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clinical-genomics-uppsala · May 8, 2024 · a611de2 · a611de2
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commit a611de2
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Showing 2 changed files with 24 additions and 12 deletions.
diff --git a/workflow/scripts/manta_to_tsv.py b/workflow/scripts/manta_to_tsv.py
@@ -11,21 +11,23 @@
 vcf = vcf.Reader(open(input_file, "r"))
 
 with open(output_file, "wt") as tsv:
-    tsv_writer = csv.writer(tsv, delimiter='\t')
+    tsv_writer = csv.writer(tsv, delimiter="\t")
     tsv_writer.writerow(["#POSITION1", "MANTAID", "BREAKEND", "GENES", "DEPTH", "ANNOTATIONINFO", "PR_ALT_FREQ", "SR_ALT_FREQ"])
     for row in vcf:
-        if "MantaBND" in row.ID and not any(x in ["MinQUAL", "MinGQ", "MinSomaticScore",
-                                                  "Ploidy", "MaxDepth", "MaxMQ0Frac", "NoPairSupport",
-                                                  "SampleFT", "HomRef"] for x in row.FILTER):
+        if "MantaBND" in row.ID and not any(
+            x
+            in ["MinQUAL", "MinGQ", "MinSomaticScore", "Ploidy", "MaxDepth", "MaxMQ0Frac", "NoPairSupport", "SampleFT", "HomRef"]
+            for x in row.FILTER
+        ):
             try:
                 genes = row.INFO["ANN"][0].split("|")
             except KeyError:
                 genes = ["NA", "NA", "NA", "NA", "NA"]
             manta_id = ":".join(row.ID.split(":")[0:2])
             last_sample_index = len(row.samples) - 1
             last_sample = row.samples[last_sample_index]
-            pr_values = last_sample.data.PR if hasattr(last_sample.data, 'PR') else None
-            sr_values = last_sample.data.SR if hasattr(last_sample.data, 'SR') else None
+            pr_values = last_sample.data.PR if hasattr(last_sample.data, "PR") else None
+            sr_values = last_sample.data.SR if hasattr(last_sample.data, "SR") else None
             if pr_values:
                 pr_denominator, pr_numerator = pr_values
                 pr_frequency = pr_numerator / (pr_denominator + pr_numerator) if pr_denominator + pr_numerator != 0 else None
@@ -39,8 +41,17 @@
                 sr_frequency = None
 
             # Format frequencies only if they are not None
-            pr_formatted = f"{pr_frequency:.4f}" if pr_frequency is not None else 'NA'
-            sr_formatted = f"{sr_frequency:.4f}" if sr_frequency is not None else 'NA'
-            tsv_writer.writerow([row.CHROM + ":" + str(row.POS), manta_id, str(row.ALT)[1:-1],
-                                genes[3] + "(" + genes[4] + ")", row.INFO["BND_DEPTH"],
-                                row.FILTER, str(pr_formatted), str(sr_formatted)])
+            pr_formatted = f"{pr_frequency:.4f}" if pr_frequency is not None else "NA"
+            sr_formatted = f"{sr_frequency:.4f}" if sr_frequency is not None else "NA"
+            tsv_writer.writerow(
+                [
+                    row.CHROM + ":" + str(row.POS),
+                    manta_id,
+                    str(row.ALT)[1:-1],
+                    genes[3] + "(" + genes[4] + ")",
+                    row.INFO["BND_DEPTH"],
+                    row.FILTER,
+                    str(pr_formatted),
+                    str(sr_formatted),
+                ]
+            )
diff --git a/workflow/scripts/sample_order_multiqc.py b/workflow/scripts/sample_order_multiqc.py
@@ -37,7 +37,8 @@
     for sample_line in sample_order:
         replacement_line = [sample_line[sample_order_index.index("sample")]]
         order_line = [sample_line[sample_order_index.index("sample")], sample_line[sample_order_index.index("lab_id")]]
-        if sample_line[sample_order_index.index("type")].lower() == "t" or sample_line[sample_order_index.index("type")].lower() == "n":
+        if (sample_line[sample_order_index.index("type")].lower() == "t" or
+                sample_line[sample_order_index.index("type")].lower() == "n"):
             replacement_tsv_dna.write("\t".join(replacement_line + ["sample_"+str(f"{i:03}")]) + "\n")
             order_tsv_dna.write("\t".join(["sample_"+str(f"{i:03}")] + order_line) + "\n")
             dna_table.write("\t".join(["sample_"+str(f"{i:03}")] + order_line)+"\n")