masster 0.5.4__py3-none-any.whl → 0.5.6__py3-none-any.whl

masster/study/processing.py

@@ -341,9 +341,6 @@ def _integrate_chrom_impl(self, **kwargs):
     uids = params.get("uids")
     rt_tol = params.get("rt_tol")
 
-    if self.consensus_map is None:
-        self.logger.error("No consensus map found.")
-        return
     if uids is None:
         # get all consensus_id from consensus_df
         ids = self.consensus_df["consensus_uid"].to_list()

masster/wizard/wizard.py

@@ -455,6 +455,9 @@ class Wizard:
         params_lines.append('    # === Processing Parameters ===')
         params_lines.append(f'    "adducts": {params_dict.get("adducts", [])!r},  # Adduct specifications for feature detection and annotation')
         params_lines.append(f'    "detector_type": {params_dict.get("detector_type", "unknown")!r},  # MS detector type ("orbitrap", "tof", "unknown")')
+        params_lines.append(f'    "noise": {params_dict.get("noise", 50.0)},  # Noise threshold for feature detection')
+        params_lines.append(f'    "chrom_fwhm": {params_dict.get("chrom_fwhm", 0.5)},  # Chromatographic peak full width at half maximum (seconds)')
+        params_lines.append(f'    "chrom_peak_snr": {params_dict.get("chrom_peak_snr", 5.0)},  # Minimum signal-to-noise ratio for chromatographic peaks')
         params_lines.append('')
         
         # Alignment & Merging
@@ -643,6 +646,7 @@ class Wizard:
             '        # Step 4: Add sample5 files to study',
             '        print("\\nStep 4/7: Adding samples to study...")',
             '        study.add(str(Path(PARAMS[\'folder\']) / "*.sample5"))',
+            '        study.features_filter(study.features_select(chrom_coherence=0.1, chrom_prominence_scaled=1))',
             '        ',
             '        # Step 5: Core processing',
             '        print("\\nStep 5/7: Processing...")',
@@ -651,29 +655,14 @@ class Wizard:
             '            rt_tol=PARAMS[\'rt_tol\']',
             '        )',
             '        ',
-            '        # Merge and create consensus features',
-            '        # 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.merge(',
+            '            method="qt",',
+            '            min_samples=PARAMS[\'min_samples_per_feature\'],',
+            '            threads=PARAMS[\'num_cores\'],',
+            '            rt_tol=PARAMS[\'rt_tol\'],'
+            '        )',
             '        study.find_iso()',
-            '        study.fill(min_samples_rel=0.0)',
+            '        study.fill()',
             '        study.integrate()',    
             '        ',
             '        # Step 6/7: Saving results',
@@ -689,8 +678,8 @@ class Wizard:
             '        study.plot_consensus_2d(filename="consensus.png")',
             '        study.plot_alignment(filename="alignment.html")',
             '        study.plot_alignment(filename="alignment.png")',
-            '        study.plot_pca(filename="pca.html")',
-            '        study.plot_pca(filename="pca.png")',
+            '        study.plot_samples_pca(filename="pca.html")',
+            '        study.plot_samples_pca(filename="pca.png")',
             '        study.plot_bpc(filename="bpc.html")',
             '        study.plot_bpc(filename="bpc.png")',
             '        study.plot_rt_correction(filename="rt_correction.html")',

{masster-0.5.4.dist-info → masster-0.5.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.5.4
+Version: 0.5.6
 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-0.5.4.dist-info → masster-0.5.6.dist-info}/RECORD

