/
notebook_environment.py
2624 lines (2396 loc) · 135 KB
/
notebook_environment.py
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# establish any minimals for the notebook environment
import os
import shutil
from distutils.spawn import find_executable
import qiime
import qiime_default_reference as qdr
import americangut as ag
from americangut.results_utils import get_repository_dir
from americangut.util import get_existing_path
_EBI_ACCESSIONS = ['ERP012803']
_TEST_ACCESSIONS = ['ag_testing']
# essential paths relative to the working_dir to be used between notebooks
paths = {
# raw files
'raw': {
'sequences': '01-raw/sequences.fna',
'metadata': '01-raw/metadata.txt',
},
# sequences filtered for blooms
'filtered': {
'sequences-notrim': '02-filtered/sequences-notrim.fna',
'sequences-100nt': '02-filtered/sequences-100nt.fna',
# only fecal sequences (for filtering for blooms)
'fecal-sequences': '02-filtered/fecal-sequences.fna',
# observed bloom sequences in samples
'observed-blooms': '02-filtered/observed-blooms',
'observed-blooms-biom': '02-filtered/observed-blooms/otu_table.biom',
'observed-blooms-otu-map':
('02-filtered/observed-blooms/sortmerna_picked_otus/'
'fecal-sequences_otus.txt'),
},
# resulting OTU data
'otus': {
'notrim': {
'ag': '03-otus/notrim/gg-13_8-97-percent',
'ag-biom': '03-otus/notrim/gg-13_8-97-percent/otu_table.biom'
},
'100nt': {
'ag': '03-otus/100nt/gg-13_8-97-percent',
'ag-biom': '03-otus/100nt/gg-13_8-97-percent/otu_table.biom'
}
},
# merged files for diversity analyses
'meta': {
'ag-gg-100nt-biom': '04-meta/ag-gg-100nt.biom',
'pgp-hmp-100nt-biom': '04-meta/pgp-hmp-100nt.biom',
'ag-pgp-hmp-gg-100nt-biom': '04-meta/ag-pgp-hmp-gg-100nt.biom',
'ag-cleaned-md': '04-meta/ag-cleaned.txt',
'gg-cleaned-md': '04-meta/gg-cleaned.txt',
'pgp-cleaned-md': '04-meta/pgp-cleaned.txt',
'hmp-cleaned-md': '04-meta/hmp-cleaned.txt',
'ag-gg-cleaned-md': '04-meta/ag-gg-cleaned.txt',
'pgp-hmp-cleaned-md': '04-meta/pgp-hmp-cleaned.txt',
'ag-pgp-hmp-gg-cleaned-md': '04-meta/ag-pgp-hmp-gg-cleaned.txt',
},
# alpha diversity analysis files
'alpha': {
'1k': {
'ag-notrim-multiple': '05-alpha/1k/ag-notrim-multiple',
'ag-notrim': '05-alpha/1k/ag-notrim',
'ag-notrim-pd': '05-alpha/1k/ag-notrim/PD_whole_tree.txt',
'ag-notrim-chao1': '05-alpha/1k/ag-notrim/chao1.txt',
'ag-notrim-observedotus': ('05-alpha/1k/ag-notrim/'
'observed_otus.txt'),
'ag-notrim-shannon': '05-alpha/1k/ag-notrim/shannon.txt',
'ag-pgp-hmp-gg-100nt-multiple': ('05-alpha/1k/'
'ag-pgp-hmp-gg-100nt-multiple'),
'ag-pgp-hmp-gg-100nt': '05-alpha/1k/ag-pgp-hmp-gg-100nt',
'ag-pgp-hmp-gg-100nt-pd':
'05-alpha/1k/ag-pgp-hmp-gg-100nt/PD_whole_tree.txt',
'ag-pgp-hmp-gg-100nt-chao1':
'05-alpha/1k/ag-pgp-hmp-gg-100nt/chao1.txt',
'ag-pgp-hmp-gg-100nt-observedotus':
'05-alpha/1k/ag-pgp-hmp-gg-100nt/observed_otus.txt',
'ag-pgp-hmp-gg-100nt-shannon':
'05-alpha/1k/ag-pgp-hmp-gg-100nt/shannon.txt',
},
'10k': {
'ag-notrim-multiple': '05-alpha/10k/ag-notrim-multiple',
'ag-notrim': '05-alpha/10k/ag-notrim',
'ag-notrim-pd': '05-alpha/10k/ag-notrim/PD_whole_tree.txt',
'ag-notrim-chao1': '05-alpha/10k/ag-notrim/chao1.txt',
'ag-notrim-observedotus': ('05-alpha/10k/ag-notrim/'
'observed_otus.txt'),
'ag-notrim-shannon': '05-alpha/10k/ag-notrim/shannon.txt',
'ag-pgp-hmp-gg-100nt-multiple': ('05-alpha/10k/'
'ag-pgp-hmp-gg-100nt-multiple'),
'ag-pgp-hmp-gg-100nt': '05-alpha/10k/ag-pgp-hmp-gg-100nt',
'ag-pgp-hmp-gg-100nt-pd':
'05-alpha/10k/ag-pgp-hmp-gg-100nt/PD_whole_tree.txt',
'ag-pgp-hmp-gg-100nt-chao1':
'05-alpha/10k/ag-pgp-hmp-gg-100nt/chao1.txt',
'ag-pgp-hmp-gg-100nt-observedotus':
'05-alpha/10k/ag-pgp-hmp-gg-100nt/observed_otus.txt',
'ag-pgp-hmp-gg-100nt-shannon':
'05-alpha/10k/ag-pgp-hmp-gg-100nt/shannon.txt',
}
},
# beta diversity analysis files
'beta': {
'notrim': {
'1k': {
'ag-biom': '06-beta/notrim/1k/ag.biom',
