python3 compatibility, fasttest th

src/zbio/io.py

@@ -31,16 +31,16 @@ def transIter(filePath, fileType = 'auto', gz = False, **kwargs):
   else : infile = open(filePath, 'r')
   if fileType == 'auto' : fileType = suffixType(filePath, gz)
   if fileType == 'bed' :
-    import bed
+    from . import bed
     return bed.bed12_iter(infile, **kwargs)
   elif fileType == 'gtf' :
-    import gtf
+    from . import gtf
     return gtf.gtftrans_iter(infile, **kwargs)
   elif fileType == 'gff' :
-    import gtf
+    from . import gtf
     return gtf.gtftrans_iter(infile, gff = True, **kwargs)
   elif fileType == 'gpd' :
-    import bed
+    from . import bed
     return bed.gpd_iter(infile, **kwargs)
   else : raise IOError('Unknown trans file type: {}'.format(fileType))
 
@@ -57,13 +57,13 @@ def geneIter(filePath, fileType = 'auto', gz = False, **kwargs):
     import bed
     return bed.bed12_iter(infile, **kwargs)
   elif fileType == 'gtf' :
-    import gtf
+    from . import gtf
     return gtf.gtfgene_iter(infile, **kwargs)
   elif fileType == 'gff' :
-    import gtf
+    from . import gtf
     return gtf.gtfgene_iter(infile, gff = True, **kwargs)
   elif fileType == 'gpd' :
-    import bed
+    from . import bed
     return bed.gpdGeneIter(infile, **kwargs)
   else : raise IOError('Unknown trans file type: {}'.format(fileType))
 
@@ -78,18 +78,18 @@ def transFetch(filePath, tid, fileType = 'auto', gz = False, **kwargs):
   else : infile = open(filePath, 'r')
   if fileType == 'auto' : fileType = suffixType(filePath, gz)
   if fileType == 'bed' :
-    import bed
+    from . import bed
     return bed.bed12_fetch(infile, id = tid, **kwargs)
   elif fileType == 'gtf' :
-    import gtf
+    from . import gtf
     gene, trans = gtf.fetch_gtf(infile, tid = tid, **kwargs)
     return trans[tid]
   elif fileType == 'gff' :
-    import gtf
+    from . import gtf
     gene, trans =  gtf.fetch_gtf(infile, tid = tid, gff = True, **kwargs)
     return trans[tid]
   elif fileType == 'gpd' :
-    import bed
+    from . import bed
     return bed.gpd_fetch(infile, id = tid, **kwargs)
   else : raise IOError('Unknown trans file type: {}'.format(fileType))
 
@@ -103,16 +103,16 @@ def transSelectIter(filePath, fileType = 'auto', gz = False,  **kwargs):
   else : infile = open(filePath, 'r')
   if fileType == 'auto' : fileType = suffixType(filePath, gz)
   if fileType == 'bed' :
-    import bed
+    from . import bed
     return bed.bed12SelectIter(infile, **kwargs) # no gene name/id annotation
   elif fileType == 'gtf' :
-    import gtf
+    from . import gtf
     return gtf.gtftransSelectIter(infile, **kwargs)
   elif fileType == 'gff' :
-    import gtf
+    from . import gtf
     return gtf.gtftransSelectIter(infile, gff = True, **kwargs)
   elif fileType == 'gpd' :
-    import bed
+    from . import bed
     return bed.gpdSelectIter(infile, **kwargs)
   else : raise IOError('Unknown trans file type: {}'.format(fileType))
 

src/zbio/orf.py

@@ -3,7 +3,7 @@
 Copyright (c) 2016 Peng Zhang <[email protected]>
 '''
 
-import fa
+from . import fa
 
 codonSize = 3
 cstart = ['ATG']

src/zbio/ribo.py

@@ -3,7 +3,7 @@
 Copyright (c) 2016 Peng Zhang <[email protected]>
 '''
 import itertools, math
-import stat, bam, gtf, exp, orf, tools, io, fa, interval
+from . import stat, bam, gtf, exp, orf, tools, io, fa, interval
 from multiprocessing import Pool
 
 codonSize = 3
@@ -163,7 +163,7 @@ def enrich_test_region(self, r1, r2, frame, delta=1e-4, glm = False, show = Fals
   def multi_orf_test(self, orflist, glm = False): 
     '''multiple ORF detection for riboseq data, not used in final version
     '''
-    import interval
+    from . import interval
     tid = self.trans.id
     blank = []
     for i in range(codonSize): ## Blank regions in different frames
@@ -243,7 +243,7 @@ def efpvalues(self, orf, blank, glm = False, show = False): # For multi_orf_test
   def max_orf(self, orf, blank): 
     '''for ribonly_orf_finder
     '''
-    import interval
+    from . import interval
     indr = indep_region(orf, blank)
     mst, mp = None, 1
     for st in orf.sts :
@@ -258,7 +258,7 @@ def ribonly_orf_finder(self, orflist, alt = False, fpth = 0.05):
     '''find likely TIS by only riboseq data, not used, similar function in pvalStatus()
     However, this function seems better
     '''
-    import interval
+    from . import interval
     blank = []
     for i in range(codonSize): ## Blank regions in different frames
       b = interval.Interval(start=self.nhead, stop=self.length-self.ntail)

src/zbio/stat.py

@@ -783,13 +783,13 @@ def tieRatio(self):
     '''
     s = sum([v**3 - v for v in self.cd.values() if v > 1])
     return s / float(self.N ** 3 - self.N)
-  def test(self, th = 20, delta = 1e-4):
+  def test(self, th = 10, delta = 1e-4):
     '''if either size <= th, use fastTest
     elif complexity <= th, use fastTest
     else use normal mwtest
     '''
     if self.n <= th or self.N - self.n <= th : return self.fastTest(delta = delta) #, True
-    if self.complexity() <= th * logarr[2] : return self.fastTest(delta = delta) #, True
+    if self.complexity() <= th: return self.fastTest(delta = delta) # * logarr[2]
     return self.mwtest() #, False
   def mwtest(self, use_continuity = True, show = False):
     '''normal mwtest, alt = greater, one-tailed