Comments (9)
I wrote a script a while ago to convert the output of genomad annotate
to a GFF. Let me know if it works for you.
from genomad.
I had this error:
$ python convert_tabular_to_gff.py virus_genes.tsv genes.gff
File "convert_tabular_to_gff.py", line 40
fout.write(f"{row.gene.rsplit('_', 1)[0]}\t")
^
SyntaxError: invalid syntax
from genomad.
That's probably because the script expects you to execute it as ./convert_tabular_to_gff.py
and not python convert_tabular_to_gff.py
. Can you try again running ./convert_tabular_to_gff.py virus_genes.tsv genes.gff
?
from genomad.
I tried as you suggest, but still give me the same error.
from genomad.
That's strange. I just executed it here and it worked as expected. Maybe it is being caused by the copy-and-paste process? Try to download from the link below and run it again.
convert_tabular_to_gff.py.zip
from genomad.
Another possibility: maybe python
links to python2
in your system. Try to replace the first line with:
#!/usr/bin/env python3
This will guarantee that the script is executed with Python 3.
from genomad.
It was exactly this, now I loaded the right python and it ran perfectly. Thank you very much!
from genomad.
No worries! Sorry that this was more complicated than it should be.
I'll leave this issue open and consider adding GFF outputs to a future release of geNomad.
from genomad.
Thank you, this would be very useful, also an .gbk output would be great!
from genomad.
Related Issues (20)
- Error downloading database HOT 2
- Inquiry on virus from MAG HOT 4
- [feature request] query database clustering HOT 1
- Whether measures have been taken by genomad to avoid identifying genomic islands as viruses? HOT 5
- AMR annotations on chromsome? HOT 1
- Errors when download and the same issue when running genomad -h HOT 3
- The virus identified by genomad weren't annotated as virus sequence by VIBRANT? HOT 3
- geNomad taxonomy about Baltimore classification HOT 1
- Error with geNomad v1.8.0, missing tensorflow.keras HOT 5
- mmseqs2 error HOT 3
- Different protein number from genomad and pyrodigal-gv HOT 2
- Small (reference) data for testing HOT 9
- Error while classifying sequences HOT 6
- Error mmseqs prefilter HOT 4
- genomad annotate fastq file is empty or contains multiple entries HOT 3
- plasmid classified as virus? HOT 7
- Optimization Request for Analyzing Large Number of MAGs with geNomad HOT 5
- Fewer viral contigs identified from genomad vs virsorter2 HOT 4
- The question about --disable-nn-classification HOT 1
- Provirus detection in genomad vs checkv HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from genomad.