def edit_taxonomies(i_datasets_folder: str, taxonomies: dict, force: bool,
prjct_nm: str, qiime_env: str, chmod: str, noloc: bool,
slurm: bool, run_params: dict, filt_raref: str, jobs: bool,
chunkit: int):
job_folder = get_job_folder(i_datasets_folder, 'taxonomy')
job_folder2 = get_job_folder(i_datasets_folder, 'taxonomy/chunks')
main_written = 0
to_chunk = []
run_pbs = '%s/1_run_taxonomy_edit_%s%s.sh' % (job_folder, prjct_nm,
filt_raref)
with open(run_pbs, 'w') as o:
for dat, (_, qza, tsv) in taxonomies.items():
if not isfile(tsv):
continue
written = 0
out_pd = pd.read_csv(tsv, dtype=str, sep='\t')
taxo = out_pd['Taxon'].tolist()
taxo_edit = get_taxa_edit(taxo)
if taxo != taxo_edit:
out_pd['Taxon'] = taxo_edit
out_pd.to_csv(tsv, index=False, sep='\t')
cmd = run_import(tsv, qza, 'FeatureData[Taxonomy]')
out_sh = '%s/run_taxonomy_edit_%s_%s%s.sh' % (
job_folder2, prjct_nm, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
main_written += 1
written += 1
if written:
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.tx.dt.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"],
run_params["n_nodes"], run_params["n_procs"],
run_params["mem_num"], run_params["mem_dim"],
chmod, written, 'single', o, noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'taxonomy_edit',
prjct_nm, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Edit features taxonomy to not contain "," characters',
'sh', run_pbs, jobs)
def run_qemistree(i_datasets_folder: str, datasets: dict, prjct_nm: str,
i_qemistree: str, taxonomies: dict, force: bool,
qiime_env: str, chmod: str, noloc: bool, slurm: bool,
run_params: dict, filt_raref: str, jobs: bool,
chunkit: int) -> None:
"""
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets_read: dataset -> [tsv table, meta table]
:param prjct_nm: Short nick name for your project.
:param i_qemistree: path to qemistree folder (feature-data and tree).
:param taxonomies: dataset -> [method, assignment qza]
:param force: Force the re-writing of scripts for all commands.
:param qiime_env: name of your qiime2 conda environment (e.g. qiime2-2019.10).
:param chmod: whether to change permission of output files (defalt: 775).
"""
job_folder = get_job_folder(i_datasets_folder, 'qemistree')
job_folder2 = get_job_folder(i_datasets_folder, 'qemistree/chunks')
written = 0
to_chunk = []
run_pbs = '%s/1_run_qemistree_%s%s.sh' % (job_folder, prjct_nm, filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds in datasets.items():
feature_data = '%s/feature-data_%s.qza' % (i_qemistree, dat)
qemistree = '%s/qemistree_%s.qza' % (i_qemistree, dat)
if not isfile(feature_data) or not isfile(qemistree):
continue
out_sh = '%s/run_qemistree_%s_%s%s.sh' % (job_folder2, prjct_nm, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
odir = get_analysis_folder(i_datasets_folder, 'qemistree/%s' % dat)
classyfire_qza = '%s/%s-classyfire.qza' % (odir, dat)
classyfire_tsv = '%s.tsv' % splitext(classyfire_qza)[0]
with open(out_sh, 'w') as cur_sh:
if force or not isfile(classyfire_tsv):
write_qemistree(feature_data, classyfire_qza,
classyfire_tsv, qemistree,
cur_sh)
written += 1
if isfile(classyfire_tsv):
odir = get_analysis_folder(i_datasets_folder, 'taxonomy/%s' % dat)
out_rad = '%s/tax_%s' % (odir, dat)
tax_qza = '%s.qza' % out_rad
tax_tsv = '%s.tsv' % out_rad
classyfire_pd = pd.read_csv(classyfire_tsv, header=0, sep='\t')
with open(tax_tsv, 'w') as o:
cols = ['id', 'kingdom', 'superclass', 'class', 'subclass', 'direct_parent']
o.write('Feature ID\tTaxon\n')
for row in classyfire_pd[cols].values:
o.write('%s\t%s\n' % (row[0], '; '.join(row[1:])))
run_export(tax_tsv, tax_qza, 'FeatureData[Taxonomy]')
taxonomies[dat] = ['direct_parent', tax_qza]
written += 1
else:
print('[Warning] Maybe run qemistree first and then re-run pipeline to '
'have the classyfire taxonomy include in the barplots!')