'ag': '06-beta/notrim/1k/ag',
'ag-unifrac':
'06-beta/notrim/1k/ag/unweighted_unifrac_ag.txt',
'ag-unifrac-pc':
'06-beta/notrim/1k/ag/unweighted_unifrac_ag-pc.txt',
'ag-oral-unifrac':
'06-beta/notrim/1k/ag/unweighted_unifrac_ag-oral.txt',
'ag-oral-unifrac-pc':
('06-beta/notrim/1k/ag/'
'unweighted_unifrac_ag-oral-pc.txt'),
'ag-skin-unifrac':
'06-beta/notrim/1k/ag/unweighted_unifrac_ag-skin.txt',
'ag-skin-unifrac-pc':
('06-beta/notrim/1k/ag/'
'unweighted_unifrac_ag-skin-pc.txt'),
'ag-fecal-unifrac':
'06-beta/notrim/1k/ag/unweighted_unifrac_ag-fecal.txt',
'ag-fecal-unifrac-pc':
('06-beta/notrim/1k/ag/'
'unweighted_unifrac_ag-fecal-pc.txt'),
'ag-wunifrac':
'06-beta/notrim/1k/ag/weighted_unifrac_ag.txt',
'ag-wunifrac-pc':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-pc.txt',
'ag-oral-wunifrac':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-oral.txt',
'ag-oral-wunifrac-pc':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-oral-pc.txt',
'ag-skin-wunifrac':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-skin.txt',
'ag-skin-wunifrac-pc':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-skin-pc.txt',
'ag-fecal-wunifrac':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-fecal.txt',
'ag-fecal-wunifrac-pc':
'06-beta/notrim/1k/ag/weighted_unifrac_ag-fecal-pc.txt',
},
'10k': {
'ag-biom': '06-beta/notrim/10k/ag.biom',
'ag': '06-beta/notrim/10k/ag',
'ag-unifrac':
'06-beta/notrim/10k/ag/unweighted_unifrac_ag.txt',
'ag-unifrac-pc':
'06-beta/notrim/10k/ag/unweighted_unifrac_ag-pc.txt',
'ag-oral-unifrac':
'06-beta/notrim/10k/ag/unweighted_unifrac_ag-oral.txt',
'ag-oral-unifrac-pc':
('06-beta/notrim/10k/ag/'
'unweighted_unifrac_ag-oral-pc.txt'),
'ag-skin-unifrac':
'06-beta/notrim/10k/ag/unweighted_unifrac_ag-skin.txt',
'ag-skin-unifrac-pc':
('06-beta/notrim/10k/ag/'
'unweighted_unifrac_ag-skin-pc.txt'),
'ag-fecal-unifrac':
'06-beta/notrim/10k/ag/unweighted_unifrac_ag-fecal.txt',
'ag-fecal-unifrac-pc':
('06-beta/notrim/10k/ag/'
'unweighted_unifrac_ag-fecal-pc.txt'),
'ag-wunifrac':
'06-beta/notrim/10k/ag/weighted_unifrac_ag.txt',
'ag-wunifrac-pc':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-pc.txt',
'ag-oral-wunifrac':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-oral.txt',
'ag-oral-wunifrac-pc':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-oral-pc.txt',
'ag-skin-wunifrac':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-skin.txt',
'ag-skin-wunifrac-pc':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-skin-pc.txt',
'ag-fecal-wunifrac':
'06-beta/notrim/10k/ag/weighted_unifrac_ag-fecal.txt',
'ag-fecal-wunifrac-pc':
('06-beta/notrim/10k/ag/'
'weighted_unifrac_ag-fecal-pc.txt'),
},
},
'100nt': {
'1k': {
'ag-biom': '06-beta/100nt/1k/ag.biom',
'ag': '06-beta/100nt/1k/ag',
'ag-pgp-hmp-gg-biom': '06-beta/100nt/1k/ag-pgp-hmp-gg.biom',
'ag-pgp-hmp-gg': '06-beta/100nt/1k/ag-pgp-hmp-gg',
'ag-unifrac':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag.txt'),
'ag-unifrac-pc':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-pc.txt'),
'ag-oral-unifrac':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-oral.txt'),
'ag-oral-unifrac-pc':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-oral-pc.txt'),
'ag-fecal-unifrac':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-fecal.txt'),
'ag-fecal-unifrac-pc':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-fecal-pc.txt'),
'ag-skin-unifrac':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-skin.txt'),
'ag-skin-unifrac-pc':
('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-skin-pc.txt'),
'ag-wunifrac':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag.txt'),
'ag-wunifrac-pc':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-pc.txt'),
'ag-oral-wunifrac':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-oral.txt'),
