based on what I saw in your screenshot, I would guess that you have used two different python virtual environments at the same time.

mpoelchau commented 4 years ago

I agree with @hsiaoyi0504 that there's an issue with your python virtual environment.

If you do pip3 list, is gff3tool one of the listed modules?

What python version are you using (python -V)?

yemao701 commented 4 years ago

@mpoelchau @hsiaoyi0504 I think taht gff3tools was properly installed by pip3 and the python version is 3.7.4 QQ截图20200806140352

mpoelchau commented 4 years ago

@yemao701 I issued an update that will hopefully fix your problem - can you pull again from the master branch?

yemao701 commented 4 years ago

@mpoelchau @hsiaoyi0504 Sorry for the delayed response, I encountered this problem because the pip3 I used is for python3.6, while my default python version was 3.7. I then use python 3.6 to run the script and it worked perfectly, thank you all for your help!

mpoelchau commented 4 years ago

Great, I am glad that you got it working!