@@ -1,8 +1,8 @@
 masster/__init__.py,sha256=ueZ224WPNRRjQEYTaQUol818nwQgJwB93HbEfmtPRmg,1041
-masster/_version.py,sha256=gwA0FHD4Z-_YF_DHvv1fia5KlwKC04Tq47mBa_FkOEo,256
+masster/_version.py,sha256=rLineW-O0OSBF7JBd31acdcshluNBFss77bXVJCx5BY,256
 masster/chromatogram.py,sha256=iYpdv8C17zVnlWvOFgAn9ns2uFGiF-GgoYf5QVVAbHs,19319
 masster/logger.py,sha256=tR65N23zfrNpcZNbZm2ot_Aual9XrGB1MWjLrovZkMs,16749
-masster/spectrum.py,sha256=XJSUrqXZSzfpWnD8v5IMClXMRZLKLYIk014qaMOS9_k,49738
+masster/spectrum.py,sha256=TWIgDcl0lveG40cLVZTWGp8-FxMolu-P8EjZyRBtXL4,49850
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil2_01_20250602151849.sample5,sha256=LdJMF8uLoDm9ixZNHBoOzBH6hX7NGY7vTvqa2Pzetb8,6539174
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_DDA_OT_C-MiLUT_QC_dil3_01_20250602150634.sample5,sha256=hWUfslGoOTiQw59jENSBXP4sa6DdkbOi40FJ68ep61Q,6956773
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008_v6_r38_01.sample5,sha256=dSd2cIgYYdRcNSzkhqlZCeWKi3x8Hhhcx8BFMuiVG4c,11382948
@@ -10,6 +10,7 @@ masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C008
 masster/data/dda/20250530_VH_IQX_KW_RP_HSST3_100mm_12min_pos_v4_MS1_C-MiLUT_C017_v5_r99_01.sample5,sha256=h2OOAWWTwKXzTNewhiYeL-cMYdp_JYLPya8Q9Nv9Lvw,12389587
 masster/data/libs/aa.csv,sha256=Sja1DyMsiaM2NfLcct4kAAcXYwPCukJJW8sDkup9w_c,1924
 masster/data/libs/ccm.csv,sha256=Q6nylV1152uTpX-ydqWeGrc6L9kgv45xN_fBZ4f7Tvo,12754
+masster/data/libs/hilic.csv,sha256=Ao2IN9t7GiFWEBJg21TmNJZjTbyHC3e0dJcfftAKsM4,671265
 masster/data/libs/urine.csv,sha256=iRrR4N8Wzb8KDhHJA4LqoQC35pp93FSaOKvXPrgFHis,653736
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.timeseries.data,sha256=01vC6m__Qqm2rLvlTMZoeKIKowFvovBTUnrNl8Uav3E,24576
 masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.wiff,sha256=go5N9gAM1rn4PZAVaoCmdteY9f7YGEM9gyPdSmkQ8PE,1447936
@@ -18,18 +19,18 @@ 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=5aEZPVcjGywCsN06ZuUWIi7h1817NsUp6o8L26P0bpY,32592
+masster/sample/adducts.py,sha256=nl5KEuat0hvktgar6Ca4PbY8JXt9SD05EeTn0HOKt64,32592
 masster/sample/h5.py,sha256=tlTPGrT9AMUhduvY_YPDzk6dZF5dI-9NRc1xeiuze5c,115442
-masster/sample/helpers.py,sha256=avW7gKT1wH47NUU0tEB3hkzm6ayQdfHpWR730kgWPSI,41342
+masster/sample/helpers.py,sha256=27eZFFidr02-DlSi4-eF4bpSk_y-qU3eoFCAOshRO20,42138
 masster/sample/lib.py,sha256=E-j9c3Wd8f9a-H8xj7CAOwlA8KcyXPoFyYm3c8r7LtI,33755
 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/plot.py,sha256=vA37dwmpeymVW8xobrsLhsD7X8x7EQIOw50Csiica84,86675
 masster/sample/processing.py,sha256=CjaLCElDKECeCvYWqzT5EH_-rPQ0Y4A30zKjZfqmS5s,55915
 masster/sample/quant.py,sha256=tHNjvUFTdehKR31BXBZnVsBxMD9XJHgaltITOjr71uE,7562
-masster/sample/sample.py,sha256=O2PY7DnRx7VkASBU4qKQcTqND1aRfd0OCjKK9Rjn5uw,20574
+masster/sample/sample.py,sha256=VhQik_ev1liRqGUtbZvV1NOjfFzgfZI1orfQT87gai4,20643
