exprmat 0.1.37__tar.gz → 0.1.39__tar.gz

{exprmat-0.1.37 → exprmat-0.1.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.37
+Version: 0.1.39
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -42,7 +42,6 @@ Requires-Dist: metacells
 Requires-Dist: sh
 Requires-Dist: networkx
 Requires-Dist: palantir
-Requires-Dist: rich
 Requires-Dist: adjusttext
 Requires-Dist: h5py
 Requires-Dist: cytoolz
@@ -55,7 +54,6 @@ Requires-Dist: hdbscan
 Requires-Dist: graphtools
 Requires-Dist: bincsync>=0.3.0
 Requires-Dist: pybigwig
-Requires-Dist: pybedgraph
 Requires-Dist: loompy
 Requires-Dist: squidpy
 Requires-Dist: zarr
@@ -75,6 +73,9 @@ Requires-Dist: formulaic>=1.0.2
 Requires-Dist: formulaic-contrasts>=0.2.0
 Requires-Dist: cython
 Requires-Dist: pyfastx
+Requires-Dist: genomicranges
+Requires-Dist: rustworkx
+Requires-Dist: xgboost
 Requires-Dist: sphinx ; extra == 'dev'
 Requires-Dist: twine ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/__init__.py

@@ -1,10 +1,19 @@
 
+# the file specification, defined as the earlieast version to handle
+# current file standard. (revision number). specification versions are not
+# continuous. historically taken [1, 39]
+
+SPECIFICATION = 39
+
+import importlib.metadata
+ver_string = importlib.metadata.version("exprmat")
+MAJOR, MINOR, REVISION = [int(x) for x in ver_string.split('.')]
+
 import os
 os.environ['OPENBLAS_NUM_THREADS'] = '1'
 os.environ['GOTO_NUM_THREADS'] = '1'
 os.environ['OMP_NUM_THREADS'] = '1'
 
-import importlib.metadata
 import mudata as mu
 import anndata as ad
 import scanpy as sc
@@ -100,6 +109,7 @@ basepath = config['data']
 from exprmat.utils import setup_styles
 from exprmat.reader.experiment import experiment, load_experiment
 from exprmat.reader.metadata import metadata, load_metadata
+from exprmat.ansi import error, warning, info, pprog, pproga
 
 setup_styles()
 
@@ -128,16 +138,33 @@ if PERFORM_DATABASE_CHECK:
         warning(f'db version: {db_ver}  package version: {importlib.metadata.version("exprmat")}')
 
 
+def cuda():
+
+    import torch
+    info(f'PyTorch version: {torch.__version__}')
+    info(f'GPU acceleration availability: {"YES" if torch.cuda.is_available() else "NO"}')
+    if torch.cuda.is_available():
+        info(f'CUDA version: {torch.version.cuda}')
+        info(f'Number of installed GPUs: {torch.cuda.device_count()}')
+        info(f'Supporting BF16 format: {"YES" if torch.cuda.is_bf16_supported() else "NO"}')
+        info(f'Devices:')
+        for i in range(torch.cuda.device_count()):
+            total_mem = torch.cuda.get_device_properties(i).total_memory / 1024 / 1024 / 1024
+            dedicated_mem = torch.cuda.memory_allocated(i) / 1024 / 1024 / 1024
+            info(f'[{i}] {torch.cuda.get_device_name(i)} {"*" if torch.cuda.current_device() == i else ""}')
+            info(f'    CUDA capability: {torch.cuda.get_device_capability(i)}')
+            info(f'    Installed VRAM (GiB): {total_mem:.2f} GiB')
+            info(f'    Supporting TensorCore: {"YES" if torch.cuda.get_device_properties(0).major >= 7 else "NO"}')
+            info(f'    Current dedicated memory: {dedicated_mem:.2f} / {total_mem:.2f} GiB ({100 * dedicated_mem / total_mem:.1f}%)')
+
+
 def version(): 
     import os
     import sys
     import platform
     from exprmat.ansi import info, error, format_file_size
 
