review py codes and remove unused codes

MACS3/Commands/bdgbroadcall_cmd.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2024-05-15 10:41:43 Tao Liu>
+# Time-stamp: <2024-10-02 15:55:43 Tao Liu>
 
 """Description: Fine-tuning script to call broad peaks from a single
 bedGraph track for scores.
@@ -13,7 +13,6 @@
 # python modules
 # ------------------------------------
 
-import sys
 import os
 from MACS3.IO import BedGraphIO
 # ------------------------------------
@@ -23,36 +22,38 @@
 # ------------------------------------
 # Misc functions
 # ------------------------------------
-import logging
-import MACS3.Utilities.Logger
+from MACS3.Utilities.Logger import logging
 
 logger = logging.getLogger(__name__)
-debug   = logger.debug
-info    = logger.info
-error   = logger.critical
-warn    = logger.warning
+debug = logger.debug
+info = logger.info
+error = logger.critical
+warn = logger.warning
+
 # ------------------------------------
 # Classes
 # ------------------------------------
 
 # ------------------------------------
 # Main function
 # ------------------------------------
-def run( options ):
+
+
+def run(options):
     info("Read and build bedGraph...")
     bio = BedGraphIO.bedGraphIO(options.ifile)
     btrack = bio.read_bedGraph(baseline_value=0)
 
     info("Call peaks from bedGraph...")
 
-    bpeaks = btrack.call_broadpeaks (options.cutoffpeak, options.cutofflink, options.minlen, options.lvl1maxgap, options.lvl2maxgap)
+    bpeaks = btrack.call_broadpeaks(options.cutoffpeak, options.cutofflink, options.minlen, options.lvl1maxgap, options.lvl2maxgap)
 
     info("Write peaks...")
 
     if options.ofile:
-        bf = open( os.path.join( options.outdir, options.ofile ), "w" )
+        bf = open(os.path.join(options.outdir, options.ofile), "w")
         options.oprefix = options.ofile
     else:
-        bf = open ( os.path.join( options.outdir, "%s_c%.1f_C%.2f_l%d_g%d_G%d_broad.bed12" % (options.oprefix,options.cutoffpeak,options.cutofflink,options.minlen,options.lvl1maxgap,options.lvl2maxgap)), "w" )
+        bf = open(os.path.join(options.outdir, "%s_c%.1f_C%.2f_l%d_g%d_G%d_broad.bed12" % (options.oprefix,options.cutoffpeak, options.cutofflink, options.minlen, options.lvl1maxgap, options.lvl2maxgap)), "w")
     bpeaks.write_to_gappedPeak(bf, name_prefix=(options.oprefix+"_broadRegion").encode(), score_column="score", trackline=options.trackline)
     info("Done")

MACS3/Commands/bdgcmp_cmd.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2024-05-15 10:13:23 Tao Liu>
+# Time-stamp: <2024-10-02 16:06:33 Tao Liu>
 
 """Description: compare bdg files
 
@@ -7,14 +7,10 @@
 the distribution).
 """
 
-import sys
 import os
-
 from MACS3.IO import BedGraphIO
 from MACS3.Utilities.OptValidator import opt_validate_bdgcmp
 
-from math import log as mlog
-
 # ------------------------------------
 # constants
 # ------------------------------------
@@ -27,15 +23,19 @@
 # Main function
 # ------------------------------------
 
-def run( options ):
-    options = opt_validate_bdgcmp( options )
+
+def run(options):
+    options = opt_validate_bdgcmp(options)
     info = options.info
-    warn = options.warn
-    debug = options.debug
-    error = options.error
-    
+    # warn = options.warn
+    # debug = options.debug
+    # error = options.error
+
     scaling_factor = options.sfactor
-    pseudo_depth = 1.0/scaling_factor   # not an actual depth, but its reciprocal, a trick to override SPMR while necessary.
+
+    # not an actual depth, but its reciprocal, a trick to override
+    # SPMR while necessary.
+    pseudo_depth = 1.0/scaling_factor
 
