Merge pull request #44 from AlexandrovLab/u59b

U59b

setup.py

@@ -14,7 +14,7 @@ def readme():
         return f.read()
 
 
-VERSION = "1.3.18"
+VERSION = "1.3.19"
 
 
 def write_version_py(filename="sigProfilerPlotting/version.py"):
@@ -23,7 +23,7 @@ def write_version_py(filename="sigProfilerPlotting/version.py"):
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
-update = 'Upgrade v1.3.18: Update SV and CNV output handling to support pdf, png, pil_image.'
+update = 'Upgrade v1.3.19: Fix plotSV input handling and refactor tests.'
     
     """
     fh = open(filename, "w")

sigProfilerPlotting/sigProfilerPlotting.py

@@ -106,7 +106,7 @@ def output_results(savefig_format, output_path, project, figs, context_type, dpi
     if savefig_format.lower() == "pdf":
         pp = PdfPages(output_path + context_type + "_plots_" + project + ".pdf")
         for fig in figs:
-            if context_type == "CNV_48" or "SV_32":
+            if context_type in ("CNV_48", "SV_32"):
                 figs[fig].savefig(pp, format="pdf", bbox_inches="tight")
             else:
                 figs[fig].savefig(pp, format="pdf")
@@ -116,7 +116,9 @@ def output_results(savefig_format, output_path, project, figs, context_type, dpi
         for fig in figs:
             if context_type in ("CNV_48", "SV_32"):
                 figs[fig].savefig(
-                    output_path + context_type + "_plots_" + fig + ".png", dpi=dpi, bbox_inches="tight"
+                    output_path + context_type + "_plots_" + fig + ".png",
+                    dpi=dpi,
+                    bbox_inches="tight",
                 )
             else:
                 figs[fig].savefig(
@@ -127,8 +129,10 @@ def output_results(savefig_format, output_path, project, figs, context_type, dpi
         image_list = {}
         for fig in figs:
             tmp_buffer = io.BytesIO()
-            if context_type == "CNV_48" or "SV_32":
-                figs[fig].savefig(tmp_buffer, format="png", bbox_inches="tight", dpi=dpi)
+            if context_type in ("CNV_48", "SV_32"):
+                figs[fig].savefig(
+                    tmp_buffer, format="png", bbox_inches="tight", dpi=dpi
+                )
             else:
                 figs[fig].savefig(tmp_buffer, format="png", dpi=dpi)
             # convert tmp_buffer to a PIL and close buffer
@@ -2063,31 +2067,25 @@ def plot(counts, labels, sample, project, percentage, aggregate=False):
 
         return fig
 
-
     # create the output directory if it doesn't exist
     if not os.path.exists(output_path):
         os.makedirs(output_path)
 
-    df = pd.read_csv(
-        matrix_path, sep=None, engine="python"
-    )  # flexible reading of tsv or csv
-
     # To reindex the input data
     df = process_input(matrix_path, "32")
     df.reset_index(inplace=True)
     label = df.columns[0]
     labels = df[label]
 
-
-    figs={}
+    figs = {}
     if aggregate:
         num_samples = len(df.columns) - 1
         df["total_count"] = df.sum(axis=1) / num_samples  # NORMALIZE BY # of SAMPLES
         counts = list(df["total_count"])
         if percentage and sum(counts) != 0:
             counts = [(x / sum(counts)) * 100 for x in counts]
         sample = ""
-        figs[sample]=plot(counts, labels, sample, project, percentage, aggregate=True)
+        figs[sample] = plot(counts, labels, sample, project, percentage, aggregate=True)
     else:
         # each column vector in dataframe contains counts for a specific sample
         samples = list(df)[1:]
@@ -2097,7 +2095,7 @@ def plot(counts, labels, sample, project, percentage, aggregate=False):
                 counts = [(x / sum(counts)) * 100 for x in counts]
             assert (len(counts)) == 32
             assert (len(labels)) == 32
-            figs[sample]=plot(counts, labels, sample, project, percentage)
+            figs[sample] = plot(counts, labels, sample, project, percentage)
 
     return output_results(savefig_format, output_path, project, figs, "SV_32", dpi=dpi)
 
@@ -2124,9 +2122,7 @@ def plotCNV(
     """
 
     # inner function to construct plot
-    def plot(
-        counts, labels, sample, project, percentage, aggregate=False
-    ):
+    def plot(counts, labels, sample, project, percentage, aggregate=False):
         counts_ordered = list()
         labels_ordered = list()
         labels_updated = list()
@@ -2652,7 +2648,9 @@ def plot(
                 counts = [(x / sum(counts)) * 100 for x in counts]
             assert len(counts) == 48
             assert len(labels) == 48
-            figs[sample] = plot(counts, labels, sample, project, percentage, aggregate=False)
+            figs[sample] = plot(
+                counts, labels, sample, project, percentage, aggregate=False
+            )
 
     return output_results(savefig_format, output_path, project, figs, "CNV_48", dpi=dpi)
 
@@ -2977,7 +2975,9 @@ def plotSBS(
                 [i.set_color("black") for i in plt.gca().get_yticklabels()]
                 sample_count += 1
 
-            return output_results(savefig_format, output_path, project, figs, "SBS_96", dpi=dpi)
+            return output_results(
+                savefig_format, output_path, project, figs, "SBS_96", dpi=dpi
+            )
         except:
             print("There may be an issue with the formatting of your matrix file.")
             pdf_path = output_path + "SBS_96_plots_" + project + ".pdf"
@@ -7730,7 +7730,9 @@ def plotSBS(
                 panel2.legend(handles[:3], labels[:3], loc="best", prop={"size": 30})
                 sample_count += 1
 
-            return output_results(savefig_format, output_path, project, figs, "SBS_288", dpi=dpi)
+            return output_results(
+                savefig_format, output_path, project, figs, "SBS_288", dpi=dpi
+            )
 
         except:
             print("There may be an issue with the formatting of your matrix file.")
@@ -8653,7 +8655,9 @@ def plotID(
                 [i.set_color("black") for i in plt.gca().get_yticklabels()]
                 sample_count += 1
 
-            return output_results(savefig_format, output_path, project, figs, "ID_83", dpi=dpi)
+            return output_results(
+                savefig_format, output_path, project, figs, "ID_83", dpi=dpi
+            )
         except:
             print("There may be an issue with the formatting of your matrix file.")
             pdf_path = output_path + "ID_83_plots_" + project + ".pdf"
@@ -10711,7 +10715,9 @@ def plotDBS(
                 [i.set_color("grey") for i in plt.gca().get_xticklabels()]
                 sample_count += 1
 
-            return output_results(savefig_format, output_path, project, figs, "DBS_78", dpi=dpi)
+            return output_results(
+                savefig_format, output_path, project, figs, "DBS_78", dpi=dpi
+            )
 
         except:
             print("There may be an issue with the formatting of your matrix file.")

sigProfilerPlotting/version.py

@@ -1,7 +1,7 @@
 
 # THIS FILE IS GENERATED FROM SIGPROFILERPLOTTING SETUP.PY
-short_version = '1.3.18'
-version = '1.3.18'
-update = 'Upgrade v1.3.18: Update SV and CNV output handling to support pdf, png, pil_image.'
+short_version = '1.3.19'
+version = '1.3.19'
+update = 'Upgrade v1.3.19: Fix plotSV input handling and refactor tests.'