masster 0.5.1__py3-none-any.whl → 0.5.4__py3-none-any.whl

masster/study/study.py

@@ -1,46 +1,38 @@
 """
 study.py
 
-This module provides tools for multi-sample mass spectrometry data analysis and cross-sample feature alignment.
-It defines the `study` class, which manages collections of DDA files, performs feature alignment across samples,
-generates consensus features, and provides study-level visualization and reporting capabilities.
-
-Key Features:
-- **Multi-Sample Management**: Handle collections of mass spectrometry files with metadata.
-- **Feature Alignment**: Align features across multiple samples using retention time and m/z tolerances.
-- **Consensus Features**: Generate consensus feature tables from aligned data.
-- **Batch Processing**: Automated processing of entire studies with configurable parameters.
-- **Study Visualization**: Generate comparative plots and alignment visualizations.
-- **Export Capabilities**: Export study results in various formats for downstream analysis.
-
-Dependencies:
-- `pyopenms`: For mass spectrometry data handling and algorithms.
-- `polars` and `pandas`: For efficient data manipulation and analysis.
-- `bokeh`, `holoviews`, `panel`: For interactive visualizations and dashboards.
-- `numpy`: For numerical computations and array operations.
-
-Classes:
-- `study`: Main class for multi-sample study management, providing methods for file loading,
-  feature alignment, consensus generation, and study-level analysis.
-
-Example Usage:
-```python
-from study import study
-
-# Create study from multiple files
-study_obj = study()
-study_obj.load_files(["sample1.mzML", "sample2.mzML", "sample3.mzML"])
-study_obj.process_all()
-study_obj.align()
-study_obj.plot_alignment_bokeh()
-study_obj.export_consensus()
-```
-
-See Also:
-- `single.py`: For individual file processing before study-level analysis.
-- `parameters.study_parameters`: For study-specific parameter configuration.
-
-
+Module providing the Study class, the main entry point for multi-sample mass spectrometry
+studies. It manages loading and metadata, cross-sample feature alignment, consensus
+generation, integration, MS2 association, plotting, exporting, and parameter/history
+management.
+
+Main class:
+- Study: high-level orchestrator. Key operations include:
+    - I/O: load/save .study5, add/add_sample, set_study_folder
+    - Processing: align, merge (consensus), fill, integrate, find_ms2, find_iso/reset_iso
+    - Selection/filtering: samples_select/delete, features_select/filter/delete,
+        consensus_select/filter/delete
+    - Retrieval: get_consensus, get_chrom, get_samples, get_*_stats, get_*_matrix
+    - Plotting: plot_alignment, plot_samples_pca/umap/2d, plot_tic/bpc/eic, plot_chrom,
+        plot_rt_correction, plot_consensus_2d/stats
+    - Export: export_mgf, export_mztab, export_xlsx, export_parquet
+    - Identification: lib_load, identify, get_id, id_reset, lib_reset
+    - Parameters: get/update parameters, update_history
+
+
+Quickstart:
+>>> from masster import Study
+>>> s = Study(folder="./study")
+>>> s.add("/data/mzML/*.mzML")            # or s.add_sample("sample.mzML", name="S1")
+>>> s.align()
+>>> s.merge()
+>>> s.plot_alignment()
+>>> s.export_parquet("consensus.parquet")
+>>> s.save("project.study5")
+
+Notes:
+- This module re-exports many functions from masster.study.* as Study methods.
+- Use Study.info() for a concise study summary.
 """
 
