update verbose mode

pydamage/cli.py

@@ -21,13 +21,13 @@
               help='Number of processes')
 @click.option('-m',
               '--mini',
-              default=2000,
+              default=1000,
               type=int,
               show_default=True,
               help='Minimum reads aligned to consider reference')
 @click.option('-c',
               '--cov',
-              default=0.5,
+              default=8,
               type=float,
               show_default=True,
               help='Minimum coverage to consider reference')

pydamage/damage.py

@@ -97,9 +97,13 @@ def test_damage(ref, bam, mode, wlen, show_al, min_al, min_cov, process, verbose
                 test_res['coverage'] = cov
                 return(check_model_fit(test_res, wlen))
         else:
+            if verbose:
+                print(f"Did not attempt to fit a model to {ref} because of too few reads aligned")
+                print(f"nb_reads_aligned: {nb_reads_aligned} - coverage: {cov} - reflen: {reflen}\n")
             pass
     except ValueError as e:
-        print(f"Could not fit a model for {ref} because of too few reads aligned")
-        print(f"Model fitting error: {e}")
-        print(f"nb_reads_aligned: {nb_reads_aligned} - coverage: {cov} - reflen: {reflen}\n")
+        if verbose:
+            print(f"Model fitting for {ref} failed because of too few reads aligned")
+            print(f"Model fitting error: {e}")
+            print(f"nb_reads_aligned: {nb_reads_aligned} - coverage: {cov} - reflen: {reflen}\n")
         return(False)

pydamage/main.py

@@ -8,6 +8,7 @@
 import pandas as pd
 import sys
 from tqdm import tqdm
+import warnings
 from pydamage import __version__
 
 def analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir="", plot = False, verbose=False, force=False):
@@ -31,6 +32,9 @@ def analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir="
         print(f"Pydamage version {__version__}\n")
     utils.makedir(outdir, force=force)
 
+    if not verbose:
+        warnings.filterwarnings("ignore")
+
     mode = utils.check_extension(bam)
     alf = pysam.AlignmentFile(bam, mode)
 
@@ -61,8 +65,9 @@ def analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir="
     test_damage_partial = partial(damage.test_damage, bam=bam, wlen=wlen,
                               min_al=mini, min_cov=cov, show_al=show_al,
                               mode=mode, process=process, verbose=verbose)
+    print("Estimating and testing Damage")
     with multiprocessing.Pool(proc) as p:
-        res = p.map(test_damage_partial, refs)
+        res = tqdm(p.imap(test_damage_partial, refs), total = len(refs))
         filt_res = [i for i in res if i]
     if plot and len(filt_res) > 0:
         print("\nGenerating pydamage plots")

pydamage/vuong.py

@@ -50,12 +50,12 @@ def vuong_closeness(ref, model_A, model_B, ct_data, ga_data, wlen, verbose):
     omega = np.std(LA-LB)
     Z = LR/(np.sqrt(len(ct_data))*omega)
     pval = norm.cdf(Z)
-    if verbose:
-        print(f"\nReference: {ref}")
-        print(f"Vuong closeness test Z-score for {ref}: {round(Z, 4)}")
-        print(f"Vuong closeness test p-value for {ref}: {round(pval, 4)}")
-        print(f"Model A parameters for {ref}: {optim_A}")
-        print(f"Model B parameters for {ref}: {optim_B}")
+    # if verbose:
+    #     print(f"\nReference: {ref}")
+    #     print(f"Vuong closeness test Z-score for {ref}: {round(Z, 4)}")
+    #     print(f"Vuong closeness test p-value for {ref}: {round(pval, 4)}")
+    #     print(f"Model A parameters for {ref}: {optim_A}")
+    #     print(f"Model B parameters for {ref}: {optim_B}")
     res.update(ydata_counts)
     res.update(ctot_out)
     res.update(gtoa_out)