I/O For other biobakery outputs

[kescobo]

• KneadData
• MetaPhlAn
• HUMAnN
• PanPhlAn
• StrainPhlAn
• PhyloPhlAn

Ideas for these tools below

KneadData

• Read in read counts as DataFrame
• Plot summaries

MetaPhlAn

Intputs

• read in single profile (see Metaphlan Profiles Function #42 )
• read in multiple profiles (see Metaphlan Profiles Function #42)
• read in table from metaphlan_merge_tables

Outputs

• write output from joined tables (fixed in Microbiome.jl)
• Write outputs with filtered species / other taxon levels (fixed in Microbiome.jl)
• Write pcl outputs with metadata from a CommunityProfile (see Metaphlan and Humann tutorials #63)

Plots

• see also Plotting #25

HUMAnN

Inputs

(many are same as for metaphlan, can maybe be combined)

(all of this was done in #63)

• read in single profile
• read in multiple profiles
• read in table from humann_join_tables
• include options to have species stratified or not
  • how to hang onto taxon info? (done with GeneFunction struct and custom writing in Microbiome.jl

Outputs

• write output from joined tables in the form of humann_join_tables
• Write pcl outputs with metadata from a CommunityProfile

Plots

see also #25

• Top X functions barplot
• humann_barplot equivalent

PanPhlAn

TBD

StrainPhlAn

TBD

PhyloPhlAn

TBD