     info("Read and build treatment bedGraph...")
     tbio = BedGraphIO.bedGraphIO(options.tfile)
@@ -46,47 +46,47 @@ def run( options ):
     cbtrack = cbio.read_bedGraph()
 
     info("Build ScoreTrackII...")
-    sbtrack = tbtrack.make_ScoreTrackII_for_macs( cbtrack, depth1 = pseudo_depth, depth2 = pseudo_depth )
+    sbtrack = tbtrack.make_ScoreTrackII_for_macs(cbtrack, depth1=pseudo_depth, depth2=pseudo_depth)
     if abs(scaling_factor-1) > 1e-6:
         # Only for the case while your input is SPMR from MACS3 callpeak; Let's override SPMR.
         info("Values in your input bedGraph files will be multiplied by %f ..." % scaling_factor)
-        sbtrack.change_normalization_method( ord('M') ) # a hack to override SPMR
-    sbtrack.set_pseudocount( options.pseudocount )
+        sbtrack.change_normalization_method(ord('M'))  # a hack to override SPMR
+    sbtrack.set_pseudocount(options.pseudocount)
 
     already_processed_method_list = []
     for (i, method) in enumerate(options.method):
         if method in already_processed_method_list:
             continue
         else:
-            already_processed_method_list.append( method )
+            already_processed_method_list.append(method)
 
         info("Calculate scores comparing treatment and control by '%s'..." % method)
         if options.ofile:
-            ofile = os.path.join( options.outdir, options.ofile[ i ] )
+            ofile = os.path.join(options.outdir, options.ofile[i])
         else:
-            ofile = os.path.join( options.outdir, options.oprefix + "_" + method + ".bdg" )
+            ofile = os.path.join(options.outdir, options.oprefix + "_" + method + ".bdg")
         # build score track
         if method == 'ppois':
-            sbtrack.change_score_method( ord('p') )
+            sbtrack.change_score_method(ord('p'))
         elif method == 'qpois':
-            sbtrack.change_score_method( ord('q') )
+            sbtrack.change_score_method(ord('q'))
         elif method == 'subtract':
-            sbtrack.change_score_method( ord('d') )
+            sbtrack.change_score_method(ord('d'))
         elif method == 'logFE':
-            sbtrack.change_score_method( ord('f') )
+            sbtrack.change_score_method(ord('f'))
         elif method == 'FE':
-            sbtrack.change_score_method( ord('F') )
+            sbtrack.change_score_method(ord('F'))
         elif method == 'logLR':             # log likelihood
-            sbtrack.change_score_method( ord('l') )
+            sbtrack.change_score_method(ord('l'))
         elif method == 'slogLR':             # log likelihood
-            sbtrack.change_score_method( ord('s') )
+            sbtrack.change_score_method(ord('s'))
         elif method == 'max':
-            sbtrack.change_score_method( ord('M') )
+            sbtrack.change_score_method(ord('M'))
         else:
             raise Exception("Can't reach here!")
 
         info("Write bedGraph of scores...")
-        ofhd = open( ofile, "w" )
+        ofhd = open(ofile, "w")
         # write_bedGraph function for ScoreTrack
-        sbtrack.write_bedGraph(ofhd,name="%s_Scores" % (method.upper()),description="Scores calculated by %s" % (method.upper()), column = 3)
+        sbtrack.write_bedGraph(ofhd, name="%s_Scores" % (method.upper()), description="Scores calculated by %s" % (method.upper()), column=3)
         info("Finished '%s'! Please check '%s'!" % (method, ofile))

MACS3/Commands/bdgdiff_cmd.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2024-05-15 10:42:27 Tao Liu>
+# Time-stamp: <2024-10-02 16:11:19 Tao Liu>
 
 """Description: Naive call differential peaks from 4 bedGraph tracks for scores.
 