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs, '%s.qmstr.%s%s' % (prjct_nm, dat, filt_raref), qiime_env,
run_params["time"], run_params["n_nodes"], run_params["n_procs"],
run_params["mem_num"], run_params["mem_dim"],
chmod, written, 'single', o, noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'qemistree',
prjct_nm, run_params["time"], run_params["n_nodes"], run_params["n_procs"],
run_params["mem_num"], run_params["mem_dim"],
qiime_env, chmod, noloc, slurm, jobs, chunkit, None)
if written:
print_message('# Make qemistree classyfire classifications', 'sh', run_pbs, jobs)
def run_barplot(i_datasets_folder: str, datasets: dict, taxonomies: dict,
force: bool, prjct_nm: str, qiime_env: str, chmod: str,
noloc: bool, slurm: bool, run_params: dict, filt_raref: str,
jobs: bool, chunkit: int) -> None:
"""Visualize taxonomy with an interactive bar plot.
Parameters
----------
i_datasets_folder : str
Path to the folder containing the data/metadata subfolders
datasets : dict
Mappig dataset name -> [tsv file path, metadata file path]
taxonomies : dict
Mappig dataset name -> [classification_method, tax_qza]
force : bool
Force the re-writing of scripts for all commands
prjct_nm : str
Short nick name for your project
qiime_env : str
Mame of a qiime2 conda environment
chmod : str
Whether to change permission of output files (defalt: 744)
noloc : bool
run_params : dict
filt_raref : str
jobs : bool
chunkit : int
Returns
-------
"""
job_folder = get_job_folder(i_datasets_folder, 'barplot')
job_folder2 = get_job_folder(i_datasets_folder, 'barplot/chunks')
written = 0
to_chunk = []
run_pbs = '%s/1_run_barplot_%s%s.sh' % (job_folder, prjct_nm, filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
out_sh = '%s/run_barplot_%s_%s%s.sh' % (job_folder2, prjct_nm, dat,
filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for tsv_meta_pds in tsv_meta_pds_:
tsv, meta = tsv_meta_pds
if dat not in taxonomies:
continue
method, tax_qza, tax_tsv = taxonomies[dat]
if not method:
method = 'taxofromfile'
qza = '%s.qza' % splitext(tsv)[0]
odir = get_analysis_folder(i_datasets_folder,
'barplot/%s' % dat)
out_qzv = '%s/bar_%s_%s.qzv' % (odir, dat, method)
if force or not isfile(out_qzv):
write_barplots(out_qzv, qza, meta, tax_qza, cur_sh)
written += 1
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.brplt.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o,
noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'barplot', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if written:
print_message('# Make sample compositions barplots', 'sh', run_pbs,
jobs)
def run_taxonomy(method: str, i_datasets_folder: str, datasets: dict,
datasets_read: dict, datasets_phylo: dict,
datasets_features: dict, datasets_filt_map: dict,
i_classifier: str, taxonomies: dict, force: bool,
prjct_nm: str, qiime_env: str, chmod: str, noloc: bool,
slurm: bool, run_params: dict, filt_raref: str, jobs: bool,
chunkit: int) -> None:
"""
Parameters
----------
method
i_datasets_folder : str
Path to the folder containing the data/metadata subfolders.
datasets : dict
Mappring dataset name -> [data file path, metadata file path].
datasets_read : dict
Mapping dataset name -> [data table, metadata table]
datasets_phylo : dict
To be updated with ('tree_to_use', 'corrected_or_not') per dataset.
datasets_features : dict
Mapping dataset name -> list of features names in
the dataset tsv / biom file.
datasets_filt_map : dict
i_classifier : str
Path to the taxonomic classifier.
taxonomies : dict
Mapping Dataset name -> [method, assignment qza]
force : bool
Force the re-writing of scripts for all commands.
prjct_nm : str
Short nick name for your project.
qiime_env : str
Name of your qiime2 conda environment (e.g. qiime2-2019.10).
chmod : str
Whether to change permission of output files (default: 744).
