Merge pull request #3 from ronin-gw/v0.2.1

V0.2.1

CHANGELOG.md

@@ -1,6 +1,11 @@
 # Change Log
 
-## V0.2.0 (2017-12-05)
+## v0.2.1 (2017-12-23)
+**Fixed bugs:**
+- BitArray length shortage for reverse strand reads
+- BitArray implementation fails for chromosomes which have no mapped reads
+
+## v0.2.0 (2017-12-05)
 **Implemented enhancements:**
 - Add BitArray implementation
 - Some refactoring

PyMaSC/__init__.py

@@ -1 +1 @@
-VERSION = "0.2.0"
+VERSION = "0.2.1"

PyMaSC/bacore/mscc.pyx

@@ -11,6 +11,7 @@ from PyMaSC.core.ncc import ReadUnsortedError
 from PyMaSC.utils.progress import ProgressBar
 
 logger = logging.getLogger(__name__)
+MAX_READLEN = 1000
 
 
 cdef class CCBitArrayCalculator(object):
@@ -91,7 +92,9 @@ cdef class CCBitArrayCalculator(object):
 
     def _init_buff(self):
         # To access by 1-based index, allocate arrays with 1 more size.
-        chromsize = self.ref2genomelen[self._chr] + 1
+        # Additionally, extra spaces same or more than (read_length - 1)
+        # is needed to contain reverse strand reads.
+        chromsize = self.ref2genomelen[self._chr] + MAX_READLEN
         self._forward_array = bitarray(chromsize)
         self._reverse_array = bitarray(chromsize)
 
@@ -102,7 +105,10 @@ cdef class CCBitArrayCalculator(object):
         if self._buff_flashed:
             return None
 
-        self._calc_correlation()
+        # keep this method safe to call; for chroms which have no reads.
+        if self._chr != '':
+            self._calc_correlation()
+
         self._buff_flashed = True
 
     cdef inline int _calc_correlation(self) except -1:

PyMaSC/handler/result.py

@@ -142,7 +142,14 @@ def _calc_cc(self, forward_sum, reverse_sum, ccbins, totlen, denom):
         sum_prod = forward_mean * reverse_mean
         var_geomean = (forward_var * reverse_var) ** 0.5
 
-        cc = (ccbins / denom - sum_prod) / var_geomean
+        try:
+            with np.errstate(divide="raise", invalid="raise"):
+                cc = (ccbins / denom - sum_prod) / var_geomean
+        except FloatingPointError as e:
+            logger.debug("catch numpy warning: " + e.message)
+            logger.debug("continue anyway.")
+            with np.errstate(divide="ignore", invalid="ignore"):
+                cc = (ccbins / denom - sum_prod) / var_geomean
 
         cc_min = min(cc)
 

PyMaSC/output/figure.py

@@ -1,6 +1,8 @@
 import logging
 import os.path
 
+import numpy as np
+
 from PyMaSC.utils.calc import moving_avr_filter
 from PyMaSC.utils.output import catch_IOError
 from PyMaSC.utils.compatible import xrange
@@ -170,7 +172,10 @@ def plot_ncc_vs_masc(pp, ccr, name):
 def _plot_ncc_vs_masc(pp, title, max_shift, read_len,
                       cc=None, cc_min=None, masc=None, masc_min=None,
                       nsc=None, rsc=None, estimated_library_len=None, expected_library_len=None):
-    assert (cc is not None) or (masc is not None)
+    assert (
+        (cc is not None and not np.all(np.isnan(cc))) or
+        (masc is not None and not np.all(np.isnan(masc)))
+    )
 
     plt.title(title)
     plt.xlabel("Reverse Strand Shift")