-    ver_string = importlib.metadata.version("exprmat")
     db_ver = version_db()
-
-    MAJOR, MINOR, REVISION = [int(x) for x in ver_string.split('.')]
     info(f'exprmat {MAJOR}.{MINOR}.{REVISION} / exprmat-db {db_ver if db_ver is not None else "(Not installed)"}')
     info(f'os: {os.name} ({sys.platform})  platform version: {platform.release()}')
     info(f'loaded configuration from {finder}')
@@ -170,6 +197,12 @@ __all__ = [
     'load_metadata',
     'version',
     'memory',
+    'cuda',
     'setwd',
-    'getwd'
+    'getwd',
+    'error',
+    'warning',
+    'info',
+    'pprog',
+    'pproga'
 ]

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/ansi.py

@@ -2,6 +2,10 @@
 import re
 import os
 
+from functools import partial
+from tqdm import tqdm
+from tqdm.auto import tqdm as tqdma
+
 
 def fore_black() -> None:
     print('\033[30m', end = '')
@@ -147,3 +151,13 @@ def yellow(x): return '\033[33m' + x + '\033[0m'
 def blue(x): return '\033[34m' + x + '\033[0m'
 def purple(x): return '\033[35m' + x + '\033[0m'
 def cyan(x): return '\033[36m' + x + '\033[0m'
+
+
+progress_styles = {
+    'ncols': 80,
+    'ascii': '-━',
+    'bar_format': '   {bar} {desc:20} {n:5d} / {total:<5d} ({elapsed} < {remaining})'
+}
+
+pprog = partial(tqdm, **progress_styles)
+pproga = partial(tqdma, **progress_styles)

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/cnv/infercnv.py

@@ -10,10 +10,9 @@ import scipy.ndimage
 import scipy.sparse
 from anndata import AnnData
 from scanpy import logging
-from tqdm.auto import tqdm
 from tqdm.contrib.concurrent import process_map
 
-from exprmat.ansi import error, warning, info
+from exprmat.ansi import error, warning, info, pproga
 from exprmat.utils import ensure_array
 
 
@@ -80,7 +79,7 @@ def infercnv(
     exclude_chromosomes
         List of chromosomes to exclude. The default is to exclude genosomes.
         For list of all available chromosomes in the dataset, you should manually check
-        the adata.var['.seqid'] column, when you are not using the pre-built genome annotations.
+        the adata.var['chr'] column, when you are not using the pre-built genome annotations.
 
     chunksize
         Process dataset in chunks of cells. This allows to run infercnv on
@@ -113,16 +112,16 @@ def infercnv(
 
     if not adata.var_names.is_unique:
         error('ensure your var_names are unique.')
-    if {'.seqid', '.start', '.end'} - set(adata.var.columns) != set():
-        warning('ensure your var table contains ".seqid", ".start", and ".end"')
+    if {'chr', 'start', 'end'} - set(adata.var.columns) != set():
+        warning('ensure your var table contains "chr", "start", and "end"')
         warning('this should be automatically queried for you if you specify a legal taxa name.')
         error('otherwise, you should parse the gff and configure these information yourself.')
 
-    var_mask = adata.var['.seqid'].isnull()
+    var_mask = adata.var['chr'].isnull()
     if np.sum(var_mask):
         warning(f'skipped {np.sum(var_mask)} genes because they don\'t have a genomic position annotated.')  # type: ignore
     if exclude_chromosomes is not None:
-        var_mask = var_mask | adata.var['.seqid'].isin(exclude_chromosomes)
+        var_mask = var_mask | adata.var['chr'].isin(exclude_chromosomes)
 
     valid_annot_adata = adata[:, ~ var_mask]
     reference = get_reference_cells(adata, reference_key, reference_cat, reference)[:, ~ var_mask]
@@ -131,7 +130,7 @@ def infercnv(
     if scipy.sparse.issparse(expr):
         expr = expr.tocsr()
 
-    var = valid_annot_adata.var.loc[:, ['.seqid', '.start', '.end']]
+    var = valid_annot_adata.var.loc[:, ['chr', 'start', 'end']]
     chr_pos, chunks, convolved_dfs = zip(
         *process_map(
             infercnv_proc,
@@ -143,7 +142,7 @@ def infercnv(
             itertools.repeat(step),
             itertools.repeat(dynamic_threshold),
             itertools.repeat(calculate_gene_values),
-            tqdm_class=tqdm,
+            tqdm_class = pproga,
             max_workers=cpu_count() if n_jobs is None else n_jobs,
         ),
         strict=False,
@@ -341,7 +340,7 @@ def running_mean_by_chr(
         and genomic position. This is a row in the plotted chromosome CNV matrix.
     '''
 
