Comments (5)
This is one of the few perl scripts left (which also rely on the bioUtils.pm module). Did you install biocode via pip? Within that python framework I can't properly place the perl module. You should be able to run this if you check out biocode instead from GitHub and then make sure biocode/lib/ is in your PERL5LIB env variable. Or copy bioUtils.pm from a checkout into a directory where perl will see it.
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Hi I'm a colleague of @arsilan324 . Got it running on my computer (thanks for your explanations), but ran into other problems:
panic! don't know what to do with feat type: 3'UTR at ./gff/correct_gff_feature_order.pl line 186, <$ifh> line 6.
found more than one gene at position 1 on molecule Transcript_100004
The gff3 looks as follows
Transcript_100004 transdecoder gene 1 813 . + . ID=Transcript_100004|g.119957;Name=ORF%20Transcript_100004%7Cg.119957%20Transcript_100004%7Cm.119957%20type%3A5prime_partial%20len%3A200%20%28%2B%29
Transcript_100004 transdecoder mRNA 1 813 . + . ID=Transcript_100004|m.119957;Parent=Transcript_100004|g.119957;Name=ORF%20Transcript_100004%7Cg.119957%20Transcript_100004%7Cm.119957%20type%3A5prime_partial%20len%3A200%20%28%2B%29
Transcript_100004 transdecoder CDS 1 600 . + . ID=cds.Transcript_100004|m.119957;Parent=Transcript_100004|m.119957
Transcript_100004 transdecoder exon 1 813 . + . ID=Transcript_100004|m.119957.exon1;Parent=Transcript_100004|m.119957
Transcript_100004 transdecoder 3'UTR 601 813 . + . ID=Transcript_100004|m.119957.utr3p1;Parent=Transcript_100004|m.119957
Transcript_100004 transdecoder gene 1 813 . - . ID=Transcript_100004|g.119958;Name=ORF%20Transcript_100004%7Cg.119958%20Transcript_100004%7Cm.119958%20type%3Acomplete%20len%3A128%20%28-%29
Transcript_100004 transdecoder mRNA 1 813 . - . ID=Transcript_100004|m.119958;Parent=Transcript_100004|g.119958;Name=ORF%20Transcript_100004%7Cg.119958%20Transcript_100004%7Cm.119958%20type%3Acomplete%20len%3A128%20%28-%29
Transcript_100004 transdecoder CDS 322 705 . - . ID=cds.Transcript_100004|m.119958;Parent=Transcript_100004|m.119958
Transcript_100004 transdecoder exon 1 813 . - . ID=Transcript_100004|m.119958.exon1;Parent=Transcript_100004|m.119958
Transcript_100004 transdecoder 5'UTR 706 813 . - . ID=Transcript_100004|m.119958.utr5p1;Parent=Transcript_100004|m.119958
Transcript_100004 transdecoder 3'UTR 1 321 . - . ID=Transcript_100004|m.119958.utr3p1;Parent=Transcript_100004|m.119958
I guess there should be only one gene with two child transcripts. Then this would be a bug in the upstream software that produced the gff file.?
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I don't mind modifying it, but in legal GFF3 that third column is supposed to correspond to a Sequence Ontology (SO) term. The parent is UTR but there are also five_prime_UTR and three_prime_UTR. You'd have to change your input file to have those feature types instead. It wouldn't hurt to make a transdecoder ticket too and tell Brian to make his GFF right. :)
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Supported added for these two types in commit 57e92bd
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great. thanks
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Related Issues (20)
- NameError: name 'utils' is not defined HOT 13
- convert_gff3_to_ncbi_tbl HOT 5
- Syntax error on gff.py HOT 4
- Exclude mRNA features in bacterial TBL exports
- Attribute error for update_selected_column9_values.py HOT 1
- Biocode.gff module error HOT 2
- [convert_genbank_to_gff3.py] key_error: locus_tag HOT 5
- AttributeError: type object 'str' has no attribute 'maketrans' HOT 2
- AttributeError: 'Gene' object has no attribute 'add_CDS' HOT 4
- Insert EC numbers into chado database issue HOT 5
- convert_augustus_to_gff3.py error HOT 6
- Conda based install HOT 2
- convert_gff3_to_ncbi_tbl.py HOT 2
- convert_gff_to_ncbi_tbl.py HOT 3
- Incorrect parent features from convert_tRNAScanSE_to_gff3.pl HOT 2
- Formatting Issue? HOT 2
- biocode error HOT 16
- product info not printout in tbl HOT 2
- fasta/fasta_simple_stats.py fails on any file with only one sequence
- [convert_genbank_to_gff3.py] No Locus_tag present in my genbank file HOT 2
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