update docstrings

maxibor · Apr 27, 2020 · 9a734d3 · 9a734d3
1 parent 64b8b38
commit 9a734d3
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Showing 5 changed files with 10 additions and 11 deletions.
diff --git a/pydamage/damage.py b/pydamage/damage.py
@@ -30,8 +30,8 @@ def get_damage(self, wlen, show_al):
             wlen (int): window length
             show_al(bool): print alignments representations
         Returns:
-            all_ct(list): positions of reads with CtoT transitions
-            all_ga(list): positions of reads with GtoA transitions
+            list: all_ct - positions of reads with CtoT transitions
+            list: all_ga - positions of reads with GtoA transitions
         """
 
         all_ct = []

diff --git a/pydamage/main.py b/pydamage/main.py
@@ -24,7 +24,7 @@ def analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir="
         verbose(bool): verbose mode
         force(bool): force overwriting of results directory
     Returns:
-        df(pd.DataFrame): pandas DataFrame containg pydamage results
+        pd.DataFrame: pandas DataFrame containg pydamage results
 
     """
     if verbose:

diff --git a/pydamage/models.py b/pydamage/models.py
@@ -31,7 +31,7 @@ def pmf(self, x, geom_p, geom_pmin, geom_pmax):
             geom_pmin (float): min y value
             geom_pmax (float): max y value
         Returns:
-            (numpy array): PMF(x)
+            np.array: PMF(x)
         """
         base_geom = ((1-geom_p)**x)*geom_p
         xmin = min(base_geom)
@@ -49,7 +49,7 @@ def log_pmf(self, x, geom_p, geom_pmin, geom_pmax):
             geom_pmin (float): min y value
             geom_pmax (float): max y value
         Returns:
-            (numpy array): LogPMF(x)
+            np.array: LogPMF(x)
         """
         return(np.log(self.pmf(x=x, geom_p=geom_p, geom_pmin=geom_pmin, geom_pmax=geom_pmax)))
 
@@ -76,7 +76,7 @@ def pmf(self, x, unif_pmin):
             x (numpy array) data
             unif_pmin (float): target y value
         Returns:
-            (numpy array): PMF(x)
+            np.array: PMF(x)
         """
         return(np.array([unif_pmin]*len(x)))
 
@@ -87,6 +87,6 @@ def log_pmf(self, x, unif_pmin):
             x (numpy array) data
             geom_pmin (float): target y value
         Returns:
-            (numpy array): LogPMF(x)
+            np.array: LogPMF(x)
         """
         return(np.log(self.pmf(x=x, unif_pmin=unif_pmin)))
diff --git a/pydamage/optim.py b/pydamage/optim.py
@@ -16,8 +16,8 @@ def optim(function, parameters, xdata, ydata, bounds, loss='huber'):
                     ((par1_min, par2_min), (par1_max, par2_max))
         loss (str): loss function. See https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares
     Returns:
-        popt_dict (dict): 'parameter_name':'parameter_value'
-        perr_dict (dict): 'parameter_name':'standard_deviation'
+        dict: popt_dict - 'parameter_name':'parameter_value'
+        dict: perr_dict - 'parameter_name':'standard_deviation'
 
     """
     popt, pcov = curve_fit(function, xdata=xdata, ydata=ydata, bounds=bounds, loss=loss)

diff --git a/pydamage/parse_damage.py b/pydamage/parse_damage.py
@@ -11,8 +11,7 @@ def damage_al(reference, query, cigartuple, wlen, show_al):
         wlen (int): window length
         print_al (bool): print alignment
     Returns:
-        CT (list): list of CtoT positions
-        GA (list): list of GtoA positions
+        dict : {'CT': list of CtoT positions, 'GA': list of GtoA positions}
     """
     r_pos = 0
     q_pos = 0