 masster/sample/sample5_schema.json,sha256=H5e2T6rHIDzul2kp_yP-ILUUWUpW08wP2pEQjMR0nSk,3977
-masster/sample/save.py,sha256=2yQtcQcRJjgAKPImTydj7LpyyMop_Q9JKRlNEK4yU6k,36339
+masster/sample/save.py,sha256=IwWfcsmWLWM-2ASdhHXWAiPyrZBv5JUynvciNPppDUs,38643
 masster/sample/sciex.py,sha256=vnbxsq_qnAQVuzcpziP1o3IC4kM5amGBcPmC2TAuDLw,46319
 masster/sample/defaults/__init__.py,sha256=A09AOP44cxD_oYohyt7XFUho0zndRcrzVD4DUaGnKH4,447
 masster/sample/defaults/find_adducts_def.py,sha256=Bu2KiBJRxD0SAnOPNMm_Nk-6fx6QYoRXjFNGzz-0_o0,13570
@@ -41,13 +42,13 @@ masster/study/__init__.py,sha256=55axdFuqRX4aXtJ8ocnhcLB32fNtmmJpCi58moO0r4g,237
 masster/study/analysis.py,sha256=L-wXBnGZCLB5UUDrjIdOiMG9zdej3Tw_SftcEmmTukM,84264
 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/helpers.py,sha256=ZhvLetoEROHMSrMKZo8jXQMJhTochITgAG_vwjs_8Mg,183129
 masster/study/id.py,sha256=r_vZQYNxqNXf_pjgk_CLkl1doLnLa956mTuVmlHN52o,80075
 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=wg2X3P-0J6mW0N0dJS0dX6KLGtt9mXj6w1j3E9nvlvo,103086
-masster/study/processing.py,sha256=O6X7wgeq0kXSyMO12g23cqB8cYO60gLRMxuJC2uhSMY,58644
+masster/study/plot.py,sha256=LEIzoYiUyq1aswh-sw8S-ESvN2DaQKN5l22yLW8gZe8,107647
+masster/study/processing.py,sha256=n5208v-JQGq3bBP-ncgl2__hHWSQQYHx2fl4Mm0THdI,58538
 masster/study/save.py,sha256=47AP518epJJ9TjaGGyrLKsMsyjIk8_J4ka7bmsnRtFQ,9268
 masster/study/study.py,sha256=TnZkTLB8Z5R-AVqoHfUNvmkTthfUI4OPmBo_LYR_e8g,38654
 masster/study/study5_schema.json,sha256=0IZxM9VVI0TUlx74BPzJDT44kySi6NZZ6iLR0j8bU_s,7736
@@ -65,9 +66,9 @@ masster/study/defaults/study_def.py,sha256=h8dYbi9xv0sesCSQik49Z53IkskMmNtW6ixl7
 masster/wizard/README.md,sha256=mL1A3YWJZOefpJ6D0-HqGLkVRmUlOpwyVFdvJBeeoZM,14149
 masster/wizard/__init__.py,sha256=a2hcZnHASjfuw1lqZhZnvTR58rc33rRnoGAY_JfvGhI,683
 masster/wizard/example.py,sha256=xEZFTH9UZ8HKOm6s3JL8Js0Uw5ChnISWBHSZCL32vsM,7983
-masster/wizard/wizard.py,sha256=6VqeOyKJ-9n0376CVbNuQo4vKLFjE0Sl2KexWZclQew,38580
-masster-0.5.4.dist-info/METADATA,sha256=wjgydggoAm3JBUOi0PrJ1oPUgUTvB3qKZ1MorC8NBOE,45113
-masster-0.5.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-masster-0.5.4.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
-masster-0.5.4.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
-masster-0.5.4.dist-info/RECORD,,
+masster/wizard/wizard.py,sha256=UobIGFZtp1s_9WJlpl6DQ2-pp7flPQ6dlYZJqYE92OM,38131
+masster-0.5.6.dist-info/METADATA,sha256=Vbsgbvaxv5TP83vvlXhTlG7vdrkUaN8fvdkSwVil3HY,45113
+masster-0.5.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+masster-0.5.6.dist-info/entry_points.txt,sha256=ZHguQ_vPmdbpqq2uGtmEOLJfgP-DQ1T0c07Lxh30wc8,58
+masster-0.5.6.dist-info/licenses/LICENSE,sha256=bx5iLIKjgAdYQ7sISn7DsfHRKkoCUm1154sJJKhgqnU,35184
+masster-0.5.6.dist-info/RECORD,,