KeyError: 'replace'

[meiyang12]

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?

[mpoelchau]

Sorry about the problems, @meiyang12! I can't tell from the gff3 snippets what might be wrong. If your gff3 and genome fasta files aren't too big and you're willing to share them, I can run the program and try to help debug. Let me know and we can figure out a way to transfer them.

If that doesn't work, you might try running the ID generator script - it might be that gff3_merge requires that all features have IDs. python lib/gff3_ID_generator.py -g in.gff3 -og out.gff -uuid -r report.txt

[meiyang12]

Sorry about the problems, @meiyang12! I can't tell from the gff3 snippets what might be wrong. If your gff3 and genome fasta files aren't too big and you're willing to share them, I can run the program and try to help debug. Let me know and we can figure out a way to transfer them.

If that doesn't work, you might try running the ID generator script - it might be that gff3_merge requires that all features have IDs. python lib/gff3_ID_generator.py -g in.gff3 -og out.gff -uuid -r report.txt

Hi, thanks for your suggestions. I am sorry for the late response. I tried the methods you say, but it occurred errors. So, I have uploaded the three file to google drive (https://drive.google.com/drive/folders/1YlQfbJuNmCWl3FHG3OavLusGKMuJDENt?usp=share_link).

[mpoelchau]

Thanks for sharing the files. It looks like there'a a bug that misinterprets the attributes sequence_ID and copy_num_ID as the ID attribute. Removing those attributes allowed the merge program to complete. We don't have a fix yet, but if you need to run the program now, I'd advise removing or renaming those attributes to exclude the ID portion of the tag.

[Ocean-Lyu]

Hi, thanks for gff3toolkit!

I also ran the gff_merge and encountered the same error. Renaming the sequence_ID and copy_num_ID did solve the problem. However, I met this error again when I tried to auto-assign replace tags for types beyond mRNA and my user defined file is as below:

mRNA exon
lnc_RNA exon
transcript exon
snoRNA exon
rRNA exon
tRNA exon
snRNA exon
V_gene_segment exon
C_gene_segment exon

The error emerged again after I added rRNA, tRNA, snRNA, V_gene_segment and C_gene_segment. Could you possibly offer some suggestions?

Some example gff entries are as follow:

[MonicaPoelchau-USDA]

Sorry you're having trouble with the gff3_merge program! Is there a way you could share the 2 gff files and your command with me? I can try to debug with that information.

[Ocean-Lyu]

I circumvented the problem by renaming 'V_gene_segment' and 'C_gene_segment' in the third column into 'mRNA' using:

sed -E -i 's/V_gene_segment/mRNA/' my.gff

and named them back after gff_merge using:

sed -E -i '/^\S+\t\S+\tmRNA.*V_segment/ s/mRNA/V_gene_segment/' my.gff

which I think worked just fine and there seems to be no missing information.
I do not konw if doing so is correct or can I carry on with the current gff?