noloc : str
run_params : dict
filt_raref : str
jobs : bool
chunkit : int
Returns
-------
"""
job_folder = get_job_folder(i_datasets_folder, 'taxonomy')
job_folder2 = get_job_folder(i_datasets_folder, 'taxonomy/chunks')
amplicon_datasets = [
dat for dat, (tree, correction) in datasets_phylo.items()
if tree == 'amplicon'
]
wol_datasets = [
dat for dat, (tree, correction) in datasets_phylo.items()
if tree == 'wol'
]
main_written = 0
to_chunk = []
run_pbs = '%s/1_run_taxonomy_%s%s.sh' % (job_folder, prjct_nm, filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets_read.items():
out_sh = '%s/run_taxonomy_%s_%s%s.sh' % (job_folder2, prjct_nm,
dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
if dat in datasets_filt_map:
taxonomies[dat] = taxonomies[datasets_filt_map[dat]]
continue
written = 0
with open(out_sh, 'w') as cur_sh:
for idx, tsv_meta_pds in enumerate(tsv_meta_pds_):
if idx:
continue
tsv, meta = datasets[dat][idx]
if not isinstance(tsv_meta_pds[0], pd.DataFrame) and \
tsv_meta_pds[0] == 'raref':
if not isfile(tsv):
print('Must have run rarefaction to use it '
'further...\nExiting')
sys.exit(0)
tsv_pd, meta_pd = get_raref_tab_meta_pds(meta, tsv)
datasets_read[dat][idx] = [tsv_pd, meta_pd]
else:
tsv_pd, meta_pd = tsv_meta_pds
odir = get_analysis_folder(i_datasets_folder,
'taxonomy/%s' % dat)
out_rad = '%s/tax_%s' % (odir, dat)
if dat in amplicon_datasets:
out_qza = '%s_%s.qza' % (out_rad, method)
out_tsv = '%s.tsv' % splitext(out_qza)[0]
taxonomies[dat] = [method, out_qza, out_tsv]
if not i_classifier:
print('No classifier passed for 16S '
'data\nExiting...')
continue
cmd = run_taxonomy_amplicon(dat, i_datasets_folder,
force, tsv_pd, out_qza,
out_tsv, i_classifier)
else:
out_qza = '%s.qza' % out_rad
out_tsv = '%s.tsv' % out_rad
if dat in wol_datasets:
cur_datasets_features = datasets_features[dat]
taxonomies[dat] = ['wol', out_qza, out_tsv]
cmd = run_taxonomy_wol(force, tsv_pd, out_qza,
out_tsv,
cur_datasets_features)
else:
if len(
[x for x in tsv_pd.index
if str(x).isdigit()]) == tsv_pd.shape[0]:
continue
taxonomies[dat] = ['feat', out_qza, out_tsv]
cmd = run_taxonomy_others(force, tsv_pd, out_qza,
out_tsv)
if cmd:
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
main_written += 1
written += 1
if written:
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.tx.sklrn.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"],
run_params["n_nodes"], run_params["n_procs"],
run_params["mem_num"], run_params["mem_dim"],
chmod, written, 'single', o, noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'taxonomy', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Classify features using classify-sklearn', 'sh',
run_pbs, jobs)
def import_datasets(i_datasets_folder: str, datasets: dict,
datasets_phylo: dict, force: bool, prjct_nm: str,
qiime_env: str, chmod: str, noloc: bool, run_params: dict,
filt_raref: str, jobs: bool, slurm: bool,
chunkit: int) -> None:
"""Initial imports of the .tsv datasets in to Qiime2 Artefacts
Parameters
----------
i_datasets_folder : str
Names identifying the datasets in the input folder
datasets : dict
Mapping dataset name -> [data file path, metadata file path]
datasets_phylo : dict
Mapping dataset name -> ('tree_to_use', 'corrected_or_not')
force : bool
Force the re-writing of scripts for all commands
prjct_nm : str
Nick name for the project.
qiime_env : str
Name of a qiime2 conda environment where analysis
tools to be run are installed
chmod : str
noloc : bool
run_params : dict
filt_raref : str
jobs : bool
chunkit : int
Returns
-------
"""
job_folder = get_job_folder(i_datasets_folder, 'import_tables')
job_folder2 = get_job_folder(i_datasets_folder, 'import_tables/chunks')
to_chunk = []
main_written = 0
run_pbs = '%s/0_run_import_%s%s.sh' % (job_folder, prjct_nm, filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
written = 0
out_sh = '%s/0_run_import_%s_%s%s.sh' % (job_folder2, prjct_nm,
dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for tsv_meta_pds in tsv_meta_pds_: # REMOVE IF FIXED NOT KEPT
tsv, meta = tsv_meta_pds
qza = '%s.qza' % splitext(tsv)[0]
if datasets_phylo[dat][1]:
cmd = run_import(tsv, qza, 'FeatureTable[Frequency]')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n' % cmd)
written += 1
elif force or not isfile(qza):
cmd = run_import(tsv, qza, 'FeatureTable[Frequency]')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n' % cmd)
written += 1
if written:
main_written += 1
to_chunk.append(out_sh)
if not chunkit:
job_name = '%s.mprt.%s%s' % (prjct_nm, dat, filt_raref)
run_xpbs(out_sh, out_pbs, job_name, qiime_env,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single',
o, noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'imports', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Import tables to qiime2', 'sh', run_pbs, jobs)
def run_rarefy(i_datasets_folder: str, datasets: dict, datasets_read: dict,
datasets_phylo: dict, datasets_filt_map: dict,
datasets_rarefs: dict, p_raref_depths: str, eval_rarefs: bool,
force: bool, prjct_nm: str, qiime_env: str, chmod: str,
noloc: bool, run_params: dict, filt_raref: str, filt_only: bool,
jobs: bool, slurm: bool, chunkit: int) -> dict:
"""
Run rarefy: Rarefy table.
