Merge pull request #597 from macs3-project/doc/macs3/3.0.0b4

MACS3 3.0.0 official release with docs updated

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,7 +20,7 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **System (please complete the following information):**
- - OS: [e.g. Linux, Mac OSX]
+ - OS: [e.g. Linux, Mac OSX] [note: Windows NOT supported]
  - Python version [e.g. 3.7.1]
  - Numpy version [e.g. 1.17.0]
  - MACS Version [e.g. 2.2.4]

.github/ISSUE_TEMPLATE/windows_issues.md

@@ -0,0 +1,21 @@
+---
+name: Windows issues
+about: Windows OS is not supported
+title: 'Windows machine: '
+labels: 'Windows'
+assignees: ''
+
+---
+
+**Please Note**
+Before opening a bug report, please take note: Windows OS is not supported, MACS is recommended to be used with either LinuxOS or MacOS.
+
+Some users have had success running through a virtual environment, discussed here: 
+- [#539](https://github.com/macs3-project/MACS/issues/539)
+- [#540](https://github.com/macs3-project/MACS/issues/540)
+- [#444](https://github.com/macs3-project/MACS/issues/444)
+- [#441](https://github.com/macs3-project/MACS/issues/441)
+
+
+
+

.github/workflows/build-and-test-MACS3-macos12.yml

@@ -3,12 +3,21 @@
 
 name: MACS3 CI MacOS 12
 
-on: [push, pull_request]
-
+on: 
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+
 jobs:
   build:
     runs-on: macos-12
     name: Build on MacOS 12 with Python 3.11
+
     steps:
       - name: Checkout MACS
         uses: actions/checkout@v3

.github/workflows/build-and-test-MACS3-non-x64.yml

@@ -3,8 +3,15 @@
 
 name: MACS3 CI non x64
 
-on: [push, pull_request]
-
+on: 
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
 jobs:
   build_job:
     runs-on: ubuntu-20.04
@@ -25,6 +32,7 @@ jobs:
         uses: actions/checkout@v3
         with:
           submodules: 'true'
+
       - name: Set up arch and run (bullseye Python 3.9)
         uses: uraimo/run-on-arch-action@v2
         id: build

.github/workflows/build-and-test-MACS3-x64.yml

@@ -3,14 +3,21 @@
 
 name: MACS3 CI x64
 
-on: [push, pull_request]
-
+on: 
+  push:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
+  pull_request:
+    paths-ignore:
+      - 'docs/**'
+      - '*.md'
 jobs:
   build:
     runs-on: ubuntu-20.04
     strategy: 
       matrix: 
-        python-version: [3.9, 3.10.11, 3.11]
+        python-version: [3.9, 3.10.11, 3.11, 3.12]
         arch: ['x64']
     name: Build on x64 with Python ${{ matrix.python-version }}
     steps:

ChangeLog

@@ -1,5 +1,5 @@
-2023-07-28  Tao Liu  <[email protected]>
-	MACS 3.0.0b3
+2023-11-14  Tao Liu  <[email protected]>
+	MACS 3.0.0
 
 	* New features in MACS3:
 

MACS3/Commands/bdgpeakcall_cmd.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2019-09-25 10:04:08 taoliu>
+# Time-stamp: <2023-11-02 11:52:48 Tao Liu>
 
 """Description: Naive call peaks from a single bedGraph track for
 scores.
@@ -43,7 +43,7 @@ def run( options ):
 
     if options.cutoff_analysis:
         info("Analyze cutoff vs number of peaks/total length of peaks/average length of peak")
-        cutoff_analysis_result = btrack.cutoff_analysis( int(options.maxgap), int(options.minlen), 50 )
+        cutoff_analysis_result = btrack.cutoff_analysis( int(options.maxgap), int(options.minlen), min_score = btrack.minvalue, max_score = btrack.maxvalue, steps = int(options.cutoff_analysis_steps) )
         info("Write report...")
         if options.ofile:
             fhd = open( os.path.join( options.outdir, options.ofile ), 'w' )

MACS3/Signal/BedGraph.pyx

@@ -1,6 +1,6 @@
 # cython: language_level=3
 # cython: profile=True
-# Time-stamp: <2023-07-28 12:06:48 Tao Liu>
+# Time-stamp: <2023-11-02 11:40:47 Tao Liu>
 
 """Module for BedGraph data class.
 