'ag-oral-wunifrac-pc':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-oral-pc.txt'),
'ag-fecal-wunifrac':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-fecal.txt'),
'ag-fecal-wunifrac-pc':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-fecal-pc.txt'),
'ag-skin-wunifrac':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-skin.txt'),
'ag-skin-wunifrac-pc':
('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-skin-pc.txt'),
'ag-pgp-hmp-gg-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg.txt'),
'ag-pgp-hmp-gg-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-pc.txt'),
'ag-pgp-hmp-gg-skin-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-skin.txt'),
'ag-pgp-hmp-gg-skin-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-skin-pc.txt'),
'ag-pgp-hmp-gg-oral-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-oral.txt'),
'ag-pgp-hmp-gg-oral-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-oral-pc.txt'),
'ag-pgp-hmp-gg-fecal-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-fecal.txt'),
'ag-pgp-hmp-gg-fecal-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-fecal-pc.txt'),
'ag-pgp-hmp-gg-skin-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-skin.txt'),
'ag-pgp-hmp-gg-skin-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-skin-pc.txt'),
'ag-pgp-hmp-gg-oral-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-oral.txt'),
'ag-pgp-hmp-gg-oral-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-oral-pc.txt'),
'ag-pgp-hmp-gg-fecal-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-fecal.txt'),
'ag-pgp-hmp-gg-fecal-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-fecal-pc.txt'),
'ag-pgp-hmp-gg-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg.txt'),
'ag-pgp-hmp-gg-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-pc.txt'),
'ag-gg-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg.txt'),
'ag-gg-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-pc.txt'),
'ag-gg-skin-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-skin.txt'),
'ag-gg-skin-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-skin-pc.txt'),
'ag-gg-oral-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-oral.txt'),
'ag-gg-oral-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-oral-pc.txt'),
'ag-gg-fecal-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-fecal.txt'),
'ag-gg-fecal-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-fecal-pc.txt'),
'ag-gg-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg.txt'),
'ag-gg-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-pc.txt'),
'ag-gg-skin-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-skin.txt'),
'ag-gg-skin-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-skin-pc.txt'),
'ag-gg-oral-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-oral.txt'),
'ag-gg-oral-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-oral-pc.txt'),
'ag-gg-fecal-wunifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-fecal.txt'),
'ag-gg-fecal-wunifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-fecal-pc.txt'),
'ag-gg-subsampled-unifrac':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-subsampled.txt'),
'ag-gg-subsampled-unifrac-pc':
('06-beta/100nt/1k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-subsampled-pc.txt'),
},
'10k': {
'ag-biom': '06-beta/100nt/10k/ag.biom',
'ag': '06-beta/100nt/10k/ag',
'ag-pgp-hmp-gg-biom': '06-beta/100nt/10k/ag-pgp-hmp-gg.biom',
'ag-pgp-hmp-gg': '06-beta/100nt/10k/ag-pgp-hmp-gg',
'ag-unifrac':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag.txt'),
'ag-unifrac-pc':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-pc.txt'),
'ag-oral-unifrac':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-oral.txt'),
'ag-oral-unifrac-pc':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-oral-pc.txt'),