https://docs.qiime2.org/2019.10/plugins/available/feature-table/rarefy/
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets: dataset -> [tsv/biom path, meta path]
:param datasets_read: dataset -> [tsv table, meta table]
:param datasets_features: dataset -> list of features names in the dataset tsv / biom file.
:param datasets_phylo: to be updated with ('tree_to_use', 'corrected_or_not') per dataset.
:param force: Force the re-writing of scripts for all commands.
:param prjct_nm: Nick name for your project.
:param qiime_env: qiime2-xxxx.xx conda environment.
:param chmod: whether to change permission of output files (defalt: 775).
:return: deta divesity matrices.
"""
evaluation = ''
eval_depths = {}
datasets_raref_depths, datasets_raref_evals = check_rarefy_need(
i_datasets_folder, datasets_read, p_raref_depths)
if eval_rarefs:
evaluation = '_eval'
set_filt_rarefy(datasets_raref_depths, datasets_filt_map)
datasets_update = {}
datasets_read_update = {}
datasets_phylo_update = {}
datasets_append = {}
main_written = 0
job_folder = get_job_folder(i_datasets_folder, 'rarefy%s' % evaluation)
job_folder2 = get_job_folder(i_datasets_folder,
'rarefy%s/chunks' % evaluation)
to_chunk = []
run_pbs = '%s/1_run_rarefy_%s%s%s.sh' % (job_folder, prjct_nm, evaluation,
filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
written = 0
if dat not in datasets_raref_depths:
continue
if filt_only and dat not in datasets_filt_map:
continue
odir = get_analysis_folder(i_datasets_folder,
'rarefy%s/%s' % (evaluation, dat))
out_sh = '%s/run_rarefy_%s%s_%s.sh' % (job_folder2, prjct_nm,
evaluation, dat)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
depths = datasets_raref_depths[dat][1]
if eval_rarefs:
depths = datasets_raref_evals[dat]
tsv_pd, meta_pd = datasets_read[dat][0]
tsv_sums = tsv_pd.sum()
for tsv_meta_pds in tsv_meta_pds_:
tsv, meta = tsv_meta_pds
for depth_ in depths:
depth = get_digit_depth(depth_, tsv_sums)
dat_raref = '%s_raref%s%s' % (dat, evaluation,
str(depth))
meta_out = '%s/meta_%s.tsv' % (odir, dat_raref)
remaining_samples = tsv_sums[
tsv_sums >= depth].index.tolist()
meta_raref_pd = meta_pd.loc[
meta_pd.sample_name.isin(remaining_samples), :]
meta_raref_pd.to_csv(meta_out, index=False, sep='\t')
qza = tsv.replace('.tsv', '.qza')
qza_out = '%s/tab_%s.qza' % (odir, dat_raref)
tsv_out = '%s.tsv' % splitext(qza_out)[0]
if force or not os.path.isfile(tsv_out):
cmd = write_rarefy(qza, qza_out, depth)
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
cmd = run_export(qza_out, tsv_out,
'FeatureTable[Frequency]')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
main_written += 1
written += 1
if eval_rarefs:
eval_depths.setdefault(dat, []).append(
'%s_%s' % (dat, str(depth)))
datasets_update['%s_%s' % (dat, str(depth))] = [[
tsv_out, meta_out
]]
datasets_read_update['%s_%s' %
(dat, str(depth))] = (
'raref', str(depth))
datasets_phylo_update[
'%s_%s' %
(dat, str(depth))] = datasets_phylo[dat]
else:
datasets_append.setdefault(dat, []).append(
[tsv_out, meta_out])
if isfile(tsv_out) and isfile(meta_out):
tab_filt_pd = pd.read_csv(tsv_out,
index_col=0,
header=0,
sep='\t')
with open(meta_out) as f:
for line in f:
break
meta_filt_pd = pd.read_csv(
meta_out,
header=0,
sep='\t',
dtype={line.split('\t')[0]: str},
low_memory=False)
datasets_read[dat].append(
[tab_filt_pd, meta_filt_pd])
else:
datasets_read[dat].append(
('raref', str(depth)))
datasets_rarefs.setdefault(dat, []).append(
'_raref%s%s' % (evaluation, str(depth)))
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(
out_sh, out_pbs,
'%s.bt%s.%s%s' % (prjct_nm, evaluation, dat, filt_raref),
qiime_env, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o, noloc,
slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'rarefy%s' % evaluation,
prjct_nm, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Get rarefied datasets', 'sh', run_pbs, jobs)
if eval_rarefs:
datasets.update(datasets_update)
datasets_read.update(datasets_read_update)
datasets_phylo.update(datasets_phylo_update)
else:
for dat, fps in datasets_append.items():
datasets[dat].extend(fps)
return eval_depths
def run_volatility(i_datasets_folder: str, datasets: dict, p_longi_column: str,
datasets_rarefs: dict, force: bool, prjct_nm: str,
qiime_env: str, chmod: str, noloc: bool, slurm: bool,
run_params: dict, filt_raref: str, jobs: bool,
chunkit: int) -> None:
"""
Run volatility: Generate interactive volatility plot.