-    chromosomes = natural_sort([x for x in var['.seqid'].unique() if x != 'MT'])
+    chromosomes = natural_sort([x for x in var['chr'].unique() if x != 'MT'])
     running_means = [
         running_mean_chr(
             chr, expr, var, window_size, step, calculate_gene_values
@@ -361,7 +360,7 @@ def running_mean_by_chr(
 
 def running_mean_chr(chr, expr, var, window_size, step, calculate_gene_values):
 
-    genes = var.loc[var['.seqid'] == chr].sort_values('.start').index.values
+    genes = var.loc[var['chr'] == chr].sort_values('start').index.values
     tmp_x = expr[:, var.index.get_indexer(genes)]
     x_conv, convolved_gene_values = running_mean(
         tmp_x, n = window_size, step = step, 

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/configuration.py

@@ -24,18 +24,21 @@ class Configuration:
         # target taxa
 
         self.config['taxa.reference'] = {
-            'mm10': 'mmu', # alias of grcm38
+            'mm10': 'mmu',   # the slightly modified version from ucsc based on grcm38
             'grcm39': 'mmu',
             'grcm38': 'mmu',
 
-            'hg19': 'hsa', # alias of grch37
+            'hg19': 'hsa',   # the slightly modified version from ucsc based on grch37
             'grch37': 'hsa',
             'grch38': 'hsa',
+
+            'dm6': 'dme'
         }
 
         self.config['default.assembly'] = {
             'mmu': 'grcm39',
-            'hsa': 'grch38'
+            'hsa': 'grch38',
+            'dme': 'dm6'
         }
 
         self.config['max.image'] = int(10000 * 50000)

exprmat-0.1.39/exprmat/data/cre.py

@@ -0,0 +1,111 @@
+
+import os
+import pandas as pd
+import pickle
+import numpy as np
+import lightmotif
+
+from exprmat.data.finders import basepath
+from exprmat.ansi import error, warning, info
+
+with open(os.path.join(basepath, 'shared', 'motifs.pkl'), 'rb') as f:
+    motif_tree = pickle.load(f)
+
+pssm_table = {}
+transcription_factor_bindings = {}
+motif_subsets = {}
+
+
+def get_motifs(subset = 'all'):
+    if subset == 'all': return motif_tree
+    elif subset in motif_subsets.keys(): return motif_subsets[subset]
+    else:
+        subtree = {}
+        for key in motif_tree.keys():
+            items = {}
+            for mot in motif_tree[key].keys():
+                if motif_tree[key][mot]['source'] == subset:
+                    items[mot] = motif_tree[key][mot]
+            subtree[key] = items
+        motif_subsets[subset] = subtree
+        return motif_subsets[subset]
+
+
+def get_transcription_factor_binding_motifs(taxa):
+
+    if not taxa in transcription_factor_bindings.keys():
+        transcription_factor_bindings[taxa] = \
+            pd.read_feather(os.path.join(basepath, taxa, 'tf', 'transcription-factors.feather'))
+    
+    return transcription_factor_bindings[taxa]
+
+
+def search_transcription_factor(taxa, factor, subset = 'all'):
+
+    tfbindings = get_transcription_factor_binding_motifs(taxa)
+    if factor in tfbindings['symbol'].tolist():
+        row = tfbindings['symbol'].tolist().index(factor)
+        row = tfbindings.iloc[row, :].copy()
+        metaclust = row['metacluster'].split(' ')
+        motifs = row['motif'].split(' ')
+
+        table = get_motifs(subset)
+        pairs = []
+        for mc in metaclust:
+            for mot in motifs:
+                if mot in table[mc].keys():
+                    pairs.append((mc, mot))
+        
+        return pairs
+    
+    else: error(f'could not find transcription factor {factor} in taxa {taxa}.')
+
+
+def plot_sequence_logo(motif, fig_height = 1, fig_width_per_base = 0.2, dpi = 100):
+
+    from exprmat.plotting.sequence import sequence_logo
+    motifs = get_motifs()
+    if isinstance(motif, tuple):
+        return sequence_logo(
+            np.array(motifs[motif[0]][motif[1]]['ppm'].T, dtype = np.float32), 
+            ppm = True, y_format = 'bits', dpi = dpi, 
+            fig_height = fig_height, fig_width_per_base = fig_width_per_base
+        )
+    
+    elif isinstance(motif, str):
+        for mc in motifs.keys():
+            if motif in motifs[mc].keys():
+                return sequence_logo(
+                    np.array(motifs[mc][motif]['ppm'].T, dtype = np.float32), 
+                    ppm = True, y_format = 'bits', dpi = dpi, 
+                    fig_height = fig_height, fig_width_per_base = fig_width_per_base
+                )
+            
+
+def motif_to_tuple(motif):
+    motifs = get_motifs()
+    for mc in motifs.keys():
+        if motif in motifs[mc].keys():
+            return (mc, motif)
+    error(f'could not find motif {motif}')
+
+
+def to_pssm(motif, eps = 0.01):
+    
+    if isinstance(motif, str): motif = motif_to_tuple(motif)
+    if motif[1] in pssm_table.keys(): return pssm_table[motif[1]]
+
+    motifs = get_motifs()
+    integral = np.array(motifs[motif[0]][motif[1]]['ppm'].T * 100000, dtype = np.int32)
+    
+    # original order: acgt.
+    pwm = lightmotif.CountMatrix({
+        'A': integral[:, 0].tolist(),
+        'C': integral[:, 1].tolist(),
+        'T': integral[:, 3].tolist(),
+        'G': integral[:, 2].tolist(),
+    }).normalize(eps)
+
+    pssm = pwm.log_odds()
+    pssm_table[motif[1]] = pssm
+    return pssm