'ag-fecal-unifrac':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-fecal.txt'),
'ag-fecal-unifrac-pc':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-fecal-pc.txt'),
'ag-skin-unifrac':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-skin.txt'),
'ag-skin-unifrac-pc':
('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-skin-pc.txt'),
'ag-wunifrac':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag.txt'),
'ag-wunifrac-pc':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-pc.txt'),
'ag-oral-wunifrac':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-oral.txt'),
'ag-oral-wunifrac-pc':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-oral-pc.txt'),
'ag-fecal-wunifrac':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-fecal.txt'),
'ag-fecal-wunifrac-pc':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-fecal-pc.txt'),
'ag-skin-wunifrac':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-skin.txt'),
'ag-skin-wunifrac-pc':
('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-skin-pc.txt'),
'ag-pgp-hmp-gg-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg.txt'),
'ag-pgp-hmp-gg-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-pc.txt'),
'ag-pgp-hmp-gg-skin-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-skin.txt'),
'ag-pgp-hmp-gg-skin-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-skin-pc.txt'),
'ag-pgp-hmp-gg-oral-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-oral.txt'),
'ag-pgp-hmp-gg-oral-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-oral-pc.txt'),
'ag-pgp-hmp-gg-fecal-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-fecal.txt'),
'ag-pgp-hmp-gg-fecal-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-pgp-hmp-gg-fecal-pc.txt'),
'ag-pgp-hmp-gg-skin-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-skin.txt'),
'ag-pgp-hmp-gg-skin-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-skin-pc.txt'),
'ag-pgp-hmp-gg-oral-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-oral.txt'),
'ag-pgp-hmp-gg-oral-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-oral-pc.txt'),
'ag-pgp-hmp-gg-fecal-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-fecal.txt'),
'ag-pgp-hmp-gg-fecal-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-fecal-pc.txt'),
'ag-pgp-hmp-gg-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg.txt'),
'ag-pgp-hmp-gg-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-pgp-hmp-gg-pc.txt'),
'ag-gg-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg.txt'),
'ag-gg-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-pc.txt'),
'ag-gg-skin-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-skin.txt'),
'ag-gg-skin-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-skin-pc.txt'),
'ag-gg-oral-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-oral.txt'),
'ag-gg-oral-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-oral-pc.txt'),
'ag-gg-fecal-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-fecal.txt'),
'ag-gg-fecal-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-fecal-pc.txt'),
'ag-gg-subsampled-unifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-subsampled.txt'),
'ag-gg-subsampled-unifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'unweighted_unifrac_ag-gg-subsampled-pc.txt'),
'ag-gg-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg.txt'),
'ag-gg-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-pc.txt'),
'ag-gg-skin-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-skin.txt'),
'ag-gg-skin-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-skin-pc.txt'),
'ag-gg-oral-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-oral.txt'),
'ag-gg-oral-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-oral-pc.txt'),
'ag-gg-fecal-wunifrac':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-fecal.txt'),
'ag-gg-fecal-wunifrac-pc':
