Commit 9468f249 authored by Theo Serralta's avatar Theo Serralta

Wrong variable in compute_mean_std

parent 09497ec1
...@@ -445,7 +445,7 @@ def dico_mappabilite(mappability_file): ...@@ -445,7 +445,7 @@ def dico_mappabilite(mappability_file):
end_time_3 = time.time() end_time_3 = time.time()
elapsed_time_3 = end_time_3 - start_time_3 elapsed_time_3 = end_time_3 - start_time_3
logging.info(f"In dico_mappability : Ending merge intervals with the same score (Time taken: {elapsed_time_2:.4f} seconds)") logging.info(f"In dico_mappability : Ending merge intervals with the same score (Time taken: {elapsed_time_3:.4f} seconds)")
end_time = time.time() end_time = time.time()
elapsed_time = end_time - start_time elapsed_time = end_time - start_time
...@@ -680,8 +680,7 @@ def calcul_med_same_gc(gc_results, depth_correction_results, chr): ...@@ -680,8 +680,7 @@ def calcul_med_same_gc(gc_results, depth_correction_results, chr):
""" """
Calculate the median depth correction for each unique GC content value. Calculate the median depth correction for each unique GC content value.
This function computes the median depth correction values for each unique GC content value in `gc_results`, This function computes the median depth correction values for each unique GC content value, filtering out zero values.
filtering out zero values from `depth_correction_results`.
Parameters Parameters
---------- ----------
...@@ -689,8 +688,6 @@ def calcul_med_same_gc(gc_results, depth_correction_results, chr): ...@@ -689,8 +688,6 @@ def calcul_med_same_gc(gc_results, depth_correction_results, chr):
A list or array of GC content values. A list or array of GC content values.
depth_correction_results : list or numpy.ndarray depth_correction_results : list or numpy.ndarray
A list or array of depth correction values. A list or array of depth correction values.
chr : str
The chromosome identifier for which the medians are calculated.
Returns Returns
------- -------
...@@ -735,15 +732,12 @@ def calcul_moy_totale(normalize_depth_results, chr): ...@@ -735,15 +732,12 @@ def calcul_moy_totale(normalize_depth_results, chr):
""" """
Calculate the mean of non-zero normalized depth results. Calculate the mean of non-zero normalized depth results.
This function filters out zero values from the normalized depth results and computes the mean This function filters out zero values from the normalized depth results and computes the mean of the remaining values.
of the remaining non-zero values.
Parameters Parameters
---------- ----------
normalize_depth_results : list or numpy.ndarray normalize_depth_results : list or numpy.ndarray
A list or array of normalized depth values. A list or array of normalized depth values.
chr : str
The chromosome identifier for which the mean is calculated.
Returns Returns
------- -------
...@@ -757,15 +751,15 @@ def calcul_moy_totale(normalize_depth_results, chr): ...@@ -757,15 +751,15 @@ def calcul_moy_totale(normalize_depth_results, chr):
# Filter results to remove zero values # Filter results to remove zero values
non_zero_results = normalize_depth_results[normalize_depth_results != 0] non_zero_results = normalize_depth_results[normalize_depth_results != 0]
# Calculate the mean of non-zero results # Calculate the mean of non-zero results
mean_chr = np.mean(non_zero_results) if non_zero_results.size > 0 else 0 mean_chr_norm = np.mean(non_zero_results) if non_zero_results.size > 0 else 0
sys.stderr.write("Chromosome : %s, mean_chr : %s\n" % (chr, mean_chr)) logging.info(f"Mean chr_norm_no_zero = {mean_chr_norm}")
end_time = time.time() end_time = time.time()
elapsed_time = end_time - start_time elapsed_time = end_time - start_time
logging.info(f"Leaving calcul_moy_totale for {chr} (Time taken: {elapsed_time:.4f} seconds)") logging.info(f"Leaving calcul_moy_totale for {chr} (Time taken: {elapsed_time:.4f} seconds)")
return mean_chr return mean_chr_norm
def calcul_std(normalize_depth_results, chr): def calcul_std(normalize_depth_results, chr):
""" """
...@@ -805,7 +799,7 @@ def calcul_std(normalize_depth_results, chr): ...@@ -805,7 +799,7 @@ def calcul_std(normalize_depth_results, chr):
return std_chr return std_chr
def compute_mean_std_med(ratio_par_window_results, chr): def compute_mean_std_med(ratio_par_window_norm_results, chr, normalize_depth_results):
""" """
Compute the mean, standard deviation, and median of non-zero ratio results per window. Compute the mean, standard deviation, and median of non-zero ratio results per window.
...@@ -814,7 +808,7 @@ def compute_mean_std_med(ratio_par_window_results, chr): ...@@ -814,7 +808,7 @@ def compute_mean_std_med(ratio_par_window_results, chr):
Parameters Parameters
---------- ----------
ratio_par_window_results : list or numpy.ndarray ratio_par_window_norm_results : list or numpy.ndarray
A list or array of ratio values per window. A list or array of ratio values per window.
chr : str chr : str
The chromosome identifier for which the statistics are calculated. The chromosome identifier for which the statistics are calculated.
...@@ -829,8 +823,9 @@ def compute_mean_std_med(ratio_par_window_results, chr): ...@@ -829,8 +823,9 @@ def compute_mean_std_med(ratio_par_window_results, chr):
start_time = time.time() start_time = time.time()
# Filter results to remove zero and -1 values # Filter results to remove zero and -1 values
ratio_par_window_results = np.array(ratio_par_window_results) ratio_par_window_norm_results = np.array(ratio_par_window_norm_results)
non_zero_results = ratio_par_window_results[ratio_par_window_results != 0] non_zero_results = ratio_par_window_norm_results[ratio_par_window_norm_results != 0]
non_zero_results = non_zero_results[np.isfinite(non_zero_results)]
# Initialize list for stats computation # Initialize list for stats computation
table = [] table = []
......
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