Comments (4)
Looking at this - can you verify that you were using python3 (and so pip3?) It would be helpful to paste the command you used to run the convert_gff3_to_gbk.py script.
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So I ran this in an anaconda python3 environment convert_gff3_to_gbk.py -i ../../032017_assembly/Pst_104E_v12_h_ctg.anno.gff3 -g ../../032017_assembly/Pst_104E_v12_h_ctg.fa -seq -o Pst_104E_v12_h_ctg.gbk
The issue was that convert_gff3_to_gbk.py is in my bin and looks for the data folder like this TEMPLATE_ENVIRONMENT = Environment(
autoescape=False,
loader=FileSystemLoader(os.path.join(PATH, '../data')),
trim_blocks=False)
. The data folder was not copied to this location. I simply pulled the data folder from git and put it in the right location so all is working now.
from biocode.
Thanks for tracking that issue down. It reminded me that when doing an installation via PyPi (rather than GitHub clone) that I wasn't handling the data/*.templates files. I've made a series of commits yesterday and today in order to fix this, and commit faee877 was the one where the actual conversion script was changed.. This will be available in the 0.2.0 release of biocode since both the python script and entire installer had to be updated.
from biocode.
Release 0.2.0 made, and tested within the docker image.
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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
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- Attribute error for update_selected_column9_values.py HOT 1
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- [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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