@@ -96,9 +96,9 @@ cdef class bedGraphTrackI:
     """
     cdef:
         dict __data
-        float32_t maxvalue
-        float32_t minvalue
-        float32_t baseline_value
+        public float32_t maxvalue
+        public float32_t minvalue
+        public float32_t baseline_value
 
     def __init__ (self, float32_t baseline_value=0 ):
         """
@@ -194,7 +194,7 @@ cdef class bedGraphTrackI:
         if value > self.maxvalue:
             self.maxvalue = value
         if value < self.minvalue:
-            self.minvalue = value        
+            self.minvalue = value
 
     cpdef add_chrom_data( self, bytes chromosome, object p, object v ):
         """Add a pv data to a chromosome. Replace the previous data.
@@ -1131,30 +1131,57 @@ cdef class bedGraphTrackI:
         #ret.merge_regions()
         return ret
 
-    cpdef str cutoff_analysis ( self, int32_t max_gap, int32_t min_length, int32_t steps = 100, float32_t max_score = 1000 ):
+    cpdef str cutoff_analysis ( self, int32_t max_gap, int32_t min_length, int32_t steps = 100, float32_t min_score = 0, float32_t max_score = 1000 ):
         """
         Cutoff analysis function for bedGraphTrackI object.
     
-        This function will try all possible cutoff values on the score column to call peaks. Then 
-        will give a report of a number of metrics (number of peaks, total length of peaks, average
-        length of peak) at varying score cutoffs. For each score cutoff, the function finds the 
-        positions where the score exceeds the cutoff, then groups those positions into "peaks" 
-        based on the maximum allowed gap (max_gap) between consecutive positions. If a peak's length
-        exceeds the minimum length (min_length), the peak is counted.
+        This function will try all possible cutoff values on the score
+        column to call peaks. Then will give a report of a number of
+        metrics (number of peaks, total length of peaks, average
+        length of peak) at varying score cutoffs. For each score
+        cutoff, the function finds the positions where the score
+        exceeds the cutoff, then groups those positions into "peaks"
+        based on the maximum allowed gap (max_gap) between consecutive
+        positions. If a peak's length exceeds the minimum length
+        (min_length), the peak is counted.
 
         Parameters
         ----------
+
         max_gap : int32_t
         Maximum allowed gap between consecutive positions above cutoff
         
-        min_length : int32_t
-        Minimum length of peak
-        
+        min_length : int32_t Minimum length of peak
         steps: int32_t
+        It will be used to calculate 'step' to increase from min_v to
+        max_v (see below).
+
+        min_score: float32_t
+        Minimum score for cutoff analysis. Note1: we will take the
+        larger value between the actual minimum value in the BedGraph
+        and min_score as min_v. Note2: the min_v won't be included in
+        the final result. We will try to output the smallest cutoff as
+        min_v+step.
+
+        max_score: float32_t
+        Maximum score for cutoff analysis. Note1: we will take the
+        smaller value between the actual maximum value in the BedGraph
+        and max_score as max_v. Note2: the max_v may not be included
+        in the final result. We will only output the cutoff that can
+        generate at least 1 peak.
 
         Returns
         -------
-        Cutoff analysis report in 'str'
+
+        Cutoff analysis report in str object.
+
+        Todos
+        -----
+
+        May need to seperate this function out as a class so that we
+        can add more ways to analyze the result. Also, we can let this
+        function return a list of dictionary or data.frame in that
+        way, instead of str object.
         
         """
         cdef:
@@ -1171,7 +1198,7 @@ cdef class bedGraphTrackI:
 
         #midvalue = self.minvalue/2 + self.maxvalue/2
         #s = float(self.minvalue - midvalue)/steps
-        minv = max( 0, self.minvalue )
+        minv = max( min_score, self.minvalue )
         maxv = min( self.maxvalue, max_score )
 
         s = float(maxv - minv)/steps

MACS3/Utilities/Constants.py

@@ -1,4 +1,4 @@
-MACS_VERSION = "3.0.0b4"
+MACS_VERSION = "3.0.0"
 MAX_PAIRNUM = 1000
 MAX_LAMBDA  = 100000
 FESTEP      = 20