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KeyError: 'replace'

Open meiyang12 opened this issue 1 year ago • 6 comments

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?

meiyang12 avatar Nov 03 '22 01:11 meiyang12