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/data/finders.py

@@ -28,23 +28,28 @@ def get_genome(taxa):
 
     if taxa not in genome.keys(): genome[taxa] = {}
     if 'genes' in genome[taxa].keys(): return genome[taxa]['genes']
-    genome[taxa]['genes'] = pandas.read_table(
-        os.path.join(basepath, f'{taxa}', 'genome.tsv.gz'),
-        # set low memory to false to allow correct adjustment to mixed dtype.
-        index_col = '.ugene', dtype = {'.seqid': str}, low_memory = False
+    genome[taxa]['genes'] = pandas.read_feather(
+        os.path.join(basepath, f'{taxa}', 'genome.feather')
     )
 
+    genome[taxa]['genes'].index = genome[taxa]['genes']['uid'].tolist()
     return genome[taxa]['genes']
 
 
-def get_genome_size(assembly):
+def get_genome_size(assembly, as_dataframe = False):
 
     import json
     taxa = cfg['taxa.reference'][assembly.lower()]
     path = os.path.join(basepath, taxa, 'assemblies', assembly.lower(), 'size.json')
     with open(path, 'r', encoding = 'utf-8') as f:
         sizes = json.load(f)
-    return sizes
+    
+    if as_dataframe: return pandas.DataFrame({
+        'seqname': sizes.keys(),
+        'len': [sizes[k] for k in sizes.keys()]
+    })
+
+    else: return sizes
 
 
 def get_genome_gff_fname(assembly):
@@ -80,12 +85,13 @@ def get_genome_ranges(assembly, fname, as_grange = False):
     taxa = cfg['taxa.reference'][assembly.lower()]
     path = os.path.join(basepath, taxa, 'assemblies', assembly.lower(), f'{fname}.feather')
     feather = pandas.read_feather(path)
+    feather = feather.loc[feather['end'] - feather['start'] > 0, :].copy()
     
     if as_grange: 
         import genomicranges
         return genomicranges.GenomicRanges.from_pandas(
-            feather[['ucsc', 'start', 'end', 'strand', 'gene']].rename(
-            columns = {'ucsc': 'seqnames', 'start': 'starts', 'end': 'ends'}
+            feather[['chr', 'start', 'end', 'strand', 'gene']].rename(
+            columns = {'chr': 'seqnames', 'start': 'starts', 'end': 'ends'}
         ))
     else: return feather
 