 from __future__ import annotations
@@ -57,6 +49,7 @@ from masster.study.helpers import _get_consensus_uids
 from masster.study.helpers import _get_features_uids
 from masster.study.helpers import _get_samples_uids
 from masster.study.helpers import compress
+from masster.study.helpers import consensus_reset
 from masster.study.helpers import decompress
 from masster.study.helpers import fill_reset
 from masster.study.helpers import get_chrom
@@ -66,6 +59,7 @@ from masster.study.helpers import get_consensus_matches
 from masster.study.helpers import get_consensus_matrix
 from masster.study.helpers import get_orphans
 from masster.study.helpers import get_sample_stats
+from masster.study.helpers import get_consensus_stats
 from masster.study.helpers import get_gaps_matrix
 from masster.study.helpers import get_gaps_stats
 from masster.study.helpers import align_reset
@@ -86,7 +80,10 @@ from masster.study.load import add
 from masster.study.load import add_sample
 from masster.study.load import fill
 from masster.study.load import load
-from masster.study.load import _load_features
+#from masster.study.load import _load_features
+from masster.study.h5 import _load_ms1
+from masster.study.h5 import _load_study5
+from masster.study.h5 import _save_study5
 from masster.study.plot import plot_alignment
 from masster.study.plot import plot_consensus_2d
 from masster.study.plot import plot_samples_2d
@@ -117,7 +114,6 @@ from masster.logger import MassterLogger
 from masster.study.defaults.study_def import study_defaults
 from masster.study.defaults.align_def import align_defaults
 from masster.study.defaults.export_def import export_mgf_defaults
-from masster.study.defaults.fill_chrom_def import fill_chrom_defaults
 from masster.study.defaults.fill_def import fill_defaults
 from masster.study.defaults.find_ms2_def import find_ms2_defaults
 from masster.study.defaults.integrate_chrom_def import integrate_chrom_defaults
@@ -352,6 +348,9 @@ class Study:
     save_consensus = save_consensus
     save_samples = save_samples
     set_study_folder = set_study_folder
+    _load_ms1 = _load_ms1
+    _load_study5 = _load_study5
+    _save_study5 = _save_study5
     
     # === Sample Management ===
     add = add
@@ -368,6 +367,7 @@ class Study:
     integrate = integrate
     
     fill = fill
+    #_estimate_rt_original_for_filled_feature = _estimate_rt_original_for_filled_feature
     
     # === Data Retrieval and Access ===
     get_consensus = get_consensus
@@ -379,6 +379,7 @@ class Study:
     get_gaps_stats = get_gaps_stats
     get_orphans = get_orphans
     get_sample_stats = get_sample_stats
+    get_consensus_stats = get_consensus_stats
     
     # === Data Selection and Filtering ===
     samples_select = samples_select
@@ -411,6 +412,7 @@ class Study:
     decompress = decompress
     
     # === Reset Operations ===
+    consensus_reset = consensus_reset
     fill_reset = fill_reset
     reset_fill = fill_reset
     align_reset = align_reset
@@ -463,19 +465,11 @@ class Study:
     _get_consensus_uids = _get_consensus_uids
     _get_features_uids = _get_features_uids
     _get_samples_uids = _get_samples_uids
-    _load_features = _load_features
-    
-    # Note: _load_study5 and _save_study5 are not exposed as class methods
-    # They are used internally by load() and save() methods only
-    
-    # === Merge Helper Methods ===
-    # (All merge helper methods are now internal to the merge module)
     
