bipartition_examiner.py
Calculate and plot the observed occurrences of clades of interest in bootstrap trees.
bipartition_examiner.py [OPTIONS] -b <input_MLBS_files> -g groups.txt
Required arguments:
-b
,--bs_files <infile>
A file that contains paths to sets of bootstrap tree files. One file name per line (Table 5). Results from files will be plotted in the order they were provided-g
,--groups <infile>
A file containing taxonomic groups/relationships of interest one per line (Table 6)
Optional arguments:
--database
Path to database if not using config.ini--chimeras
A .tsv containing a Unique ID, higher taxonomy, and lower taxonomy for each chimera within the input bootstrap files. The file contains three columns:- Chimera_ID 1
- Higher_Tax
- Lower_Tax
--bar_plot
Plot categorical data as a barplot- Default: Plot series data as a line graph.
-o
,--output <out_dir>
Path to user-defined output directory- Default:
./bipartition_examiner_out_<M.D.Y>
- Default:
-h
,--help
Show this help message and exit.
bipartion_examiner.py
output:
bipartion_examiner.pdf
- a plot (line graph or histogram) with MLBS values on the y-axis file names on the x-axis. Groups of interest are color coded.bipartion_examiner.tsv
- a .tsv file that contains the values plotted inbipartion_examiner.pdf
/home/myworkingdirectory/MLbootstrap.experiment1 |
/home/myworkingdirectory/MLbootstrap.experiment2 |
/home/myworkingdirectory/MLbootstrap.experiment3 |
Amoebozoa |
Amoebozoa+Obazoa+CRuMs |
Fungi+Metazoa |
Homosapi+Gallgall |
Fungi:Sacccere,Candalbi,Aspefumi,Coprcine |