('06-beta/100nt/10k/ag-pgp-hmp-gg/'
'weighted_unifrac_ag-gg-fecal-pc.txt'),
}
},
},
# taxonomy summaries
'taxa': {
'100nt': {
'base': '07-taxa/100nt',
'L2': {
'ag-tsv': '07-taxa/100nt/otu_table_L2.txt',
'ag-biom': '07-taxa/100nt/otu_table_L2.biom',
'ag-md': '07-taxa/100nt/ag-cleaned_L2.txt',
'ag-skin-biom': '07-taxa/100nt/otu_table_skin_L2.biom',
'ag-oral-biom': '07-taxa/100nt/otu_table_oral_L2.biom',
'ag-fecal-biom': '07-taxa/100nt/otu_table_fecal_L2.biom',
},
'L3': {
'ag-tsv': '07-taxa/100nt/otu_table_L3.txt',
'ag-biom': '07-taxa/100nt/otu_table_L3.biom',
'ag-md': '07-taxa/100nt/ag-cleaned_L3.txt',
'ag-skin-biom': '07-taxa/100nt/otu_table_skin_L3.biom',
'ag-oral-biom': '07-taxa/100nt/otu_table_oral_L3.biom',
'ag-fecal-biom': '07-taxa/100nt/otu_table_fecal_L3.biom',
},
'L6': {
'ag-tsv': '07-taxa/100nt/otu_table_L6.txt',
'ag-biom': '07-taxa/100nt/otu_table_L6.biom',
'ag-md': '07-taxa/100nt/ag-cleaned_L6.txt',
'ag-skin-biom': '07-taxa/100nt/otu_table_skin_L6.biom',
'ag-oral-biom': '07-taxa/100nt/otu_table_oral_L6.biom',
'ag-fecal-biom': '07-taxa/100nt/otu_table_fecal_L6.biom',
}
},
'notrim': {
'base': '07-taxa/notrim',
'L2': {
'ag-tsv': '07-taxa/notrim/otu_table_L2.txt',
'ag-biom': '07-taxa/notrim/otu_table_L2.biom',
'ag-md': '07-taxa/notrim/ag-cleaned_L2.txt',
'ag-skin-biom': '07-taxa/notrim/otu_table_skin_L2.biom',
'ag-oral-biom': '07-taxa/notrim/otu_table_oral_L2.biom',
'ag-fecal-biom': '07-taxa/notrim/otu_table_fecal_L2.biom',
},
'L3': {
'ag-tsv': '07-taxa/notrim/otu_table_L3.txt',
'ag-biom': '07-taxa/notrim/otu_table_L3.biom',
'ag-md': '07-taxa/notrim/ag-cleaned_L3.txt',
'ag-skin-biom': '07-taxa/notrim/otu_table_skin_L3.biom',
'ag-oral-biom': '07-taxa/notrim/otu_table_oral_L3.biom',
'ag-fecal-biom': '07-taxa/notrim/otu_table_fecal_L3.biom',
},
'L6': {
'ag-tsv': '07-taxa/notrim/otu_table_L6.txt',
'ag-biom': '07-taxa/notrim/otu_table_L6.biom',
'ag-md': '07-taxa/notrim/ag-cleaned_L6.txt',
'ag-skin-biom': '07-taxa/notrim/otu_table_skin_L6.biom',
'ag-oral-biom': '07-taxa/notrim/otu_table_oral_L6.biom',
'ag-fecal-biom': '07-taxa/notrim/otu_table_fecal_L6.biom',
}
}
},
# collapsed samples
'collapsed': {
'100nt': {
'alpha-map': '08-collapsed/100nt/alpha_map.txt',
'1k': {
'ag-biom': '08-collapsed/100nt/1k/ag.biom',
'ag-fecal-biom': '08-collapsed/100nt/1k/ag-fecal.biom',
'ag-skin-biom': '08-collapsed/100nt/1k/ag-oral.biom',
'ag-oral-biom': '08-collapsed/100nt/1k/ag-skin.biom',
'ag-fecal-sex-biom': ('08-collapsed/100nt/1k/'
'ag-fecal-sex.biom'),
'ag-fecal-diet-biom': ('08-collapsed/100nt/1k/'
'ag-fecal-diet.biom'),
'ag-fecal-age-biom': ('08-collapsed/100nt/1k/'
'ag-fecal-age.biom'),
'ag-fecal-bmi-biom': ('08-collapsed/100nt/1k/'
'ag-fecal-bmi.biom'),
'ag-oral-sex-biom': '08-collapsed/100nt/1k/ag-oral-sex.biom',
'ag-oral-diet-biom': '08-collapsed/100nt/1k/ag-oral-diet.biom',
'ag-oral-age-biom': '08-collapsed/100nt/1k/ag-oral-age.biom',
'ag-oral-flossing-biom': ('08-collapsed/100nt/1k/'
'ag-oral-flossing.biom'),
'ag-skin-sex-biom': '08-collapsed/100nt/1k/ag-skin-sex.biom',
'ag-skin-cosmetics-biom': ('08-collapsed/100nt/1k/'
'ag-skin-cosmetics.biom'),
'ag-skin-age-biom': '08-collapsed/100nt/1k/ag-skin-age.biom',
'ag-skin-hand-biom': ('08-collapsed/100nt/1k/'
'ag-skin-hand.biom'),
},
'10k': {
'ag-biom': '08-collapsed/100nt/10k/ag.biom',
'ag-fecal-biom': '08-collapsed/100nt/10k/ag-fecal.biom',
'ag-skin-biom': '08-collapsed/100nt/10k/ag-oral.biom',
'ag-oral-biom': '08-collapsed/100nt/10k/ag-skin.biom',
'ag-fecal-sex-biom': ('08-collapsed/100nt/10k/'
'ag-fecal-sex.biom'),
'ag-fecal-diet-biom': ('08-collapsed/100nt/10k/'
'ag-fecal-diet.biom'),
'ag-fecal-age-biom': ('08-collapsed/100nt/10k/'
'ag-fecal-age.biom'),
'ag-fecal-bmi-biom': ('08-collapsed/100nt/10k/'
'ag-fecal-bmi.biom'),
'ag-oral-sex-biom': '08-collapsed/100nt/10k/ag-oral-sex.biom',
'ag-oral-diet-biom': ('08-collapsed/100nt/10k/'
