def alpha_plot(opts, sample_ids):
"""Produces digestable alpha diversity distribution plots per sample
Parameters
----------
opts : dict
A dict of relevant opts.
sample_ids : Iterable of str
A list of sample IDs of interest
Returns
-------
dict
A dict containing each sample ID and any errors observed or None if
no error was observed for the sample. {str: str or None}
"""
results = {}
alpha_map = pd.read_csv(
agu.get_existing_path(opts['collapsed']['100nt']['alpha-map']),
sep='\t',
dtype=str,
)
alpha_metrics = ['shannon_1k', 'PD_whole_tree_1k']
# Checks the alpha_field is in the mapping file
for metric in alpha_metrics:
if metric not in alpha_map.columns:
raise ValueError('%s is not a valid alpha diversity field name.'
% metric)
# Checks the group_field is in the mapping file
if 'SIMPLE_BODY_SITE' not in alpha_map.columns:
raise ValueError('SIMPLE_BODY_SITE is not a valid field name.')
alpha_map[alpha_metrics] = alpha_map[alpha_metrics].astype(float)
alpha_map.set_index('#SampleID', inplace=True)
results = {}
for id_ in sample_ids:
if id_ not in alpha_map.index:
results[id_] = 'ID not found'
else:
results[id_] = None
shannon_path = os.path.join(_result_path(opts, id_),
'shannon_%s.png' % id_)
_plot_alpha(id_, alpha_map, 'shannon_1k',
xlabel='Shannon Diversity',
fp=shannon_path)
# Generates the pd whole tree diversity figure
pd_path = os.path.join(_result_path(opts, id_),
'pd_%s.png' % id_)
_plot_alpha(id_, alpha_map, 'PD_whole_tree_1k',
xlabel='PD Whole Tree Diversity',
fp=pd_path)
return results
def test_cat_taxa_summaries(self):
cat_taxa_summaries()
path = get_existing_path(
'../agp_processing/10-populated-templates/taxa')
exp = ['ag-oral-flossing-Daily.txt', 'ag-oral-flossing-Never.txt',
'ag-oral-flossing-Occasionally.txt',
'ag-oral-flossing-Rarely.txt', 'ag-oral-flossing-Regularly.txt',
'ag-stool-average.txt']
files = listdir(path)
self.assertItemsEqual(files, exp)
with open(join(path, 'ag-oral-flossing-Rarely.txt')) as f:
obs = f.read()
exp = """k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Fusobacteriaceae; g__Fusobacterium\t0.0110430107527
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Planococcaceae; g__\t0.00196774193548
k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__[Weeksellaceae]; g__Chryseobacterium\t0.0125913978495
k__Bacteria; p__Bacteroidetes; c__Sphingobacteriia; o__Sphingobacteriales; f__Sphingobacteriaceae; g__Sphingobacterium\t0.00608602150538
k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Bulleidia\t0.00269892473118
k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria\t0.074935483871
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Oribacterium\t0.00749462365591
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Xanthomonadales; f__Xanthomonadaceae; g__\t0.017311827957
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Moraxellaceae; g__Enhydrobacter\t0.000150537634409
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__\t0.00667741935484
k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Caulobacterales; f__Caulobacteraceae; g__Brevundimonas\t0.00996774193548
k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__[Weeksellaceae]; g__\t0.00139784946237
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Klebsiella\t0.00174193548387
k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus\t0.00756989247312
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella\t0.0509569892473
k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Leptotrichiaceae; g__Leptotrichia\t0.0143333333333
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus\t0.138817204301
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__\t0.0051935483871
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae]; g__[Prevotella]\t0.00132258064516
k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter\t0.00133333333333
k__Bacteria; p__Firmicutes; c__Bacilli; o__Gemellales; f__Gemellaceae; g__\t0.0097311827957
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__\t0.0135268817204
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__Haemophilus\t0.0668279569892
k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Brucellaceae; g__Ochrobactrum\t0.00575268817204
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Veillonella\t0.0709247311828
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas\t0.0165698924731
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__Aggregatibacter\t0.00410752688172
k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__\t0.00394623655914
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Moraxellaceae; g__Acinetobacter\t0.0247634408602
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Aerococcaceae; g__Alloiococcus\t0.000225806451613
k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Moryella\t0.000612903225806
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Micrococcaceae; g__Rothia\t0.114602150538
k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__Atopobium\t0.00761290322581
k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Alicycliphilus\t0.00530107526882
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Actinomycetaceae; g__Actinomyces\t0.0204408602151
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Xanthomonadales; f__Xanthomonadaceae; g__Stenotrophomonas\t0.0443655913978
k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium\t0.000440860215054
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Morganella\t0.000161290322581
k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Carnobacteriaceae; g__Granulicatella\t0.025247311828
k__Bacteria; p__SR1; c__; o__; f__; g__\t0.00222580645161
k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas\t0.0665268817204
"""
self.assertEqual(obs, exp)
def get_bloom_sequences():
"""Get the filepath to the bloom sequences
Returns
-------
str
The filepath to the bloom sequences
Raises
------
IOError
If the path does not exist
"""
repo = get_repository_dir()
return get_existing_path(os.path.join(repo, 'data/AG/BLOOM.fasta'))
def get_bloom_sequences():
"""Get the filepath to the bloom sequences
Returns
-------
str
The filepath to the bloom sequences
Raises
------
IOError
If the path does not exist
"""
repo = get_repository_dir()
return get_existing_path(os.path.join(repo, 'data/AG/BLOOM.fasta'))