@@ -185,7 +191,7 @@ def get_mapper_ensembl(taxa):
     else:
 
         gtable = get_genome(taxa)
-        ensembl_list = gtable[['ensembl']].values.transpose()[0].tolist()
+        ensembl_list = gtable[['id']].values.transpose()[0].tolist()
         id_list = gtable.index.tolist()
         ensembl_finder = {}
 

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/data/geneset.py

@@ -59,13 +59,13 @@ def translate_id(taxa, genes, idfrom = 'entrez', idto = 'ugene', keep_nones = Tr
 
         # construct multi-platform convertion table.
         gtable = get_genome(taxa)
-        gtable = gtable[['ensembl', 'gene']].copy()
+        gtable = gtable[['id', 'gene']].copy()
         gtable['ugene'] = gtable.index.tolist()
-        gtable.index = gtable['ensembl'].tolist()
+        gtable.index = gtable['id'].tolist()
         gtable['uppercase'] = gtable['gene'].str.upper().tolist()
 
         # deduplicate
-        gtable = gtable.loc[~ gtable['ensembl'].duplicated(), :].copy()
+        gtable = gtable.loc[~ gtable['id'].duplicated(), :].copy()
         gtable['ugene'] = taxa + ':' + gtable['ugene']
 
         entrez = pandas.read_table(

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/data/presets.py

@@ -40,5 +40,40 @@ g2m_genesets = {
 
 preset_genesets = {
     's': s_gene_sets,
-    'g2m': g2m_genesets
+    'g2m': g2m_genesets,
+    'custom': {
+        'mmu': {
+            't': [
+                'Cd3d', 'Cd8a', 'Cd4', 'Sell', 
+                'Il7r', 'Tcf7', 'Ifng', 'Gzmb', 
+                'Tox', 'Pdcd1', 'Havcr2', 'Lag3',
+                'Mki67', 'Icos', 'Foxp3', 'Id2',
+                'Id3', 'Gata3', 'Tbx21', 'Cd69',
+                'Cxcr5', 'Bach1', 'Cxcr5', 'Xcl1',
+                'Etv6', 'Ikzf3', 'Zbed2', 'Batf',
+                'Klrb1c', 'Klrg1', 'Prf1'
+            ],
+            'chemokines': {
+                "CCL": [
+                    "Ccl1", "Ccr1l1", "Ccl2", "Ccl3", "Ccl4", "Ccl5", "Ccl6",
+                    "Ccl7", "Ccl17", "Ccl8", "Ccl9", "Ccl11", "Ccl12", "Ccl19",
+                    "Ccl19-ps2", "Ccl20", "Ccl22", "Ccl24", "Ccl25", "Ccl26",
+                    "Ccl27a", "Ccl28",
+                ],
+                "CCR": [
+                    "Ccr1", "Ccr2", "Ccr3", "Ccr4", "Ccr5", "Ccr6",
+                    "Ccr7", "Ccr8", "Ccr9", "Ccr10",
+                ],
+                "CXCL": [
+                    "Cxcl1", "Cxcl2", "Cxcl3", "Cxcl5", "Cxcl9", "Cxcl10", "Cxcl11",
+                    "Cxcl12", "Cxcl13", "Cxcl14", "Cxcl15", "Cxcl16", "Cxcl17",
+                ],
+                "CXCR": ["Cxcr1", "Cxcr2", "Cxcr3", "Cxcr4", "Cxcr5", "Cxcr6"],
+                "XCL": ["Xcl1"],
+                "XCR": ["Xcr1"],
+                "CX3CL": ["Cx3cl1"],
+                "CX3CR": ["Cx3cr1"],
+            }
+        }
+    }
 }

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/descriptive/aucell.py

@@ -9,7 +9,7 @@ import numpy as np
 import pandas as pd
 from boltons.iterutils import chunked
 from exprmat.descriptive.recovery import enrich_cells
-from rich.progress import track
+from exprmat import pprog
 
 # to reduce the memory footprint of a ranking matrix we use unsigned 32bit 
 # integers which provides a range from 0 through 4,294,967,295. this should be 
@@ -96,7 +96,7 @@ def aucell4r(
                     module.noweights() if noweights else module,
                     auc_threshold = auc_threshold,
                 )
-                for module in track(signatures, description = 'auc')
+                for module in pprog(signatures, desc = 'auc')
             ]
         ).unstack("regulon")
         aucs.columns = aucs.columns.droplevel(0)