     # === Default Parameters ===
     study_defaults = study_defaults
     align_defaults = align_defaults
     export_mgf_defaults = export_mgf_defaults
-    fill_chrom_defaults = fill_chrom_defaults
     fill_defaults = fill_defaults
     find_ms2_defaults = find_ms2_defaults
     integrate_chrom_defaults = integrate_chrom_defaults
@@ -566,84 +560,7 @@ class Study:
             self.logger.debug("Module reload completed")
         except Exception as e:
             self.logger.error(f"Failed to reload current module {current_module}: {e}")
-
-    def _sanitize_null_ids(self):
-        """
-        Sanitize null feature_id and consensus_id values by replacing them with new integer IDs.
-        For feature_id: generates large sequential integers that can be converted by merge/align functions.
-        For consensus_id: uses 16-character UUID strings (as expected by merge function).
-        """
-        import uuid
-        import polars as pl
-        import time
-        
-        # Sanitize features_df feature_id column
-        if hasattr(self, 'features_df') and self.features_df is not None and not self.features_df.is_empty():
-            # Check for null feature_ids
-            null_feature_ids = self.features_df.filter(pl.col("feature_id").is_null()).shape[0]
-            if null_feature_ids > 0:
-                self.logger.info(f"Sanitizing {null_feature_ids} null feature_id values with new integer IDs")
-                
-                # Find the maximum existing feature_id (convert strings to int if possible)
-                max_existing_id = 0
-                existing_ids = self.features_df.filter(pl.col("feature_id").is_not_null())["feature_id"].to_list()
-                for fid in existing_ids:
-                    try:
-                        int_id = int(fid)
-                        max_existing_id = max(max_existing_id, int_id)
-                    except (ValueError, TypeError):
-                        # Skip non-integer IDs
-                        pass
-                
-                # Generate new sequential integer IDs starting from max + timestamp offset
-                # Use timestamp to ensure uniqueness across different sanitization runs
-                base_id = max(max_existing_id + 1, int(time.time() * 1000000))  # Microsecond timestamp
-                new_int_ids = [str(base_id + i) for i in range(null_feature_ids)]
-                uid_index = 0
-                
-                # Create a list to store all feature_ids
-                feature_ids = []
-                for feature_id in self.features_df["feature_id"].to_list():
-                    if feature_id is None:
-                        feature_ids.append(new_int_ids[uid_index])
-                        uid_index += 1
-                    else:
-                        feature_ids.append(feature_id)
-                
-                # Update the DataFrame with sanitized feature_ids
-                self.features_df = self.features_df.with_columns(
-                    pl.Series("feature_id", feature_ids, dtype=pl.Utf8)
-                )
-                
-                self.logger.info(f"Successfully sanitized {null_feature_ids} feature_id values")
-        
-        # Sanitize consensus_df consensus_id column
-        if hasattr(self, 'consensus_df') and self.consensus_df is not None and not self.consensus_df.is_empty():
-            if "consensus_id" in self.consensus_df.columns:
-                null_consensus_ids = self.consensus_df.filter(pl.col("consensus_id").is_null()).shape[0]
-                if null_consensus_ids > 0:
-                    self.logger.info(f"Sanitizing {null_consensus_ids} null consensus_id values with new UIDs")
-                    
-                    # Generate new UIDs for null values using the same method as merge()
-                    new_uids = [str(uuid.uuid4()).replace('-', '')[:16] for _ in range(null_consensus_ids)]
-                    uid_index = 0
-                    
-                    # Create a list to store all consensus_ids
-                    consensus_ids = []
-                    for consensus_id in self.consensus_df["consensus_id"].to_list():
-                        if consensus_id is None:
-                            consensus_ids.append(new_uids[uid_index])
-                            uid_index += 1
-                        else:
-                            consensus_ids.append(consensus_id)
-                    
-                    # Update the DataFrame with sanitized consensus_ids
-                    self.consensus_df = self.consensus_df.with_columns(
-                        pl.Series("consensus_id", consensus_ids, dtype=pl.Utf8)
-                    )
-                    
-                    self.logger.info(f"Successfully sanitized {null_consensus_ids} consensus_id values")
-
+    
     def __dir__(self):
         """
         Custom __dir__ implementation to hide internal methods starting with '_' 
@@ -699,12 +616,19 @@ class Study:
 
     def __str__(self):
         """
-        Returns a string representation of the study.
-
-        Returns:
-            str: A summary string of the study.
+        Return a short summary string with number of samples and consensus features.
         """
-        return ""
+        samples = (
+            len(self.samples_df)
+            if (self.samples_df is not None and not self.samples_df.is_empty())
+            else 0
+        )
+        consensus = (
+            len(self.consensus_df)
+            if (self.consensus_df is not None and not self.consensus_df.is_empty())
+            else 0
+        )
+        return f"{samples} samples, {consensus} consensus"
 
     def logger_update(
         self,
@@ -993,6 +917,5 @@ class Study:
 
         print(summary)
 
-if __name__ == "__main__":
-    # This block is executed when the script is run directly
+if __name__ == "__main__":    
     pass

masster/wizard/wizard.py

@@ -652,12 +652,26 @@ class Wizard:
             '        )',
             '        ',
             '        # Merge and create consensus features',
-            '        study.merge(',
-            '            min_samples=PARAMS[\'min_samples_per_feature\'],',
-            '            threads=PARAMS[\'num_cores\'],',
-            '            rt_tol=PARAMS[\'rt_tol\'],',
-            '            mz_tol=PARAMS[\'mz_tol\']',
-            '        )',
+            '        # Use optimized method for large datasets (>500 samples)',
+            '        num_samples = len(study.samples)',
+            '        if num_samples > 500:',
+            '            print(f"  Large dataset detected ({num_samples} samples), using optimized qt_chunked + hierarchical method")',
+            '            study.merge(',
+            '                method="qt_chunked",',
+            '                dechunking="hierarchical",', 
+            '                min_samples=PARAMS[\'min_samples_per_feature\'],',
+            '                threads=PARAMS[\'num_cores\'],',
+            '                rt_tol=PARAMS[\'rt_tol\'],',
+            '                mz_tol=PARAMS[\'mz_tol\']',
+            '            )',
+            '        else:',
+            '            print(f"  Using standard merge method for {num_samples} samples")',
+            '            study.merge(',
+            '                min_samples=PARAMS[\'min_samples_per_feature\'],',
+            '                threads=PARAMS[\'num_cores\'],',
+            '                rt_tol=PARAMS[\'rt_tol\'],',
+            '                mz_tol=PARAMS[\'mz_tol\']',
+            '            )',
             '        study.find_iso()',
             '        study.fill(min_samples_rel=0.0)',
             '        study.integrate()',    