'ag-oral-diet.biom'),
'ag-oral-age-biom': '08-collapsed/100nt/10k/ag-oral-age.biom',
'ag-oral-flossing-biom': ('08-collapsed/100nt/10k/'
'ag-oral-flossing.biom'),
'ag-skin-sex-biom': '08-collapsed/100nt/10k/ag-skin-sex.biom',
'ag-skin-cosmetics-biom': ('08-collapsed/100nt/10k/'
'ag-skin-cosmetics.biom'),
'ag-skin-age-biom': '08-collapsed/100nt/10k/ag-skin-age.biom',
'ag-skin-hand-biom': ('08-collapsed/100nt/10k/'
'ag-skin-hand.biom'),
}
},
'notrim': {
'alpha-map': '08-collapsed/notrim/alpha-map.txt',
'1k': {
'ag-biom': '08-collapsed/notrim/1k/ag.biom',
'ag-fecal-biom': '08-collapsed/notrim/1k/ag-fecal.biom',
'ag-skin-biom': '08-collapsed/notrim/1k/ag-oral.biom',
'ag-oral-biom': '08-collapsed/notrim/1k/ag-skin.biom',
'ag-fecal-sex-biom': ('08-collapsed/notrim/1k/'
'ag-fecal-sex.biom'),
'ag-fecal-diet-biom': ('08-collapsed/notrim/1k/'
'ag-fecal-diet.biom'),
'ag-fecal-age-biom': ('08-collapsed/notrim/1k/'
'ag-fecal-age.biom'),
'ag-fecal-bmi-biom': ('08-collapsed/notrim/1k/'
'ag-fecal-bmi.biom'),
'ag-oral-sex-biom': '08-collapsed/notrim/1k/ag-oral-sex.biom',
'ag-oral-diet-biom': ('08-collapsed/notrim/1k/'
'ag-oral-diet.biom'),
'ag-oral-age-biom': '08-collapsed/notrim/1k/ag-oral-age.biom',
'ag-oral-flossing-biom': ('08-collapsed/notrim/1k/'
'ag-oral-flossing.biom'),
'ag-skin-sex-biom': '08-collapsed/notrim/1k/ag-skin-sex.biom',
'ag-skin-cosmetics-biom': ('08-collapsed/notrim/1k/'
'ag-skin-cosmetics.biom'),
'ag-skin-age-biom': '08-collapsed/notrim/1k/ag-skin-age.biom',
'ag-skin-hand-biom': ('08-collapsed/notrim/1k/'
'ag-skin-hand.biom'),
},
'10k': {
'ag-biom': '08-collapsed/notrim/10k/ag.biom',
'ag-fecal-biom': '08-collapsed/notrim/10k/ag-fecal.biom',
'ag-skin-biom': '08-collapsed/notrim/10k/ag-oral.biom',
'ag-oral-biom': '08-collapsed/notrim/10k/ag-skin.biom',
'ag-fecal-sex-biom': ('08-collapsed/notrim/10k/'
'ag-fecal-sex.biom'),
'ag-fecal-diet-biom': ('08-collapsed/notrim/10k/'
'ag-fecal-diet.biom'),
'ag-fecal-age-biom': ('08-collapsed/notrim/10k/'
'ag-fecal-age.biom'),
'ag-fecal-bmi-biom': ('08-collapsed/notrim/10k/'
'ag-fecal-bmi.biom'),
'ag-oral-sex-biom': '08-collapsed/notrim/10k/ag-oral-sex.biom',
'ag-oral-diet-biom': ('08-collapsed/notrim/10k/'
'ag-oral-diet.biom'),
'ag-oral-age-biom': '08-collapsed/notrim/10k/ag-oral-age.biom',
'ag-oral-flossing-biom': ('08-collapsed/notrim/10k/'
'ag-oral-flossing.biom'),
'ag-skin-sex-biom': '08-collapsed/notrim/10k/ag-skin-sex.biom',
'ag-skin-cosmetics-biom': ('08-collapsed/notrim/10k/'
'ag-skin-cosmetics.biom'),
'ag-skin-age-biom': '08-collapsed/notrim/10k/ag-skin-age.biom',
'ag-skin-hand-biom': ('08-collapsed/notrim/10k/'
'ag-skin-hand.biom'),
}
}
},
# per-sample results
'per-sample': {
'successful-ids': '09-per-sample/successful_ids.txt',
'unsuccessful-ids': '09-per-sample/unsuccessful_ids.txt',
'results': '09-per-sample/results',
'statics-fecal': '09-per-sample/statics-fecal',
'statics-oral': '09-per-sample/statics-oral',
'statics-skin': '09-per-sample/statics-skin',
},
'populated-templates': {
'result-pdfs': '10-populated-templates/pdfs/',
'result-taxa': '10-populated-templates/taxa/',
'successful-pdfs': '10-populated-templates/successful_ids.txt',
'unsuccessful-pdfs': '10-populated-templates/unsuccessful_ids.txt',
},
'demux': {},
'otu-map': {},
'package': {
'split': {
'notrim-map': '01-raw/metadata.txt',
'notrim-raw-otu': ('03-otus/notrim/gg-13_8-97-percent/'
'otu_table.biom'),
'notrim-raw-dir': '11-packaged/split/notrim/raw/',
'notrim-1k-otu': '06-beta/notrim/1k/ag.biom',
'notrim-1k-dir': '11-packaged/split/notrim/1k/',
'notrim-10k-otu': '06-beta/notrim/10k/ag.biom',
'notrim-10k-dir': '11-packaged/split/notrim/10k/',
'100nt-map': '01-raw/metadata.txt',
'100nt-raw-otu': '03-otus/100nt/gg-13_8-97-percent/otu_table.biom',
'100nt-raw-dir': '11-packaged/split/100nt/raw/',
'100nt-1k-otu': '06-beta/100nt/1k/ag.biom',
