Blacked.

oligo_melting/secstr.py

@@ -1,11 +1,11 @@
 # -*- coding: utf-8 -*-
 
-'''
+"""
 @author: Gabriele Girelli
 @contact: gigi.ga90@gmail.com
 @description: methods for melting temperature calculation and correction for
               single-strand oligonucleotide secondary structures.
-'''
+"""
 
 # DEPENDENCIES =================================================================
 
@@ -15,26 +15,27 @@
 # CONSTANTS ====================================================================
 
 # Gas constant
-R = 1.987 / 1000    # kcal / (K mol)
+R = 1.987 / 1000  # kcal / (K mol)
 
 # FUNCTIONS ====================================================================
 
-def adj_fa(tm, fa_conc, fa_conc_0 = None):
-    '''Adjust secondary structure melting temperature based on formamide
+
+def adj_fa(tm, fa_conc, fa_conc_0=None):
+    """Adjust secondary structure melting temperature based on formamide
     concentration. Method adapted to work with OligoArrayAux output.
     Based on McConaughy, Biochemistry(8), 1969
     Method based on Wright et al not implemented, as m-value is not available.
-    
+
     Args:
       tm (float): melting temperature, in K.
       fa_conc (float): formamide concentration in %v,v.
       fa_mode (string): formamide correction lavel.
       fa_conc_0 (float): initial formamide concentration in %v,v.
-    
+
     Returns:
       float: corrected melting temperature.
-    '''
-    
+    """
+
     # Default initial concentration
     if type(None) == type(fa_conc_0):
         fa_conc_0 = 0
@@ -44,29 +45,30 @@ def adj_fa(tm, fa_conc, fa_conc_0 = None):
 
     # Correct
     if 0 == dfac:
-        return(tm)
+        return tm
     else:
-        return(tm - 0.72 * dfac)
+        return tm - 0.72 * dfac
+
 
 def melt_curve(h, s, tm, fa_conc, trange, tstep):
-    '''Generate melting curve
-    
+    """Generate melting curve
+
     Args:
       tm (float): melting temperature.
       fa_conc (float): formamide concentration in %v,v.
       trange (float): melting curve temperature range.
       tstep (float): melting curve temperature step.
-      
+
     Returns:
       list: melting curve data (x, y)
-    '''
+    """
 
     # Empty list for melting table
     data = []
 
     # Explore the temperature range
-    t = tm - trange / 2.
-    while t <= tm + trange / 2.:
+    t = tm - trange / 2.0
+    while t <= tm + trange / 2.0:
         # Calculate dissociated fraction
         k = unfolded_fraction(h, t, s)
 
@@ -80,20 +82,21 @@ def melt_curve(h, s, tm, fa_conc, trange, tstep):
         t += tstep
 
     # Return melting table
-    return(data)
+    return data
+
 
 def unfolded_fraction(h, t, s):
-    '''Calculate secondary structure unfolded fraction
-    
+    """Calculate secondary structure unfolded fraction
+
     Args:
       h (float): enthalpy.
       t (float): current temperature.
       s (float): enthropy.
-    
+
     Returns:
       float: dissociated fraction.
-    '''
-    
+    """
+
     # Calculate free energy at current temperature
     dg = h - t * s
 
@@ -104,7 +107,8 @@ def unfolded_fraction(h, t, s):
     k = 1 / (1 + factor)
 
     # Output
-    return(k)
+    return k
+
 
 # END ==========================================================================
 

oligo_melting/seq.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 
-'''
+"""
 @author: Gabriele Girelli
 @contact: gigi.ga90@gmail.com
 @description: methods for basic nucleic acid sequence management.
-'''
+"""
 
 # CONSTANTS ====================================================================
 
@@ -13,27 +13,28 @@
 
 # FUNCTIONS ====================================================================
 
+
 def rc(na, t):
-    '''
+    """
     Args:
         na (string): nucleic acid sequence.
         t (string): nucleic acid type, either 'dna' or 'rna'.
 
     Return:
         string: reverse complement of na.
-    '''
+    """
 
     # Identify type
     t = t.lower()
 
     # Select alphabet
-    if t == 'dna':
+    if t == "dna":
         ab = AB_DNA
-    elif t == 'rna':
+    elif t == "rna":
         ab = AB_RNA
     else:
-        print('ERROR: unknown na type.')
-        return()
+        print("ERROR: unknown na type.")
+        return ()
 
     rab = ab[1].strip().lower()
     ab = ab[0].strip().lower()
@@ -43,8 +44,8 @@ def rc(na, t):
 
     for c in na:
         if not c in ab:
-            print('ERROR: provided string conflicts with selected alphabet.')
-            return()
+            print("ERROR: provided string conflicts with selected alphabet.")
+            return ()
 
     # Calculate reverse
     r = na[::-1]
@@ -54,9 +55,10 @@ def rc(na, t):
     for c in r:
         rc.append(rab[ab.index(c)])
 
-    rc=''.join([str(c) for c in rc]).upper()
+    rc = "".join([str(c) for c in rc]).upper()
+
+    return rc
 
-    return(rc)
 
 # END ==========================================================================