https://docs.qiime2.org/2019.10/plugins/available/longitudinal/volatility/
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets: list of datasets.
:param p_longi_column: metadata column that is the time stratification.
:param force: Force the re-writing of scripts for all commands.
:param prjct_nm: Nick name for your project.
:param qiime_env: qiime2-xxxx.xx conda environment.
:param chmod: whether to change permission of output files (defalt: 775).
"""
job_folder = get_job_folder(i_datasets_folder, 'longitudinal')
job_folder2 = get_job_folder(i_datasets_folder, 'longitudinal/chunks')
main_written = 0
first_print = 0
first_print2 = 0
to_chunk = []
run_pbs = '%s/5_run_volatility_%s%s.sh' % (job_folder, prjct_nm,
filt_raref)
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
written = 0
out_sh = '%s/run_volatility_%s_%s%s.sh' % (job_folder2, prjct_nm,
dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for idx, tsv_meta_pds in enumerate(tsv_meta_pds_):
tsv, meta = tsv_meta_pds
cur_raref = datasets_rarefs[dat][idx]
meta_alphas = '%s_alphas.tsv' % splitext(meta)[0]
if not isfile(meta_alphas):
if not first_print:
print(
'\nWarning: First make sure you run alpha -> alpha merge/export (2_run_merge_alphas.sh) '
' before running volatility\n\t(if you need the alpha as a response variable)!'
)
first_print += 1
continue
with open(meta) as f:
for line in f:
break
time_point = [
x for x in line.strip().split('\t')
if p_longi_column in x
][0]
if not time_point:
if not first_print2:
print('Variable %s not in metadata %s\n' %
(p_longi_column, meta_alphas))
first_print2 += 1
continue
odir = get_analysis_folder(
i_datasets_folder,
'longitudinal/%s%s' % (dat, cur_raref))
out_fp = '%s/%s_volatility.qzv' % (odir, dat)
if force or not isfile(out_fp):
write_longitudinal_volatility(out_fp, meta_alphas,
time_point, cur_sh)
written += 1
main_written += 1
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.vltlt.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o,
noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'volatility', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Longitudinal change in alpha diversity indices', 'sh',
run_pbs, jobs)
def run_alpha_rarefaction(i_datasets_folder: str, datasets: dict,
datasets_rarefs: dict, datasets_phylo: dict,
trees: dict, force: bool, prjct_nm: str,
qiime_env: str, chmod: str, noloc: bool, slurm: bool,
As: tuple, run_params: dict, filt_raref: str,
jobs: bool, chunkit: int) -> None:
"""
Run alpha-rarefaction: Alpha rarefaction
https://docs.qiime2.org/2019.10/plugins/available/diversity/alpha-rarefaction/
"""
alpha_metrics = get_metrics('alpha_metrics', As)
job_folder = get_job_folder(i_datasets_folder, 'alpha_rarefaction')
job_folder2 = get_job_folder(i_datasets_folder, 'alpha_rarefaction/chunks')
main_written = 0
run_pbs = '%s/4_run_alpha_rarefaction_%s%s.sh' % (job_folder, prjct_nm,
filt_raref)
to_chunk = []
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
written = 0
out_sh = '%s/run_alpha_rarefaction_%s_%s%s.sh' % (
job_folder2, prjct_nm, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for idx, tsv_meta_pds in enumerate(tsv_meta_pds_):
tsv, meta = tsv_meta_pds
qza = '%s.qza' % splitext(tsv)[0]
cur_raref = datasets_rarefs[dat][idx]
odir = get_analysis_folder(
i_datasets_folder,
'alpha_rarefaction/%s%s' % (dat, cur_raref))
for metric in alpha_metrics:
out_fp = '%s/rarefcurve_%s%s_%s.qzv' % (
odir, dat, cur_raref, metric)
if force or not isfile(out_fp):
if write_diversity_alpha_rarefaction(
out_fp, qza, metric, datasets_phylo, trees,
dat, meta, cur_sh):
continue
written += 1
main_written += 1
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.lphrrf.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o,
noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'alpha_rarefaction',
prjct_nm, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Compute rarefaction curve on alpha diversity indices',
'sh', run_pbs, jobs)
def run_correlations(i_datasets_folder: str, datasets: dict, diversities: dict,
datasets_rarefs: dict, force: bool, prjct_nm: str,
qiime_env: str, chmod: str, noloc: bool, slurm: bool,
run_params: dict, filt_raref: str, jobs: bool,
chunkit: int) -> None:
"""
Run alpha-correlation: Alpha diversity correlation
https://docs.qiime2.org/2019.10/plugins/available/diversity/alpha-correlation/
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets: list of datasets.