@@ -11,7 +11,6 @@
 # python modules
 # ------------------------------------
 
-import sys
 import os
 from MACS3.IO import BedGraphIO
 from MACS3.Signal import ScoreTrack
@@ -23,28 +22,26 @@
 # ------------------------------------
 # Misc functions
 # ------------------------------------
-import logging
-import MACS3.Utilities.Logger
+from MACS3.Utilities.Logger import logging
 
 logger = logging.getLogger(__name__)
-debug   = logger.debug
-info    = logger.info
-error   = logger.critical
-warn    = logger.warning
+debug = logger.debug
+info = logger.info
+error = logger.critical
+warn = logger.warning
 # ------------------------------------
 # Classes
 # ------------------------------------
 
 # ------------------------------------
 # Main function
 # ------------------------------------
-def run( options ):
+
+
+def run(options):
     if options.maxgap >= options.minlen:
         error("MAXGAP should be smaller than MINLEN! Your input is MAXGAP = %d and MINLEN = %d" % (options.maxgap, options.minlen))
 
-    LLR_cutoff = options.cutoff
-    ofile_prefix = options.oprefix
-
     info("Read and build treatment 1 bedGraph...")
     t1bio = BedGraphIO.bedGraphIO(options.t1bdg)
     t1btrack = t1bio.read_bedGraph()
@@ -68,44 +65,43 @@ def run( options ):
         depth1 = depth2 / depth1
         depth2 = 1.0
     elif depth1 < depth2:       # scale down condition 2 to size of condition 1
-        depth2 = depth1/ depth2
+        depth2 = depth1 / depth2
         depth1 = 1.0
     else:                       # no need to scale down any
         depth1 = 1.0
         depth2 = 1.0
 
-    twoconditionscore = ScoreTrack.TwoConditionScores( t1btrack,
-                                                        c1btrack,
-                                                        t2btrack,
-                                                        c2btrack,
-                                                        depth1,
-                                                        depth2 )
+    twoconditionscore = ScoreTrack.TwoConditionScores(t1btrack,
+                                                      c1btrack,
+                                                      t2btrack,
+                                                      c2btrack,
+                                                      depth1,
+                                                      depth2)
     twoconditionscore.build()
     twoconditionscore.finalize()
-    (cat1,cat2,cat3) = twoconditionscore.call_peaks(min_length=options.minlen, max_gap=options.maxgap, cutoff=options.cutoff)
+    (cat1, cat2, cat3) = twoconditionscore.call_peaks(min_length=options.minlen, max_gap=options.maxgap, cutoff=options.cutoff)
 
     info("Write peaks...")
 
     if options.ofile:
-        ofiles = [os.path.join( options.outdir, x ) for x in options.ofile]
-        name_prefix = [ x.encode() for x in options.ofile ]
+        ofiles = [os.path.join(options.outdir, x) for x in options.ofile]
+        name_prefix = [x.encode() for x in options.ofile]
     else:
-        ofiles = [ os.path.join( options.outdir, "%s_c%.1f_cond1.bed" % (options.oprefix,options.cutoff)),
-                   os.path.join( options.outdir, "%s_c%.1f_cond2.bed" % (options.oprefix,options.cutoff)),
-                   os.path.join( options.outdir, "%s_c%.1f_common.bed" % (options.oprefix,options.cutoff))
-                   ]
-        name_prefix = [ x.encode() for x in [ options.oprefix+"_cond1_", options.oprefix+"_cond2_", options.oprefix+"_common_" ]]
-
-    nf = open( ofiles[ 0 ], 'w' )
-    cat1.write_to_bed(nf, name_prefix=name_prefix[ 0 ], name=b"condition 1", description=b"unique regions in condition 1", score_column="score")
+        ofiles = [os.path.join(options.outdir, "%s_c%.1f_cond1.bed" % (options.oprefix, options.cutoff)),
+                  os.path.join(options.outdir, "%s_c%.1f_cond2.bed" % (options.oprefix, options.cutoff)),
+                  os.path.join(options.outdir, "%s_c%.1f_common.bed" % (options.oprefix, options.cutoff))
+                  ]
+        name_prefix = [x.encode() for x in [options.oprefix+"_cond1_", options.oprefix+"_cond2_", options.oprefix+"_common_"]]
+
+    nf = open(ofiles[0], 'w')
+    cat1.write_to_bed(nf, name_prefix=name_prefix[0], name=b"condition 1", description=b"unique regions in condition 1", score_column="score")
     nf.close()
 
