NBISweden EMBLmyGFF3 issues

NBISweden / EMBLmyGFF3

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

GNU General Public License v3.0

59 stars 16 forks source link

issues

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CDS translation is broken with bacterial trans_table=11

#86 lfalquet opened 2 days ago
3
Add option to pad locus tag number with zeros

#85 bartns closed 6 months ago
5
Bug when specifying -g mitochrondrion (or plastid)

#84 olekto opened 7 months ago
0
Gene sorting compared to fasta

#83 stephan-nylinder opened 8 months ago
4
unexpected keyword argument 'strand'

#82 webbchen opened 8 months ago
3
Translation when circular genome and ORF in the cut of the assembly

#81 BenjaminGuinet opened 1 year ago
1
2.2.1

#80 Juke34 closed 1 year ago
0
Installation issue EMBLmyGFF3 & python version requirements

#79 rhinoplax closed 1 year ago
0
Not for ENA submission: Sequence too short

#78 CEPHAS-01 closed 1 year ago
0
if I can specify certain python source during python setup.py install

#77 njliangdong closed 1 year ago
2
BioPython 1.81 installs via conda, but needs an older version

#76 AdamStuckert closed 1 year ago
2
Reporting the line number of the problematic input GFF3 files when parsing error is triggered

#75 yjx1217 closed 1 year ago
2
Update README.md

#74 Juke34 closed 2 years ago
0
Update to verssion 2.2

#73 Juke34 closed 2 years ago
0
Translation problem

#72 nicolasginet closed 1 year ago
2
Warning qualifier unknown db_xref

#71 girouxem closed 2 years ago
1
Contigs are disorganised in the EMBL file

#70 ireneortega closed 1 year ago
10
Use of example data

#69 yamaton closed 2 years ago
2
attribute formats broken across several lines

#68 LornaMGnify closed 3 years ago
2
Fix error with --expose_translations option

#67 yamaton closed 3 years ago
1
TypeError: read() takes 1 positional argument but 2 were given?

#66 VibrantStarling closed 2 years ago
3
What the option "-a accesion" parameter should to be set(means:What type？)

#65 chemy-cm closed 3 years ago
3
ImportError Bio.Alphabet error

#64 emmannaemeka closed 2 years ago
1
thank you

#63 KamilSJaron opened 3 years ago
1
Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file

#62 rstewa03 closed 3 years ago
2
Speed

#61 Juke34 closed 3 years ago
0
How to add in comment or CC line

#60 katherinedougan opened 3 years ago
1
EMBL to fasta ?

#59 ptranvan closed 1 year ago
1
Download

#58 henricheng closed 3 years ago
27
Confusion with the locus tag

#57 ptranvan closed 3 years ago
1
Bio.Alphabet has been removed from Biopython

#56 metalichen closed 3 years ago
3
Bio.Alphabet issue

#55 AdamStuckert closed 3 years ago
3
Is the option --locus_numbering_start working?

#54 Jeepee8820 closed 4 years ago
5
--translate option does not work anymore

#53 Juke34 closed 3 years ago
11
question: what additional options for mitochondria

#52 rob123king closed 4 years ago
4
update tests to throw exit code

#51 Juke34 closed 4 years ago
0
ID not taken as locus tag

#50 rob123king closed 4 years ago
2
Py3

#49 Juke34 closed 4 years ago
0
Error with embl file during ENA webin-cli validation

#48 Anto007 closed 4 years ago
2
Feature/1.3

#47 Juke34 closed 4 years ago
0
Joining of intron features

#46 sophietandonnet closed 4 years ago
1
update to version 1.2.7 and 1.2.8

#45 Juke34 closed 4 years ago
0
Installation inconveniences

#44 apredeus closed 4 years ago
2
Spread feature like CDS are not collectively linked when L1 and/or L2 feature missing

#43 Juke34 opened 5 years ago
0
When no strand for CDS by default the negative strand is used

#42 Juke34 closed 4 years ago
0
Add warning for unknown sequence

#41 Juke34 closed 4 years ago
0
ZeroDivisionError (when --no_progress activated)

#40 psur9757 closed 4 years ago
1
EMBL flatfile not compatible with PAGIT RATT

#39 peritob closed 5 years ago
4
string index out of range (when sequence end by Ns)

#38 Juke34 closed 4 years ago
4
Warning regarding protein ID

#37 VenithaB closed 5 years ago
7