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taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
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Add support for new metagenomic tool: metaphlan3 #8

Closed maxibor closed 1 year ago

maxibor commented 2 years ago

metaphlan3: github.com/biobakery/MetaPhlAn

Default output:

#mpa_v30_CHOCOPhlAn_201901
#/n/huttenhower_lab/tools/metaphlan3/bin/metaphlan SRS014476-Supragingival_plaque.fasta.gz --input_type fasta
#SampleID       Metaphlan_Analysis
#clade_name     NCBI_tax_id     relative_abundance      additional_species
k__Bacteria     2       100.0   
k__Bacteria|p__Actinobacteria   2|201174        100.0   
k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760   100.0   
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales    2|201174|1760|85007     65.25681        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales        2|201174|1760|85006     34.74319        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae      2|201174|1760|85007|1653        65.25681        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae      2|201174|1760|85006|1268        34.74319        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium   2|201174|1760|85007|1653|1716   65.25681        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia    2|201174|1760|85006|1268|32207  34.74319        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_matruchotii    2|201174|1760|85007|1653|1716|43768     65.25681        
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_dentocariosa     2|201174|1760|85006|1268|32207|2047     34.74319        k__Bacteria|p__Actinobacteria|