Comments (6)
Thank you for your feedback. That would be definitely useful, we will add this information.
from emblmygff3.
Done.
Will be included in the next release (not planned yet. I will wait for more modifications). To have this improvement before the next EMBLmyGFF3 release, install EMBLmyGFF3 using git clone:
pip uninstall EMBLmyGFF3 #could be needed twice
git clone https://github.com/NBISweden/EMBLmyGFF3.git
cd EMBLmyGFF3/
python setup.py install
If you already installed the tool using git clone you will have to do so:
pip uninstall EMBLmyGFF3 #could be needed twice
git pull #from the EMBLmyGFF3 git repository. It will update the code
python setup.py install #from the EMBLmyGFF3 git repository
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Thanks!
Would it be possible to catch all exceptions with a clue on the location into the GFF3 file ? The error examples number 1 and 3 in my comment above are not addressed by this commit, unless I'm mistaken (although, for error number 1, I admit that I can search for non ASCII character by a simple shell command)
from emblmygff3.
Actually having a CDS not multiple of three is allowed. So it is not an error, but translation method (which is part of biopython and not EMBLmyGFF3) raise a warning to inform you.
To fulfil your request I have now added an internal (in EMBLmyGFF3) Warning with the CDS ID when the CDS is not multiple of three. I'm not sure about the pertinence to add this warning, but it is now done.
For the following error
UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 5: ordinal not in range(128)
I don't have any test case to work with. Could you provide me a sample of your data ?
from emblmygff3.
I had a look on your commit (6816aa8). I agree with you that this may not be pertinent to add this warning... I thought it could be possible quite easy to catch all kind of errors indifferently from biopython and provide the feature ID where it occurs, but maybe I am mistaken... I thank you anyway.
For the ASCII error, you should have the error only by copy-paste this character into an attribute of the 9th column of the GFF3: "α" (greek alpha). Tell me if not.
Thank you
from emblmygff3.
The last commit (7398bd4) should have addressed the UnicodeDecodeError error.
Thank you for having catched this issue.
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Related Issues (20)
- How to add in comment or CC line HOT 1
- Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file HOT 2
- thank you HOT 1
- ImportError Bio.Alphabet error HOT 1
- What the option "-a accesion" parameter should to be set(means:What type?) HOT 3
- TypeError: read() takes 1 positional argument but 2 were given? HOT 3
- attribute formats broken across several lines HOT 2
- Use of example data HOT 2
- Contigs are disorganised in the EMBL file HOT 10
- Warning qualifier unknown db_xref HOT 1
- Translation problem HOT 2
- Reporting the line number of the problematic input GFF3 files when parsing error is triggered HOT 2
- BioPython 1.81 installs via conda, but needs an older version HOT 2
- if I can specify certain python source during python setup.py install HOT 2
- Not for ENA submission: Sequence too short
- Installation issue EMBLmyGFF3 & python version requirements
- Translation when circular genome and ORF in the cut of the assembly HOT 1
- unexpected keyword argument 'strand' HOT 3
- Gene sorting compared to fasta HOT 4
- Bug when specifying -g mitochrondrion (or plastid)
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