Comments (4)
edit
I see there are 4 columns and the fourth is space separated!
OK!
Hello!
Thank you so much for doing this!
One small thing - in the output, some lines have 5 columns and others only have four..... e.g. species here:
contig tax_level assignment count_of_genes_assigned
single_ERR2027929.96_k87_3848 kingdom 2 Bacteria 4
single_ERR2027929.96_k87_3848 phylum 1239 Firmicutes 4
single_ERR2027929.96_k87_3848 family 186803 Lachnospiraceae 3
single_ERR2027929.96_k87_3848 family 31979 Clostridiaceae 1
single_ERR2027929.96_k87_3848 genus 841 Roseburia 2
single_ERR2027929.96_k87_3848 genus 1855714 Anaerobium 1
single_ERR2027929.96_k87_3848 genus 1485 Clostridium 1
single_ERR2027929.96_k87_3848 species specI_v3_07704 1
single_ERR2027929.96_k87_3848 species specI_v3_08779 1
single_ERR2027929.96_k87_3848 species specI_v3_11370 1
single_ERR2027929.96_k87_3848 species specI_v3_10000 1
Can this be fixed somehow? :-D
Cheers
Mick
from gunc.
Hi Mick!
I am confused by the output of gunc - I thought it would be able to identify those contigs which do not match with the rest of the genome - can gunc not do that?
We are currently working on this as a feature. Our aim is to have an automated 'chopping away' of problematic contigs, but we want to do it properly and benchmark before letting lose a tool that wreaks havoc with your previous MAGs...
Or at least I thought it would be able to tell me the taxonomic assignments of each contig so I could make the decision myself - does gunc not do this?
It certainly looks from the visualisation (https://grp-bork.embl-community.io/gunc/_images/GUNC_PLOT_example.png) that gunc is able to label contigs - can I get those labels out as a text file?
The visualisation module uses a heuristic to limit the number of displayed contigs (to avoid cluttering). But we'll add the option to get flat files with per-contig tax labels – basically, all labels assigned to a given contig at a taxonomic level, plus frequency. This would still require some further parsing to do what you intend, but it's the least biased output we can provide. This will come as a new option to gunc run
, called --contig_taxonomy_output
. @fullama is working to release this feature asap :-)
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Thank you!
I guess in the meantime I can parse the diamond file to add taxonomic labels per protein and then use whatever summarisation algorithm I need to get per-contig taxonomies
Cheers
Mick
from gunc.
Hi, I just released GUNC v1.0.4... (available via pip now and conda in a little while when it goes through)
you can now use gunc with the --contig_taxonomy_output
option which hopefully gives you the kind of output you are looking for..
it will out put a tsv of the form:
contig | tax_level | assignment | count_of_genes_assigned |
---|---|---|---|
k141_21019_1 | kingdom | 2 Bacteria | 1 |
k141_21019_1 | phylum | 200795 Chloroflexi | 1 |
k141_21019_1 | family | 475964 Caldilineaceae | 1 |
k141_21019_1 | genus | 233191 Caldilinea | 1 |
Any questions just let us know!
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Related Issues (20)
- installation failure using conda HOT 5
- **conda install** no longer finds **diamond=2.0.4** HOT 9
- Diamond parameters - max-target-seqs HOT 4
- file_suffix flag HOT 24
- panda KeyError: 'contig' HOT 5
- false positives HOT 8
- NAN in the output result HOT 13
- apply GUNC to a large dataset of MAGs HOT 1
- Failed to run Diamond HOT 4
- Incompatibility with pandas 2.0 HOT 2
- diamond error HOT 4
- Command 'diamond --version' returned non-zero exit status 132 HOT 3
- --use_species_level is not a better choice? HOT 1
- --use_species_level is not a better choice? HOT 5
- Suppress deprecation warning from pandas HOT 1
- Threshold CSS values when dealing with genomes in reference database HOT 4
- New GTDB database release HOT 1
- GUNC gene_counts.json file not found! HOT 5
- GUNC diamond output filename HOT 1
- Database update for gunc
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