'100nt-1k-dir': '11-packaged/split/100nt/1k/',
'100nt-10k-otu': '06-beta/100nt/10k/ag.biom',
'100nt-10k-dir': '11-packaged/split/100nt/10k/',
},
'single_ids': {
'fecal-1k': '11-packaged/fecal/single_ids_1k.txt',
'fecal-10k': '11-packaged/fecal/single_ids_10k.txt',
'fecal-unrare': '11-packaged/fecal/single_ids_unrarefied.txt',
'oral-1k': '11-packaged/oral/single_ids_1k.txt',
'oral-10k': '11-packaged/oral/single_ids_10k.txt',
'oral-unrare': '11-packaged/oral/single_ids_unrarefied.txt',
'skin-1k': '11-packaged/skin/single_ids_1k.txt',
'skin-10k': '11-packaged/skin/single_ids_10k.txt',
'skin-unrare': '11-packaged/skin/single_ids_unrarefied.txt',
},
'all_participants_all_samples': {
'fecal': {
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'source-unrare-otu': ('11-packaged/split/notrim/raw/'
'otu_table__BODY_HABITAT_UBERON:'
'feces__.biom'),
'source-unrare-map': ('11-packaged/split/notrim/raw/'
'metadata__BODY_HABITAT_UBERON:'
'feces__.txt'),
'sink-unrare-dir': ('11-packaged/fecal/notrim'),
'sink-unrare-otu': ('11-packaged/fecal/notrim/ag_fecal.'
'biom'),
'sink-unrare-map': ('11-packaged/fecal/notrim/ag_fecal.'
'txt'),
'source-1k-otu': ('11-packaged/split/notrim/1k/'
'ag__BODY_HABITAT_UBERON:feces__.biom'),
'source-1k-map': ('11-packaged/split/notrim/1k/'
'metadata__BODY_HABITAT_UBERON:'
'feces__.txt'),
'source-1k-pd': '05-alpha/1k/ag-notrim/PD_whole_tree.txt',
'source-1k-chao1': '05-alpha/1k/ag-notrim/chao1.txt',
'source-1k-observedotus': ('05-alpha/1k/ag-notrim/'
'observed_otus.txt'),
'source-1k-shannon': '05-alpha/1k/ag-notrim/shannon.txt',
'source-1k-unweighted-unifrac': ('06-beta/notrim/1k/ag/'
'unweighted_unifrac_ag-'
'fecal.txt'),
'source-1k-weighted-unifrac': ('06-beta/notrim/1k/ag/'
'weighted_unifrac_ag-'
'fecal.txt'),
'source-10k-otu': ('11-packaged/split/notrim/10k/'
'ag__BODY_HABITAT_UBERON:feces__.biom'),
'source-10k-map': ('11-packaged/split/notrim/10k/'
'metadata__BODY_HABITAT_UBERON:feces__.'
'txt'),
'source-10k-pd': ('05-alpha/10k/ag-notrim/PD_whole_tree.'
'txt'),
'source-10k-chao1': ('05-alpha/10k/ag-notrim/chao1.'
'txt'),
'source-10k-observedotus': ('05-alpha/10k/ag-notrim/'
'observed_otus.txt'),
'source-10k-shannon': '05-alpha/10k/ag-notrim/shannon.txt',
'source-10k-unweighted-unifrac': ('06-beta/notrim/10k/ag/'
'unweighted_unifrac_ag'
'-fecal.txt'),
'source-10k-weighted-unifrac': ('06-beta/notrim/10k/ag/'
'weighted_unifrac_ag-'
'fecal.txt'),
'sink-1k-dir': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/1k'),
'sink-1k-otu': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/1k/'
'ag_1k_fecal.biom'),
'sink-1k-map': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/1k/'
'ag_1k_fecal.txt'),
'sink-1k-unweighted-unifrac': ('11-packaged/fecal/notrim/'
'all_participants/'
'all_samples/1k/'
'unweighted_unifrac_ag_1k_'
'fecal.txt'),
'sink-1k-weighted-unifrac': ('11-packaged/fecal/notrim/'
'all_participants/'
'all_samples/1k/'
'weighted_unifrac_ag_1k_'
'fecal.txt'),
'sink-10k-dir': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/10k'),
'sink-10k-otu': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/10k/'
'ag_10k_fecal.biom'),
'sink-10k-map': ('11-packaged/fecal/notrim/'
'all_participants/all_samples/10k/'
'ag_10k_fecal.txt'),
'sink-10k-unweighted-unifrac': ('11-packaged/fecal/notrim/'
'all_participants/'
'all_samples/10k/'
'unweighted_unifrac_ag_'
'10k_fecal.txt'),
'sink-10k-weighted-unifrac': ('11-packaged/fecal/notrim/'
'all_participants/'
'all_samples/10k/'
'weighted_unifrac_ag_10k_'
'fecal.txt'),
},
'100nt': {
'source-unrare-otu': ('11-packaged/split/100nt/raw/'
'otu_table__BODY_HABITAT_UBERON:'
'feces__.biom'),
'source-unrare-map': ('11-packaged/split/100nt/raw/'
'metadata__BODY_HABITAT_UBERON:'
'feces__.txt'),
'sink-unrare-dir': ('11-packaged/fecal/100nt'),
'sink-unrare-otu': ('11-packaged/fecal/100nt/ag_fecal.'
