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jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
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report_gff3_statistics.py, 'Gene' object has no attribute 'length' #16

Closed pezhmansafdari closed 10 years ago

pezhmansafdari commented 10 years ago

Hi, When I am trying to run "report_gff3_statistics.py" script for a file which looks like what I have pasted below, I get this error: Traceback (most recent call last): File "report_gff_stat.py", line 113, in main() File "report_gff_stat.py", line 56, in main type_lengths['gene'] += gene.length AttributeError: 'Gene' object has no attribute 'length' T he gff3 file: 28 scaffold_936 phytozome9_0 gene 5553 6897 . - . ID=gene4;Name=Aquca_936_00001 29 scaffold_936 phytozome9_0 mRNA 5553 6897 . - . ID=mRNA4;Parent=gene4;Name=Aquca_936_00001.1;pacid=22051342;longest=1 30 scaffold_936 phytozome9_0 three_prime_UTR 5553 5787 . - . Parent=mRNA4;pacid=22051342 31 scaffold_936 phytozome9_0 exon 5553 5897 . - . Parent=mRNA4;pacid=22051342 32 scaffold_936 phytozome9_0 CDS 5788 5897 . - 2 Parent=mRNA4;pacid=22051342 33 scaffold_936 . intron 5898 6021 . - . Parent=mRNA4 34 scaffold_936 phytozome9_0 exon 6022 6086 . - . Parent=mRNA4;pacid=22051342 35 scaffold_936 phytozome9_0 CDS 6022 6086 . - 1 Parent=mRNA4;pacid=22051342 36 scaffold_936 . intron 6087 6219 . - . Parent=mRNA4 37 scaffold_936 phytozome9_0 exon 6220 6305 . - . Parent=mRNA4;pacid=22051342 38 scaffold_936 phytozome9_0 CDS 6220 6305 . - 0 Parent=mRNA4;pacid=22051342 39 scaffold_936 . intron 6306 6802 . - . Parent=mRNA4 40 scaffold_936 phytozome9_0 CDS 6803 6895 . - 0 Parent=mRNA4;pacid=22051342 41 scaffold_936 phytozome9_0 exon 6803 6897 . - . Parent=mRNA4;pacid=22051342 42 scaffold_936 phytozome9_0 five_prime_UTR 6896 6897 . - . Parent=mRNA4;pacid=22051342

Thanks,

Pezhman

jorvis commented 10 years ago

The only issue I see there that makes your GFF non-standard is that it lacks IDs on the exon and CDS features, but I'm not sure that should cause this particular script to fail. Do you think you could mail the whole GFF to me or make it available somewhere for me to test against?

jorvis commented 10 years ago

Closing due to lack of response. Please re-open if you can post an example file somewhere that reproduces this issue.