GFF3toolkit
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KeyError: 'replace'
I ran gff3_merge program, and I got the error
Traceback (most recent call last):
File "/home/meiyang/anaconda3/bin/gff3_merge", line 33, in <module>
sys.exit(load_entry_point('gff3tool==2.1.0', 'console_scripts', 'gff3_merge')())
File "/home/meiyang/anaconda3/lib/python3.9/site-packages/gff3tool-2.1.0-py3.9.egg/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 "/home/meiyang/anaconda3/lib/python3.9/site-packages/gff3tool-2.1.0-py3.9.egg/gff3tool/bin/gff3_merge.py", line 70, in main
gff3_merge.revision.main(gff_file=gff_file1, revision_file=autoFILE, output_gff=autoReviseGff, report_file=autoReviseReport, user_defined1=user_defined1, auto=auto, logger=logger)
File "/home/meiyang/anaconda3/lib/python3.9/site-packages/gff3tool-2.1.0-py3.9.egg/gff3tool/lib/gff3_merge/revision.py", line 227, in main
tag = ','.join(child['attributes']['replace']).replace(' ','')
KeyError: 'replace'
and my gff3 files were like these: one:
##gff-version 3
##sequence-region BMSK_chr10_RagTag 64593 17730062
BMSK_chr10_RagTag Liftoff gene 64593 65277 . + . ID=gene5668;name=BMSK0005247;coverage=1.0;sequence_ID=1.0;valid_ORFs=1;extra_copy_number=0;copy_num_ID=BMSK0005247_0
BMSK_chr10_RagTag Liftoff mRNA 64593 65277 . + . ID=mRNA5668;Parent=gene5668;name=BMSK0005247.1;matches_ref_protein=True;valid_ORF=True;extra_copy_number=0
BMSK_chr10_RagTag Liftoff exon 64593 64628 . + . Parent=mRNA5668;extra_copy_number=0
BMSK_chr10_RagTag Liftoff five_prime_UTR 64593 64628 . + . Parent=mRNA5668;extra_copy_number=0
BMSK_chr10_RagTag Liftoff five_prime_UTR 64752 64818 . + . Parent=mRNA5668;extra_copy_number=0
BMSK_chr10_RagTag Liftoff exon 64752 65277 . + . Parent=mRNA5668;extra_copy_number=0
BMSK_chr10_RagTag Liftoff CDS 64819 65028 . + 0 Parent=mRNA5668;extra_copy_number=0
BMSK_chr10_RagTag Liftoff three_prime_UTR 65029 65277 . + . Parent=mRNA5668;extra_copy_number=0
two:
##gff-version 3
##sequence-region BMSK_chr10_RagTag 60014 17730543
BMSK_chr10_RagTag Liftoff gene 60014 62435 . - . ID=gene6047;Name=KWMTBOMO05391;coverage=0.997;sequence_ID=0.996;valid_ORFs=0;extra_copy_number=0;copy_num_ID=KWMTBOMO05391_0
BMSK_chr10_RagTag Liftoff mRNA 60014 62435 . - . ID=mRNA6047;Name=KWMTBOMO05391;Parent=gene6047;matches_ref_protein=False;valid_ORF=False;missing_stop_codon=True;extra_copy_number=0
BMSK_chr10_RagTag Liftoff transcription_end_site 60014 60014 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff exon 60014 60869 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff stop_codon 60169 60171 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff CDS 60169 60869 . - 1 Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff terminal 60169 60869 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff CDS 62184 62227 . - 0 Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff initial 62184 62227 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff exon 62184 62338 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff start_codon 62225 62227 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff exon 62427 62435 . - . Parent=mRNA6047;extra_copy_number=0
BMSK_chr10_RagTag Liftoff transcription_start_site 62435 62435 . - . Parent=mRNA6047;extra_copy_number=0
anyone can help?