{masster-0.5.1.dist-info → masster-0.5.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.1
+Version: 0.5.4
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.5.1.dist-info → masster-0.5.4.dist-info}/RECORD

@@ -1,5 +1,5 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=dkqPLCQGfsGL65orxLHNgDpbEE9aMOWq4b_vYspojyk,256
+masster/_version.py,sha256=gwA0FHD4Z-_YF_DHvv1fia5KlwKC04Tq47mBa_FkOEo,256
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
 masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
@@ -18,16 +18,16 @@ masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecR
 masster/lib/__init__.py,sha256=TcePNx3SYZHz6763TL9Sg4gUNXaRWjlrOtyS6vsu-hg,178
 masster/lib/lib.py,sha256=SSN06UtiM-hIdjS3eCiIHsJ_8S4YHRGOLGmdPIh-efo,27481
 masster/sample/__init__.py,sha256=HL0m1ept0PMAYUCQtDDnkdOS12IFl6oLAq4TZQz83uY,170
-masster/sample/adducts.py,sha256=S7meba3L1tSdjoDhkSiTI71H2NJLu4i1dtJwfDKWI1M,32591
-masster/sample/h5.py,sha256=B0gAmhrnoFoybotqsqiT8s-PkeZWUdIQfI-4cnM52Zc,115430
-masster/sample/helpers.py,sha256=JhzFpNh7j7YVUibIMuPQ50hBcGDEBCaBbmwA3Z5OhgM,41336
+masster/sample/adducts.py,sha256=5aEZPVcjGywCsN06ZuUWIi7h1817NsUp6o8L26P0bpY,32592
+masster/sample/h5.py,sha256=tlTPGrT9AMUhduvY_YPDzk6dZF5dI-9NRc1xeiuze5c,115442
+masster/sample/helpers.py,sha256=avW7gKT1wH47NUU0tEB3hkzm6ayQdfHpWR730kgWPSI,41342
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
-masster/sample/load.py,sha256=CSJnNfJ6EpWEIbDj92mJK0qFao0ycxuGf_w9DzWhlnY,51721
+masster/sample/load.py,sha256=swjRBCoFGni9iPztHIKPVB5ru_xDMVryB_inPXdujTw,51819
 masster/sample/parameters.py,sha256=Gg2KcuNbV_wZ_Wwv93QlM5J19ji0oSIvZLPV1NoBmq0,4456
 masster/sample/plot.py,sha256=0v4FzO_yzpUdATjdHZU4YO7UoW73Xlf51vVQByQ33X0,82574
-masster/sample/processing.py,sha256=Sh6IFxuFcmCspyizUPghd4Qqqk1mTPCNtvdxmyy0eKQ,55914
+masster/sample/processing.py,sha256=CjaLCElDKECeCvYWqzT5EH_-rPQ0Y4A30zKjZfqmS5s,55915
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=_IUvUIlW2F4NRxsOdtBb1NePJJX_9FDcT5ZgM4O7ZRs,20534
+masster/sample/sample.py,sha256=O2PY7DnRx7VkASBU4qKQcTqND1aRfd0OCjKK9Rjn5uw,20574
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
 masster/sample/save.py,sha256=2yQtcQcRJjgAKPImTydj7LpyyMop_Q9JKRlNEK4yU6k,36339
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
@@ -39,36 +39,35 @@ masster/sample/defaults/get_spectrum_def.py,sha256=o62p31PhGd-LiIkTOzKQhwPtnO2At
 masster/sample/defaults/sample_def.py,sha256=keoXyMyrm_iLgbYqfIbqCpJ3XHBVlNwCNmb5iMQL0iY,14579
 masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
 masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
-masster/study/export.py,sha256=Rp1vc5iDl-XFWo_RBVCJDGBNSKakq9f8aC2FeUCP9GA,59398
-masster/study/h5.py,sha256=6_nyjMGg_dkKkrx_Mv77wGg5SmWsVOZxu7HZasoXbRU,84916
-masster/study/helpers.py,sha256=dU2YxAGPmu1w55mpcgNoHPpg2fNW-vK944aJy3YwLsU,163555