-    nf = open( ofiles[ 1 ], 'w' )
-    cat2.write_to_bed(nf, name_prefix=name_prefix[ 1 ], name=b"condition 2", description=b"unique regions in condition 2", score_column="score")
+    nf = open(ofiles[1], 'w')
+    cat2.write_to_bed(nf, name_prefix=name_prefix[1], name=b"condition 2", description=b"unique regions in condition 2", score_column="score")
     nf.close()
 
-    nf = open( ofiles[ 2 ], 'w' )
-    cat3.write_to_bed(nf, name_prefix=name_prefix[ 2 ], name=b"common", description=b"common regions in both conditions", score_column="score")
+    nf = open(ofiles[2], 'w')
+    cat3.write_to_bed(nf, name_prefix=name_prefix[2], name=b"common", description=b"common regions in both conditions", score_column="score")
     nf.close()
     info("Done")
-

MACS3/Commands/bdgopt_cmd.py

@@ -1,4 +1,4 @@
-# Time-stamp: <2024-05-15 11:15:48 Tao Liu>
+# Time-stamp: <2024-10-02 16:12:50 Tao Liu>
 
 """Description: Modify bedGraph file
 
@@ -10,7 +10,6 @@
 # ------------------------------------
 # python modules
 # ------------------------------------
-import sys
 import os
 
 from MACS3.IO import BedGraphIO
@@ -31,13 +30,15 @@
 # ------------------------------------
 # Main function
 # ------------------------------------
-def run( options ):
-    options = opt_validate_bdgopt( options )
+
+
+def run(options):
+    options = opt_validate_bdgopt(options)
     info = options.info
-    warn = options.warn
-    debug = options.debug
-    error = options.error
-    
+    # warn = options.warn
+    # debug = options.debug
+    # error = options.error
+
     info("Read and build bedGraph...")
     bio = BedGraphIO.bedGraphIO(options.ifile)
     btrack = bio.read_bedGraph(baseline_value=0)
@@ -49,18 +50,15 @@ def run( options ):
     else:
         extraparam = float(options.extraparam[0])
         if options.method.lower() == "multiply":
-            btrack.apply_func( lambda x: x * extraparam)
+            btrack.apply_func(lambda x: x * extraparam)
         elif options.method.lower() == "add":
-            btrack.apply_func( lambda x: x + extraparam)
+            btrack.apply_func(lambda x: x + extraparam)
         elif options.method.lower() == "max":
-            btrack.apply_func( lambda x: x if x> extraparam else extraparam )
+            btrack.apply_func(lambda x: x if x > extraparam else extraparam)
         elif options.method.lower() == "min":
-            btrack.apply_func( lambda x: x if x< extraparam else extraparam )
+            btrack.apply_func(lambda x: x if x < extraparam else extraparam)
 
-    ofile = BedGraphIO.bedGraphIO( os.path.join( options.outdir, options.ofile ), data = btrack )
+    ofile = BedGraphIO.bedGraphIO(os.path.join(options.outdir, options.ofile), data=btrack)
     info("Write bedGraph of modified scores...")
-    ofile.write_bedGraph(name="%s_modified_scores" % (options.method.upper()),description="Scores calculated by %s" % (options.method.upper()))
+    ofile.write_bedGraph(name="%s_modified_scores" % (options.method.upper()), description="Scores calculated by %s" % (options.method.upper()))
     info("Finished '%s'! Please check '%s'!" % (options.method, ofile.bedGraph_filename))
-
-
-