:param diversities: alpha diversity qiime2 Arfetact per dataset.
:param force: Force the re-writing of scripts for all commands.
:param prjct_nm: Nick name for your project.
:param qiime_env: qiime2-xxxx.xx conda environment.
:param chmod: whether to change permission of output files (defalt: 775).
"""
job_folder = get_job_folder(i_datasets_folder, 'alpha_correlations')
job_folder2 = get_job_folder(i_datasets_folder,
'alpha_correlations/chunks')
main_written = 0
run_pbs = '%s/4_run_alpha_correlation_%s%s.sh' % (job_folder, prjct_nm,
filt_raref)
to_chunk = []
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
if dat not in diversities:
continue
written = 0
out_sh = '%s/run_alpha_correlation_%s_%s%s.sh' % (
job_folder2, prjct_nm, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for idx, tsv_meta_pds in enumerate(tsv_meta_pds_):
tsv, meta = tsv_meta_pds
cur_raref = datasets_rarefs[dat][idx]
for method in ['spearman', 'pearson']:
for group, divs in diversities[dat][idx].items():
if group:
odir = get_analysis_folder(
i_datasets_folder,
'alpha_correlations/%s%s/%s' %
(dat, cur_raref, group))
else:
odir = get_analysis_folder(
i_datasets_folder,
'alpha_correlations/%s%s' %
(dat, cur_raref))
for qza in [x[0] for x in divs]:
out_fp = '%s/alpha_corr_%s' % (
odir, basename(qza).replace(
'.qza', '_%s.qzv' % method))
if force or not isfile(out_fp):
write_diversity_alpha_correlation(
out_fp, qza, method, meta, cur_sh)
written += 1
main_written += 1
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(out_sh, out_pbs,
'%s.lphcrr.%s%s' % (prjct_nm, dat, filt_raref),
qiime_env, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o,
noloc, slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'alpha_correlations',
prjct_nm, run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message(
'# Correlate numeric metadata variables with alpha diversity indices',
'sh', run_pbs, jobs)
def run_alpha(i_datasets_folder: str, datasets: dict, datasets_read: dict,
datasets_phylo: dict, datasets_rarefs: dict,
p_alpha_subsets: str, trees: dict, force: bool, prjct_nm: str,
qiime_env: str, chmod: str, noloc: bool, slurm: bool, As: tuple,
dropout: bool, run_params: dict, filt_raref: str,
eval_depths: dict, jobs: bool, chunkit: int) -> dict:
"""
Computes the alpha diversity vectors for each dataset.
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets: dataset -> [tsv, meta]
:param datasets_read: dataset -> [tsv table, meta table]
:param datasets_phylo: to be updated with ('tree_to_use', 'corrected_or_not') per dataset.
:param p_alpha_subsets: Subsets for alpha diversity.
:param trees: to be update with tree to use for a dataset phylogenetic analyses.
:param force: Force the re-writing of scripts for all commands.
:param prjct_nm: Short nick name for your project.
:param qiime_env: name of your qiime2 conda environment (e.g. qiime2-2019.10).
:param chmod: whether to change permission of output files (defalt: 775).
