v0.2.0

CHANGELOG

@@ -1,3 +1,9 @@
+2018-2-7 ribotish 0.2.0
+
+	Lower the threshold between fasttest and normal test to increase testing speed.
+
+	Some python3 compatibility updates.
+
 2018-1-15 ribotish 0.1.11
 
 	Update codes to allow genes with transcripts in different strands in chromosome.

README.rst

@@ -1,6 +1,6 @@
-README for Ribo-TISH (0.1.11)
+README for Ribo-TISH (0.2.0)
 ==================================
-<2018-1-15 Peng Zhang>
+<2018-2-7 Peng Zhang>
 
 Introduction
 ============

bin/ribotish

@@ -5,8 +5,8 @@ Copyright (c) 2016 Peng Zhang <[email protected]>
 This code is free software; you can redistribute it and/or modify it
 under the terms of the BSD License (see the file COPYING included with
 the distribution).
-@status: experimental
-@version: 0.1.9
+@status: Alpha
+@version: 0.2.0
 @author:  Peng Zhang
 @contact: [email protected]
 """

setup.py

@@ -10,7 +10,7 @@
 # the distribution).
 # 
 # @status:  Alpha
-# @version: 0.1.11
+# @version: 0.2.0
 # @author:  Peng Zhang
 # @contact: [email protected]
 

src/__init__.py

@@ -1,2 +1,2 @@
 __all__=["run"]
-__version__ = '0.1.11'
+__version__ = '0.2.0'

src/zbio/interval.py

@@ -221,7 +221,40 @@ def contradict(self, other) :
     si = self.intersect([(p1, p2)])
     oi = other.intersect([(p1, p2)])
     return si.sub(oi), oi.sub(si)
-
+  def genome_pos(self, p, strand = '+', bias = 1): # exon only
+    if len(self) == 0: return None
+    m = self.rlen() # cdna_length()
+    if p < 0 or p > m: return None
+    if strand == '-': 
+      p = m - p
+      bias = 1 - bias
+    if p == 0 : return self.start
+    if p == m: return self.stop
+    p1 = p
+    for itv in self.lst:
+      l = itv[1] - itv[0]
+      if l - p1 >= bias:
+        return p1 + itv[0] # e.start
+      else:
+        p1 -= l
+    return None
+  def cdna_pos(self, p, strand = '+', strict = False):
+    '''if strict is True, the 3' end of exon will be considered as not in the transcript,
+    if strict is False, 3' end of exon will be considered as start of the next exon, 
+    or transcript end (self.cdna_length()) if in the last exon.
+    '''
+    if len(self.lst) == 0 : return None
+    i, c = self.nearest(p)
+    if c != 0 : return None
+    if strict:
+      if strand != '-' and p == self.lst[i][1]: return None
+      if strand == '-' and p == self.lst[i][0]: return None
+    pos = sum([self.lst[j][1] - self.lst[j][0] for j in range(i)])
+    pos += p - self.lst[i][0]
+    if strand == '-': 
+      pos = self.rlen() - pos
+    return pos
+
 def trans2interval(t, start = 0, stop = None):
   '''generate intervals for a transcript
   start, stop are cDNA positions
@@ -302,4 +335,8 @@ def allTransRegions(trans):
   for chr in regions: regions[t.chr].check()
   return regions
 
-
+def str2interval(s, blocksep = ',', rangesep = '-', id = ''):
+  itvs = [map(int, b.split(rangesep)) for b in s.split(blocksep)]
+  return Interval(itvs=itvs, id=id)
+
+