Comments (4)
Potentially yes. Do you have any other error / trace before this ?
If you can send me your files I can have a look more in detail.
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There is no trace before this one.
The files I was trying to use are attached to this reply.
from emblmygff3.
Thank you for having reported this problem. This is indeed a bug.
Line 194 of EMBLmyGFF3.py
while end:
has to be replaced by
while end < len(seq):
It will be fixed in a future release.
Until then, you can fix it yourself that way:
Uninstall EMBLmyGFF3:
pip unistall EMBLmyGFF3
clone the repo in a nice place:
mkdir ~/git
cd ~/git
git clone https://github.com/NBISweden/EMBLmyGFF3.git
cd EMBLmyGFF3
replace line 194 of EMBLmyGFF3.py as indicated before (here using the nano text editor but you can use what ever you want):
nano EMBLmyGFF3/modules/feature.py
install:
python setup.py install
or if you do not have administartive rights on your machine:
python setup.py install --user
Except this bug I can point 2 other problems:
- The fasta headers are different from those reported in column 1 of the gff file. Be sure the annotation has been done using this fasta sequences. If it is the case fix the name they must be similar in both files otherwise EMBLmyGFF3 will not be able to match the features (gene,cds,etc) to the proper sequence. Currently no feature at all will be attached to the sequences.
- if you plan to submit the EMBL file created like that, you will have a rejection from ENA. Indeed they do not accept sequences that start or/and end with
N
(gaps). You have plenty of cases like that. This is also related to the current bug. If you shrink the N from extremities you will passthrough the current bug in EMBLmyGFF3 and do not encounter any rejection due to trailing Ns during ENA submission.
To do so first you must fix names between your gff and fasta files as indicated point 1 and then you can use the scriptgff3_sp_clipN_seqExtremities_and_fixCoordinates.pl
from the GAAS repository.
from emblmygff3.
I realised about the headers after having a problem related with that with another species, the hedears will be changed, the EMBL sequences are not going to be submitted, I needed them to make some analysis.
Thank you, I really apreciate your help.
from emblmygff3.
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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