'biom'),
'sink-unrare-map': ('11-packaged/fecal/100nt/ag_fecal.'
'txt'),
'source-1k-otu': ('11-packaged/split/100nt/1k/'
'ag__BODY_HABITAT_UBERON:feces__.biom'),
'source-1k-map': ('11-packaged/split/100nt/1k/'
'metadata__BODY_HABITAT_UBERON:'
'feces__.txt'),
'source-1k-pd': ('05-alpha/1k/ag-pgp-hmp-gg-100nt/'
'PD_whole_tree.txt'),
'source-1k-chao1': ('05-alpha/1k/ag-pgp-hmp-gg-100nt/'
'chao1.txt'),
'source-1k-observedotus': ('05-alpha/1k/'
'ag-pgp-hmp-gg-100nt/'
'observed_otus.txt'),
'source-1k-shannon': ('05-alpha/1k/ag-pgp-hmp-gg-100nt/'
'shannon.txt'),
'source-1k-unweighted-unifrac': ('06-beta/100nt/1k/ag/'
'unweighted_unifrac_ag-'
'fecal.txt'),
'source-1k-weighted-unifrac': ('06-beta/100nt/1k/ag/'
'weighted_unifrac_ag-'
'fecal.txt'),
'source-10k-otu': ('11-packaged/split/100nt/10k/'
'ag__BODY_HABITAT_UBERON:feces__.biom'),
'source-10k-map': ('11-packaged/split/100nt/10k/metadata'
'__BODY_HABITAT_UBERON:feces__.txt'),
'source-10k-pd': ('05-alpha/10k/ag-pgp-hmp-gg-100nt/'
'PD_whole_tree.txt'),
'source-10k-chao1': ('05-alpha/10k/ag-pgp-hmp-gg-100nt/'
'chao1.txt'),
'source-10k-observedotus': ('05-alpha/10k/'
'ag-pgp-hmp-gg-100nt/'
'observed_otus.txt'),
'source-10k-shannon': ('05-alpha/10k/ag-pgp-hmp-gg-100nt/'
'shannon.txt'),
'source-10k-unweighted-unifrac': ('06-beta/100nt/10k/ag/'
'unweighted_unifrac_ag-'
'fecal.txt'),
'source-10k-weighted-unifrac': ('06-beta/100nt/10k/ag/'
'weighted_unifrac_ag-'
'fecal.txt'),
'sink-1k-dir': ('11-packaged/fecal/100nt/all_participants/'
'all_samples/1k'),
'sink-1k-otu': ('11-packaged/fecal/100nt/all_participants/'
'all_samples/1k/ag_1k_fecal.biom'),
'sink-1k-map': ('11-packaged/fecal/100nt/all_participants/'
'all_samples/1k/ag_1k_fecal.txt'),
'sink-1k-unweighted-unifrac': ('11-packaged/fecal/100nt/'
'all_participants/'
'all_samples/1k/'
'unweighted_unifrac_ag_1k_'
'fecal.txt'),
'sink-1k-weighted-unifrac': ('11-packaged/fecal/100nt/'
'all_participants/'
'all_samples/1k/'
'weighted_unifrac_ag_1k_'
'fecal.txt'),
'sink-10k-dir': ('11-packaged/fecal/100nt/'
'all_participants/all_samples/10k'),
'sink-10k-otu': ('11-packaged/fecal/100nt/'
'all_participants/all_samples/10k/'
'ag_10k_fecal.biom'),
'sink-10k-map': ('11-packaged/fecal/100nt/'
'all_participants/all_samples/10k/'
'ag_10k_fecal.txt'),
'sink-10k-unweighted-unifrac': ('11-packaged/fecal/100nt/'
'all_participants/'
'all_samples/10k/'
'unweighted_unifrac_ag_'
'10k_fecal.txt'),
'sink-10k-weighted-unifrac': ('11-packaged/fecal/100nt/'
'all_participants/'
'all_samples/10k/'
'weighted_unifrac_ag_10k_'
'fecal.txt'),
},
},
'oral': {
'notrim': {
'source-unrare-otu': ('11-packaged/split/notrim/raw/'