make all plots

maxibor · May 7, 2020 · 26b0713 · 26b0713
1 parent 780e413
commit 26b0713
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Showing 2 changed files with 5 additions and 8 deletions.
diff --git a/pydamage/main.py b/pydamage/main.py
@@ -74,9 +74,11 @@ def analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir="
 
     if plot and len(filt_res) > 0:
         print("\nGenerating Pydamage plots")
+        plotdir = f"{outdir}/plots"
+        utils.makedir(plotdir, confirm=False)
+
         for ref in tqdm(filt_res):
-            dam_plot = damageplot(damage_dict=ref, wlen=wlen, qlen = ref['qlen'], outdir=outdir)
-            dam_plot.makedir()
+            dam_plot = damageplot(damage_dict=ref, wlen=wlen, qlen = ref['qlen'], outdir=plotdir)
             dam_plot.draw()
     df = utils.pandas_processing(res_dict=filt_res, outdir=outdir)
     return(df)

diff --git a/pydamage/plot.py b/pydamage/plot.py
@@ -31,12 +31,7 @@ def __init__(self, damage_dict, wlen, qlen, outdir):
         self.contig = damage_dict['reference']
         self.pvalue = damage_dict['pvalue']
         self.coverage = damage_dict['coverage']
-        self.outdir = outdir
-
-
-    def makedir(self):
-        self.plotdir = f"{self.outdir}/plots"
-        utils.makedir(self.plotdir, confirm=False)
+        self.plotdir = outdir
 
     def draw(self):
         """Draw pydamage plots