Comments (5)
There is currently no option to do this, but I could implement it as a feature in the future. In the meantime, you can obtain the nucleotide sequences of the CDSs by extracting them from the genomes using the gene coordinates.
from genomad.
I also had a seemingly simple question about whether I could format the output at taxonomy, such as converting it to k__; p__; c__; o__; f__; g__; s__.
Thanks!
from genomad.
You can use taxopy
for that. geNomad's taxdump is inside the database directory, and you can find the TaxIds in the <prefox>_annotate/<prefox>_taxonomy.tsv
file.
For instance:
import taxopy
taxdb = taxopy.TaxDb(
nodes_dmp="genomad_db/nodes.dmp",
names_dmp="genomad_db/names.dmp",
keep_files=True
)
taxon = taxopy.Taxon(5797, taxdb)
for rank, name in reversed(taxon.ranked_name_lineage):
if name != "root":
print(f"{rank}__{name}")
realm__Duplodnaviria
kingdom__Heunggongvirae
phylum__Uroviricota
class__Caudoviricetes
order__Crassvirales
from genomad.
What's the difference between "Unclassified" and "Viruses;;;;;;" ?
from genomad.
"Unclassified" means that the genes in the sequence had no matches to markers with taxonomy information. "Viruses" means that the classification is uncertain at a high rank.
from genomad.
Related Issues (20)
- 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
- Error mmseqs prefilter HOT 2
- Genetic codes HOT 2
- question about integrase identification during provirus identification HOT 3
- Number of contigs in the assembly HOT 1
- Chromosome classification result HOT 2
- Discrepancy in Output Counts in Genomad HOT 1
- line 19 in aggregated_classfication.py HOT 2
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from genomad.