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andreaminio / AnnotationPipeline-EVM_based-DClab

Cantù Lab @ UC Davis - Annotation pipeline - EVM based
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Error about "GFF_extract_features.py" #3

Closed unavailable-2374 closed 2 years ago

unavailable-2374 commented 2 years ago

Commnd：“python3 tools/Scripts/GFF_extract_features.py -g mmpt_1.fa -a R1.stringtie.transdecoder.gff3 -p R1.stringtie.transdecoder.clean > R1.stringtie.transdecoder.clean.log”

Error： File "/public/agis/zhouyongfeng_group/caoshuo/anno/tools/Scripts/GFF_extract_features.py", line 1189 for g_key, g_value in sorted(genes.iteritems(), key=lambda (k, v): itemgetter(1, 2)(v)): ^ SyntaxError: expected ':'

Python 3.10.3

thanks!

andreaminio commented 2 years ago

Hi,

The issue is with the python version. The script is made in python 2, not python 3.

Try running it like this requiring explicitly python 2: python2 tools/Scripts/GFF_extract_features.py -g mmpt_1.fa -a R1.stringtie.transdecoder.gff3 -p R1.stringtie.transdecoder.clean > R1.stringtie.transdecoder.clean.log

unavailable-2374 commented 2 years ago

thanks！