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jorvis / biocode

Bioinformatics code libraries and scripts
MIT License
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convert_gff3_to_ncbi_tbl.py error generated #41

Closed wyim-pgl closed 7 years ago

wyim-pgl commented 7 years ago

Dear Joshua,

I've got error during convert_gff3_to_ncbi_tbl.py.

Can you please check ?

convert_gff3_to_ncbi_tbl.py -i ../gene.gff -o aasdasdasd -ln JC0 -nap adsadasd

Traceback (most recent call last): File "/Users/wyim/bin/biocode/gff/convert_gff3_to_ncbi_tbl.py", line 92, in main() File "/Users/wyim/bin/biocode/gff/convert_gff3_to_ncbi_tbl.py", line 55, in main (assemblies, features) = biocodegff.get_gff3_features( args.input_file ) File "/Users/wyim/bin/biocode/lib/biocodegff.py", line 272, in get_gff3_features raise Exception("Error in GFF3: Parent {0} referenced by a child feature before it was defined".format(parent_id) ) Exception: Error in GFF3: Parent Mecry000010.1 referenced by a child feature before it was defined

jorvis commented 7 years ago

Some of the parsing libraries have issues with misordered GFF. That is, where features like a CDS appear which reference an mRNA parent, but in which that parent has not been seen yet in the file. Fortunately, this has come up before and there's a script which attempts to correct for it. Could you try running your input through the gff/correct_gff_feature_order.pl script and then use that output to try again?

jorvis commented 7 years ago

Closing this, assuming that fixed the issue. If not, please re-open and post example input file.