+masster/study/export.py,sha256=joFK9jip2UM4lVAvhkdKVeUdNdM4D8uP2WE49IaVJgw,60172
+masster/study/h5.py,sha256=84plxM7gYFdn_mNbcg8XxE_NRZmiIBqs_XhfHMiXshk,95364
+masster/study/helpers.py,sha256=s5jLUmxDAs_Qn6dVwpkwlwuwliMDEBjmeikS6OrxdSE,183137
 masster/study/id.py,sha256=r_vZQYNxqNXf_pjgk_CLkl1doLnLa956mTuVmlHN52o,80075
-masster/study/load.py,sha256=W4mljmYVR71sas4no7vKWIVfdnQjb-rTcEUhE0ZMr0k,71696
-masster/study/merge.py,sha256=XF4NxNuLSxwf2j1__ReIInXVRGDRoSHFeKdcCSayKU4,164298
+masster/study/load.py,sha256=7d11294YYEGrSKox3cwvetv2vqcstYT1SnyAhHH5V_Q,107706
+masster/study/merge.py,sha256=D9xNRlEaMPTPZQAZhiBBSzQ-27lD60fCDmKb0cYST-M,149764
 masster/study/parameters.py,sha256=bTvmcwX9INxzcrEAmTiFH8qeWVhwkvMTZjuP394pz5o,3279
-masster/study/plot.py,sha256=pAN5uQKYPUpupQVtKBloWjKOKpM_C9o2e3VWkJ-aZN8,102041
-masster/study/processing.py,sha256=TKeTzRLmaMxUKCt66pXPfx_7xc-R5__ZwEZdFHOxg6A,55916
+masster/study/plot.py,sha256=wg2X3P-0J6mW0N0dJS0dX6KLGtt9mXj6w1j3E9nvlvo,103086
+masster/study/processing.py,sha256=O6X7wgeq0kXSyMO12g23cqB8cYO60gLRMxuJC2uhSMY,58644
 masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
-masster/study/study.py,sha256=vbP_bPa62-KYN0OTUN6PpSyCoFcW-TdbLbx67ShkEx0,42930
+masster/study/study.py,sha256=TnZkTLB8Z5R-AVqoHfUNvmkTthfUI4OPmBo_LYR_e8g,38654
 masster/study/study5_schema.json,sha256=0IZxM9VVI0TUlx74BPzJDT44kySi6NZZ6iLR0j8bU_s,7736
 masster/study/defaults/__init__.py,sha256=m3Z5KXGqsTdh7GjYzZoENERt39yRg0ceVRV1DeCt1P0,610
-masster/study/defaults/align_def.py,sha256=hHQbGgsOqMRHHr0Wn8Onr8XeaRz3-fFE0qGE-OMst80,20324
+masster/study/defaults/align_def.py,sha256=Du0F592ej2einT8kOx8EUs610axSvur8_-6N19O-uJY,10209
 masster/study/defaults/export_def.py,sha256=eXl3h4aoLX88XkHTpqahLd-QZ2gjUqrmjq8IJULXeWo,1203
-masster/study/defaults/fill_chrom_def.py,sha256=hB6-tyC9bhx-IpGj2HC8FinQdW4VLYj_pn5t1rlj-Ew,8887
-masster/study/defaults/fill_def.py,sha256=H-ZNKyiXxBLWdLoCMqxfvphNyc9wrDVFMC7TyRNYEm0,8869
+masster/study/defaults/fill_def.py,sha256=pdH-lwknaMqnB_lXdGmeSqk9KgLMoOgNlp82eEunx6U,9124
 masster/study/defaults/find_consensus_def.py,sha256=2KRRMsCDP7pwNrLCC6eI5uQgMXqiNdiI6pSvxNJ8L5M,8598
 masster/study/defaults/find_ms2_def.py,sha256=RL0DFG41wQ05U8UQKUGr3vzSl3mU0m0knQus8DpSoJE,5070
 masster/study/defaults/identify_def.py,sha256=96rxoCAPQj_yX-3mRoD2LTkTLJgG27eJQqwarLv5jL0,10580
 masster/study/defaults/integrate_chrom_def.py,sha256=0MNIWGTjty-Zu-NTQsIweuj3UVqEY3x1x8pK0mPwYak,7264
 masster/study/defaults/integrate_def.py,sha256=Vf4SAzdBfnsSZ3IRaF0qZvWu3gMDPHdgPfMYoPKeWv8,7246
-masster/study/defaults/merge_def.py,sha256=K7sfwEGfgcWU85zorbWNFaxDhqRH52pxQoKv9Jn2qhY,15030
+masster/study/defaults/merge_def.py,sha256=3W13QSZaIzxHTDFifW-Nncu_phIqZgf0TpcllaKwbHE,12978
 masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7it5pL0,16033
 masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
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