### Preparing the input files
### Download files from:
### http://qiita.ucsd.edu/study/description/1741
### Getting only female samples
## ~6m41.536s
## filter_fasta.py -f all_seqs.fna -o just_female.fna --mapping_fp mapping_file.txt --valid_states='sex:female'
## ~2m31.414s
## subsample_fasta.py -i just_female.fna -p .025 -o workshop_seqs.fna

## ~0m1.217s
validate_mapping_file.py -m mapping_file.txt -o validate_mappping_file

## ~2m45.257s
pick_closed_reference_otus.py -i workshop_seqs.fna -o pick_close_ref

## do not run with the full mapping file as it will take ~1hr
## ~30m35.601s
echo "compare_alpha_diversity:num_permutations 10" > params.txt
echo "make_distance_boxplots:num_permutations 10" >> params.txt
core_diversity_analyses.py -t ~/svn_programs/gg_13_8_otus/trees/97_otus.tree -i pick_close_ref/otu_table.biom -o core_diversity -m mapping_file.txt -e 250 -p params.txt

## do some tests by body_site
## ~2m
core_diversity_analyses.py -t ~/svn_programs/gg_13_8_otus/trees/97_otus.tree -i pick_close_ref/otu_table.biom -o core_diversity -m mapping_file.txt -e 250 -p params.txt -c body_site --recover_from_failure
