revert back to full covars

macs3-project · Oct 4, 2022 · 77ffc3c · 77ffc3c
1 parent 9ec2922
commit 77ffc3c
Show file tree

Hide file tree

Showing 4 changed files with 1,167 additions and 961 deletions.
diff --git a/MACS3/Commands/hmmratac_cmd.py b/MACS3/Commands/hmmratac_cmd.py
@@ -1,4 +1,4 @@
-# Time-stamp: <2022-10-04 12:12:26 Tao Liu>
+# Time-stamp: <2022-10-04 15:13:57 Tao Liu>
 
 """Description: Main HMMR command
 
@@ -217,7 +217,7 @@ def run( args ):
         options.info( f"#4 Load Hidden Markov Model from given model file")
         hmm_model, i_open_region, i_background_region, i_nucleosomal_region, options.hmm_binsize = hmm_model_init( options.hmm_file )
     else:
-        options.info( f"#4 Train Hidden Markov Model with Multinormal Emission" )
+        options.info( f"#4 Train Hidden Markov Model with Multivariate Gaussian Emission" )
 
         # extract signals within peak using the given binsize
         options.info( f"#  Extract signals in training regions with bin size of {options.hmm_binsize}")
@@ -238,7 +238,7 @@ def run( args ):
 
         options.info( f"#  Use Baum-Welch algorithm to train the HMM")
 
-        hmm_model = hmm_training( training_data, training_data_lengths, random_seed = options.hmm_randomSeed, covar="diag" )
+        hmm_model = hmm_training( training_data, training_data_lengths, random_seed = options.hmm_randomSeed, covar="full" )
 
         options.info( f"#   HMM converged: {hmm_model.monitor_.converged}")
 

diff --git a/MACS3/Signal/HMMR_HMM.pyx b/MACS3/Signal/HMMR_HMM.pyx
@@ -1,6 +1,6 @@
 # cython: language_level=3
 # cython: profile=True
-# Time-stamp: <2022-10-04 12:31:15 Tao Liu>
+# Time-stamp: <2022-10-04 15:14:15 Tao Liu>
 
 """Module description:
 
@@ -25,9 +25,6 @@ from cpython cimport bool
 from hmmlearn import hmm
 import json
 # from hmmlearn cimport hmm
-# from sklearn.cluster import KMeans 
-# from sklearn.cluster cimport KMeans
-
 
 # ------------------------------------
 # MACS3 modules

diff --git a/bin/macs3 b/bin/macs3
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# Time-stamp: <2022-10-04 12:14:31 Tao Liu>
+# Time-stamp: <2022-10-04 13:48:15 Tao Liu>
 
 """Description: MACS v3 main executable.
 
@@ -812,7 +812,7 @@ def add_hmmratac_parser( subparsers ):
     # group for peak calling arguments
     group_call = argparser_hmmratac.add_argument_group( "Peak calling arguments" )
     group_call.add_argument( "-c", "--prescan-cutoff", dest = "prescan_cutoff", type = float,
-                             help = "The fold change cutoff for prescanning candidate regions in the whole dataset. The we will use HMM to predict states on these candidate regions. Higher the prescan cutoff, fewer regions will be considered. Must > 1. Default: 1.2",
+                             help = "The fold change cutoff for prescanning candidate regions in the whole dataset. Then we will use HMM to predict states on these candidate regions. Higher the prescan cutoff, fewer regions will be considered. Must > 1. Default: 1.2",
                              default = 1.2 )
 
     group_call.add_argument( "--minlen", dest = "openregion_minlen", type = int,