:return: {'dataset1': [ 'meta', {'div_index1': '.qza', 'div_index2': '.qza', ... }],
'dataset2': [ 'meta', {'div_index1': '.qza', 'div_index2': '.qza', ... }], '...'}
"""
evaluation = ''
if len(eval_depths):
evaluation = '_eval'
alpha_metrics = get_metrics('alpha_metrics', As)
alpha_subsets = read_yaml_file(p_alpha_subsets)
job_folder = get_job_folder(i_datasets_folder, 'alpha%s' % evaluation)
job_folder2 = get_job_folder(i_datasets_folder,
'alpha%s/chunks' % evaluation)
diversities = {}
run_pbs = '%s/1_run_alpha_%s%s%s.sh' % (job_folder, prjct_nm, evaluation,
filt_raref)
main_written = 0
to_chunk = []
with open(run_pbs, 'w') as o:
for dat, tsv_meta_pds_ in datasets.items():
written = 0
diversities[dat] = []
out_sh = '%s/run_alpha_%s%s_%s%s.sh' % (
job_folder2, prjct_nm, evaluation, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for idx, tsv_meta_pds in enumerate(tsv_meta_pds_):
tsv, meta = tsv_meta_pds
if not isinstance(
datasets_read[dat][idx][0], pd.DataFrame
) and datasets_read[dat][idx][0] == 'raref':
if not isfile(tsv):
print(
'Must have run rarefaction to use it further...\nExiting'
)
sys.exit(0)
tsv_pd, meta_pd = get_raref_tab_meta_pds(meta, tsv)
datasets_read[dat][idx] = [tsv_pd, meta_pd]
else:
tsv_pd, meta_pd = datasets_read[dat][idx]
cur_raref = datasets_rarefs[dat][idx]
qza = '%s.qza' % splitext(tsv)[0]
divs = {}
for metric in alpha_metrics:
odir = get_analysis_folder(
i_datasets_folder, 'alpha/%s%s' % (dat, cur_raref))
out_fp = '%s/%s_%s.qza' % (
odir, basename(splitext(qza)[0]), metric)
out_tsv = '%s.tsv' % splitext(out_fp)[0]
if force or not isfile(out_fp):
ret_continue = write_diversity_alpha(
out_fp, datasets_phylo, trees, dat, qza,
metric, cur_sh, qiime_env)
if ret_continue:
continue
cmd = run_export(out_fp, out_tsv, '')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
written += 1
main_written += 1
divs.setdefault('', []).append((out_fp, metric))
if alpha_subsets and dat in alpha_subsets:
for subset, subset_regex in alpha_subsets[dat].items():
odir = get_analysis_folder(
i_datasets_folder,
'alpha/%s%s/%s' % (dat, cur_raref, subset))
if dropout:
qza_subset_ = '%s/%s_%s.qza' % (
odir, basename(splitext(qza)[0]), subset)
else:
qza_subset_ = '%s/%s_%s_noDropout.qza' % (
odir, basename(splitext(qza)[0]), subset)
feats_subset = '%s.meta' % splitext(qza_subset_)[0]
feats = get_subset(tsv_pd, subset_regex)
if not len(feats):
continue
subset_pd = pd.DataFrame({
'Feature ID':
feats,
'Subset': [subset] * len(feats)
})
subset_pd.to_csv(feats_subset,
index=False,
sep='\t')
write_filter_features(tsv_pd, feats, qza,
qza_subset_, feats_subset,
cur_sh, dropout)
for metric in alpha_metrics:
if metric in [
'faith_pd'
] and datasets_phylo[dat][1] and dat in trees:
tree_in_qza = trees[dat][0]
tree_in_tsv = '%s.tsv' % splitext(
tree_in_qza)[0]
if dropout:
qza_subset = '%s/%s_%s.qza' % (
odir,
basename(splitext(tree_in_qza)[0]),
subset)
else:
qza_subset = '%s/%s_%s_noDropout.qza' % (
odir,
basename(splitext(tree_in_qza)[0]),
subset)
write_filter_features(
pd.read_csv(tree_in_tsv,
header=0,
index_col=0,
sep='\t'), feats,
tree_in_qza, qza_subset, feats_subset,
cur_sh, dropout)
else:
qza_subset = qza_subset_
out_fp = '%s/%s__%s.qza' % (
odir, basename(
splitext(qza_subset)[0]), metric)
out_tsv = '%s.tsv' % splitext(out_fp)[0]
if force or not isfile(out_fp):
ret_continue = write_diversity_alpha(
out_fp, {dat: [1, 0]}, trees, dat,
qza_subset, metric, cur_sh, qiime_env)
if ret_continue:
continue
cmd = run_export(out_fp, out_tsv, '')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
written += 1
main_written += 1
divs.setdefault(subset, []).append(
(out_fp, metric))
diversities[dat].append(divs)
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(
out_sh, out_pbs, '%s.mg.lph%s.%s%s' %
(prjct_nm, evaluation, dat, filt_raref), qiime_env,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o, noloc,
slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'alpha', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Calculate alpha diversity indices', 'sh', run_pbs,
jobs)
return diversities
def merge_meta_alpha(i_datasets_folder: str, datasets: dict,
datasets_rarefs: dict, diversities: dict, force: bool,
prjct_nm: str, qiime_env: str, chmod: str, noloc: bool,
slurm: bool, dropout: bool, run_params: dict,
filt_raref: str, eval_depths: dict, jobs: bool,
chunkit: int) -> dict:
"""
Computes the alpha diversity vectors for each dataset.
