In my prior post on ubiome Json files, or taxon number based files, I gave code and the pattern to use. Unfortunately, not every one provides such easy to use data. Look at the following download file format (AmericanGut) #taxon relative_abundance k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides 0.287722 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__ 0.130347 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__ 0.116602 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Faecalibacterium 0.045869 k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Parabacteroides 0.042162 k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__ 0.039537 k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__ 0.034286 … Continue reading Upload Taxon Name based Files
