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gff3_merge iteritems error #110
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Thanks for the bug report, @chklopp ! We'll look into this in the next couple of days. In the meantime, would you be willing to share the datasets/command you used so we can make sure we can reproduce the error? |
We have replaced iteritems by items in the code and it worked. Here is a link a data subset including fasta and both gff files : |
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, args.output_gff, args.all, args.auto_assignment, args.user_defined_file1, args.user_defined_file2, logger=logger_stderr)
File "/tools/python/3.6.3/lib/python3.6/site-packages/gff3tool/bin/gff3_merge.py", line 85, in main
gff3_merge.merge.main(autoReviseGff, gff_file2, output_gff, report, user_defined1, user_defined2, logger)
File "/tools/python/3.6.3/lib/python3.6/site-packages/gff3tool/lib/gff3_merge/merge.py", line 22, in main
gff3_sort.main(gff_file1, output='WA_sorted.gff', logger=logger)
File "/tools/python/3.6.3/lib/python3.6/site-packages/gff3tool/bin/gff3_sort.py", line 279, in main
report.write(TwoParent(child['attributes']['ID'],exon))
File "/tools/python/3.6.3/lib/python3.6/site-packages/gff3tool/bin/gff3_sort.py", line 138, in TwoParent
attributes_line = ";".join("=".join((str(k),str(v))) for k,v in attributes.iteritems())
AttributeError: 'dict' object has no attribute 'iteritems'
There seems to be a python2 syntax used in the gff3_sort.py script.
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