:param i_datasets_folder: Path to the folder containing the data/metadata subfolders.
:param datasets: list of datasets.
:param datasets_rarefs: list of rarefied datasets.
:param diversities: paths to [alpha_divs]
:param force: Force the re-writing of scripts for all commands.
:param prjct_nm: Short nick name for your project.
:param qiime_env: name of your qiime2 conda environment (e.g. qiime2-2019.10).
:param chmod: whether to change permission of output files (defalt: 775).
:return:
"""
evaluation = ''
if len(eval_depths):
evaluation = '_eval'
job_folder = get_job_folder(i_datasets_folder, 'tabulate%s' % evaluation)
job_folder2 = get_job_folder(i_datasets_folder,
'tabulate%s/chunks' % evaluation)
to_export = {}
to_chunk = []
main_written = 0
run_pbs = '%s/2_run_merge_alphas_%s%s%s.sh' % (job_folder, prjct_nm,
evaluation, filt_raref)
with open(run_pbs, 'w') as o:
for dat, group_divs_list in diversities.items():
written = 0
to_export[dat] = []
out_sh = '%s/run_merge_alpha_%s%s_%s%s.sh' % (
job_folder2, prjct_nm, evaluation, dat, filt_raref)
if slurm:
out_pbs = '%s.slm' % splitext(out_sh)[0]
else:
out_pbs = '%s.pbs' % splitext(out_sh)[0]
with open(out_sh, 'w') as cur_sh:
for idx, group_divs in enumerate(group_divs_list):
tsv, meta = datasets[dat][idx]
cur_raref = datasets_rarefs[dat][idx]
base = basename(splitext(tsv)[0]).lstrip('tab_')
to_export_groups = []
for group, divs in group_divs.items():
if group:
output_folder = get_analysis_folder(
i_datasets_folder, 'tabulate%s/%s%s/%s' %
(evaluation, dat, cur_raref, group))
else:
output_folder = get_analysis_folder(
i_datasets_folder, 'tabulate%s/%s%s' %
(evaluation, dat, cur_raref))
if dropout:
out_fp = '%s/%s_alphas__%s.qzv' % (output_folder,
base, group)
else:
out_fp = '%s/%s_alphas_noDropout__%s.qzv' % (
output_folder, base, group)
out_fp_tsv = '%s.tsv' % splitext(out_fp)[0]
if isfile(out_fp_tsv):
with open(out_fp_tsv) as f:
for line in f:
indices = line.strip().split('\t')[1:]
break
divs_alphas = [x[1] for x in divs]
if len(indices) < len(divs_alphas):
force = True
to_export_groups.append(out_fp_tsv)
if force or not isfile(out_fp):
write_metadata_tabulate(out_fp, divs, meta, cur_sh)
cmd = run_export(out_fp, out_fp_tsv, '')
cur_sh.write('echo "%s"\n' % cmd)
cur_sh.write('%s\n\n' % cmd)
main_written += 1
written += 1
to_export[dat].append(to_export_groups)
to_chunk.append(out_sh)
if not chunkit:
run_xpbs(
out_sh, out_pbs, '%s.mrg.lph%s.%s%s' %
(prjct_nm, evaluation, dat, filt_raref), qiime_env,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], chmod, written, 'single', o, noloc,
slurm, jobs)
if to_chunk and chunkit:
simple_chunks(run_pbs, job_folder2, to_chunk, 'tabulate', prjct_nm,
run_params["time"], run_params["n_nodes"],
run_params["n_procs"], run_params["mem_num"],
run_params["mem_dim"], qiime_env, chmod, noloc, slurm,
jobs, chunkit, None)
if main_written:
print_message('# Merge and export alpha diversity indices', 'sh',
run_pbs, jobs)
return to_export