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/dynamics/parallel.py

@@ -3,11 +3,10 @@ import os
 from multiprocessing import Manager
 from threading import Thread
 from joblib import delayed, Parallel
-from rich.progress import TextColumn, BarColumn, TimeRemainingColumn, TimeElapsedColumn
 
 import numpy as np
 from scipy.sparse import issparse, spmatrix
-from exprmat.ansi import error, warning, info
+from exprmat.ansi import error, warning, info, pprog
 
 
 def get_n_jobs(n_jobs):
@@ -67,10 +66,10 @@ def parallelize(
         Whether to show a progress bar.
     """
 
-    if show_progress_bar: from rich.progress import Progress as progress
+    if show_progress_bar: progress = pprog
     else: progress = None
 
-    def update(pbar, task, queue, n_total):
+    def update(pbar, queue, n_total):
         
         n_finished = 0
         while n_finished < n_total:
@@ -83,32 +82,17 @@ def parallelize(
             assert res in (None, (1, None), 1)  # (None, 1) means only 1 job
             if res == (1, None):
                 n_finished += 1
-                if pbar is not None: pbar.advance(task, advance = 1)
+                if pbar is not None: pbar.update(1)
             elif res is None: n_finished += 1
-            elif pbar is not None: pbar.advance(task, advance = 1)
-
-        if pbar is not None:
-            pbar.stop()
+            elif pbar is not None: pbar.update(1)
 
 
     def wrapper(*args, **kwargs):
 
         if pass_queue and show_progress_bar:
-            pbar = None if progress is None else progress(
-                TextColumn("[progress.description]"),
-                BarColumn(),
-                TextColumn("[progress.percentage]{task.percentage:>4.1f}%"),
-                TimeRemainingColumn(),
-                TimeElapsedColumn()
-            )
-
-            pbartask = None
-            if pbar is not None: 
-                pbartask = pbar.add_task(description = "", total = col_len)
-                pbar.start()
-
+            pbar = None if progress is None else progress(total = col_len)
             queue = Manager().Queue()
-            thread = Thread(target = update, args = (pbar, pbartask, queue, len(collections)))
+            thread = Thread(target = update, args = (pbar, queue, len(collections)))
             thread.start()
 
         else: pbar, queue, thread = None, None, None

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/grn/infergrn.py

@@ -6,11 +6,10 @@ from functools import partial
 from multiprocessing import Pool, cpu_count
 from pathlib import PurePath
 import pandas as pd
-from rich.progress import track
 
 from exprmat.utils import choose_layer
 from exprmat.data.tf import get_tfs
-from exprmat.ansi import info, warning, error
+from exprmat.ansi import info, warning, error, pprog
 from exprmat.grn.regressors import (
     EARLY_STOP_WINDOW_LENGTH,
     kwargs_random_forest,
@@ -67,7 +66,7 @@ def adjacencies(
 
     with Pool(ncpus) as p:
         adjs = list(
-            track(
+            pprog(
                 p.imap(
                     partial(
                         run_infer_partial_network,
@@ -82,7 +81,7 @@ def adjacencies(
                     chunksize = 1,
                 ),
                 total = len(gene_names),
-                description = 'inferring partial network '
+                desc = 'inferring partial network'
             )
         )
 

{exprmat-0.1.37 → exprmat-0.1.39}/exprmat/lr/utils.py

@@ -4,10 +4,9 @@ from numpy import log10, finfo, exp
 from numpy import union1d
 import anndata
 import numpy as np
-from tqdm import tqdm
 
 from joblib import Parallel, delayed
-from exprmat.ansi import warning, error
+from exprmat.ansi import warning, error, pprog
 
 
 class default_params():
@@ -211,7 +210,7 @@ def generate_perms_cube(X, n_perms, labels_mask, seed, agg_fun, n_jobs, verbose)
     results = Parallel(n_jobs = n_jobs)(
         delayed(permute_and_aggregate)
         (perm, rng.permutation(idx), X, labels_mask, agg_fun)
-        for perm in tqdm(range(n_perms), disable = not verbose, ncols = 80)
+        for perm in pprog(range(n_perms), disable = not verbose)
     )
 
     # unpack results