Add option to skip coverage plots (issue #19)

dariober · Mar 15, 2020 · 44fdd18 · 44fdd18
1 parent b4a6f09
commit 44fdd18
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Showing 2 changed files with 22 additions and 7 deletions.
diff --git a/bin/cnv_facets.R b/bin/cnv_facets.R
@@ -31,7 +31,7 @@ suppressMessages(library(gridExtra))
 
 # -----------------------------------------------------------------------------
 
-VERSION= sprintf('0.15.0; facets=%s', packageVersion('facets'))
+VERSION= sprintf('0.16.0; facets=%s', packageVersion('facets'))
 
 docstring<- sprintf('DESCRIPTION \\n\\
 Detect somatic copy number variants (CNVs) and estimate purity and ploidy in a\\n\\
@@ -131,6 +131,10 @@ parser$add_argument('--unmatched', '-u', help=
 'Normal sample is unmatched. If set, heterozygote SNPs are\\n\\
 called using tumor reads only and logOR calculations are different', action= 'store_true')
 
+parser$add_argument('--no-cov-plot', '-np', help= 
+'Do not produce coverage plots (they can be memory intensive).\\n\\
+Other plots remain unaffected', action= 'store_true')
+
 def_rnd<- 'The name of the input file'
 parser$add_argument('--rnd-seed', '-s', help= sprintf(
 'Seed for random number generator. Default: %s', def_rnd), type= 'character', default= def_rnd)
@@ -812,11 +816,13 @@ if(sys.nframe() == 0){
     }
     rcmat_flt<- filter_rcmat(rcmat= rcmat[['pileup']], min_ndepth= xargs$depth[1], 
         max_ndepth= xargs$depth[2], target_bed= targets)
-
-    write(sprintf('[%s] Plotting histogram of coverage...', Sys.time()), stderr())
-    plot_coverage(rcmat= rcmat[['pileup']], rcmat_flt= rcmat_flt, 
-        fname= paste0(xargs$out, '.cov.pdf'), title= paste0('Depth of coverage\n', xargs$out))
-
+
+    if(xargs$no_cov_plot == FALSE){
+        write(sprintf('[%s] Plotting histogram of coverage...', Sys.time()), stderr())
+        plot_coverage(rcmat= rcmat[['pileup']], rcmat_flt= rcmat_flt, 
+            fname= paste0(xargs$out, '.cov.pdf'), title= paste0('Depth of coverage\n', xargs$out))
+    }
+
     rcmat[['pileup']]<- NULL
 
     x_ <- gc(verbose= FALSE)
@@ -887,7 +893,7 @@ if(sys.nframe() == 0){
     par(las= 1, mar= c(3, 3, 1, 1), mgp= c(1.5, 0.5, 0), tcl= -0.3)
     logRlogORspider(facets$proc_out$out, facets$proc_out$dipLogR)
     x_ <- dev.off()
-
+    
     si<- capture.output(sessionInfo())
     write(si, stderr())
 }
diff --git a/test/test_cnv_facets.py b/test/test_cnv_facets.py
@@ -84,6 +84,15 @@ def testBamInput(self):
         self.assertTrue(os.path.exists('test_out/out.csv.gz'))
         self.assertEqual('', vcf_validator('test_out/out.vcf.gz'))
 
+    def testDoNotPlot(self):
+        p = sp.Popen("""../bin/cnv_facets.R --no-cov-plot -t data/TCRBOA6-T-WEX.sample.bam -n data/TCRBOA6-N-WEX.sample.bam -vcf data/common.sample.vcf.gz -o test_out/out""", shell=True, stdout= sp.PIPE, stderr= sp.PIPE)
+        stdout, stderr = p.communicate()
+        self.assertEqual(0, p.returncode)
+        self.assertTrue(os.path.exists('test_out/out.vcf.gz'))
+        self.assertTrue(os.path.exists('test_out/out.cnv.png'))
+        self.assertTrue(os.path.exists('test_out/out.spider.pdf'))
+        self.assertTrue(not os.path.exists('test_out/out.cov.pdf'))
+
     def testBamInputNotProperlyPaired(self):
         # Prepare a bam files with 'properly paired' flag removed
         p = sp.Popen(r"""