Merge pull request #21 from mskcc/Removing_NA

Removing NA
mskcc · Jun 13, 2017 · 3c5a9dd · 3c5a9dd
2 parents db50618 + b8aa768
commit 3c5a9dd
Show file tree

Hide file tree

Showing 9 changed files with 2,253 additions and 2,252 deletions.
diff --git a/data/sample_output.maf b/data/sample_output.maf
diff --git a/filter_blacklist_regions.R b/filter_blacklist_regions.R
@@ -66,6 +66,6 @@ if (!interactive()) {
   rmsk[, Chromosome := gsub("chr", "", Chromosome)]
 
   maf.out <- annotate_maf(maf, blacklist, rmsk)
-  if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-  } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+  if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F)
+  } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
 }
diff --git a/filter_cohort_normals.R b/filter_cohort_normals.R
@@ -84,6 +84,6 @@ if( ! interactive() ) {
   }
 
   maf.out <- annotate_maf(maf, fillout, normal.samples)
-  if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F, na="")
-  } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F, na="") }
+  if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F, na="")
+  } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F, na="") }
 }
diff --git a/filter_dmp.R b/filter_dmp.R
@@ -41,6 +41,6 @@ if (!interactive()) {
     outfile <- args$outfile
 
     maf.out <- annotate_maf(maf)
-    if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-    } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+    if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F)
+    } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
 }
diff --git a/filter_ffpe.R b/filter_ffpe.R
@@ -107,7 +107,7 @@ if (!interactive()) {
     } else if(args$filter) {
         maf <- add_mut_tri(maf)
         maf.out <- filter_artifacts(maf)
-        if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-        } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+        if (outfile == 'stdout') { write.table(maf.out, na="", stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
+        } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
     }
 }
diff --git a/filter_ffpe_pool.R b/filter_ffpe_pool.R
@@ -85,6 +85,6 @@ if(fillout.format == 2){
 }
 
   maf.out <- annotate_maf(maf, parsed_fillout,alt.reads)
-  if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-  } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+  if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F)
+  } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
 }
diff --git a/filter_low_conf.R b/filter_low_conf.R
@@ -40,6 +40,6 @@ if (!interactive()) {
     outfile <- args$outfile
 
     maf.out <- annotate_maf(maf)
-    if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-    } else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+    if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F)
+    } else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
 }
diff --git a/filter_normal_panel.R b/filter_normal_panel.R
@@ -101,6 +101,6 @@ if( ! interactive() ) {
 	}
 
 	maf.out <- annotate_maf(maf, parsed_fillout, normal.count)
-	if (outfile == 'stdout') { write.table(maf.out, stdout(), sep = "\t", col.names = T, row.names = F, quote = F)
-	} else { write.table(maf.out, outfile, sep = "\t", col.names = T, row.names = F, quote = F) }
+	if (outfile == 'stdout') { write.table(maf.out, stdout(), na="", sep = "\t", col.names = T, row.names = F, quote = F)
+	} else { write.table(maf.out, outfile, na="", sep = "\t", col.names = T, row.names = F, quote = F) }
 }
diff --git a/tests/test_run_ngs-filters.py b/tests/test_run_ngs-filters.py
@@ -43,7 +43,8 @@ def setup_module():
         sys.exit(1)
 
 def teardown_module():
-     shutil.rmtree(new_dir)
+     #shutil.rmtree(new_dir)
+     pass
 
 def test_maf_fileSimilarity():
     outFileMaf = os.path.join(new_dir, "sample_output.maf")