add check to skip parsing of blank lines in SampleSheets

add a check to skip parsing of blank lines in SampleSheets.csv files,
and a unit test with a representative sample sheet

illumina.py

@@ -461,6 +461,9 @@ def _detect_and_load_sheet(self, infile):
                 miseq_skip = False
                 row_num = 0
                 for line in inf:
+                    # if this is a blank line, skip parsing and continue to the next line...
+                    if len(line.rstrip('\n').rstrip('\r').strip()) == 0:
+                        continue
                     csv.register_dialect('samplesheet', quoting=csv.QUOTE_MINIMAL, escapechar='\\')
                     row = next(csv.reader([line.strip().rstrip('\n')], dialect="samplesheet"))
                     row = [item.strip() for item in row] # remove leading/trailing whitespace from each item

test/input/TestSampleSheet/SampleSheet-with-blanklines.csv

@@ -0,0 +1,35 @@
+[Header],,,,,,,,,
+IEMFileVersion,4,,,,,,,,
+Investigator Name,Anne,,,,,,,,
+Experiment Name,AP081616,,,,,,,,
+Date,8/16/16,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,
+Application,FASTQ Only,,,,,,,,
+Assay,Nextera XT,,,,,,,,
+Description,CSF,,,,,,,,
+Chemistry,Amplicon,,,,,,,,
+,,,,,,,,,
+[Reads],,,,,,,,,
+101,,,,,,,,,
+101,,,,,,,,,
+,,,,,,,,,
+[Settings],,,,,,,,,
+ReverseComplement,0,,,,,,,,
+Adapter,CTGTCTCTTATACACATCT,,,,,,,,
+,,,,,,,,,
+[Data],,,,,,,,,
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+BWH001lib1,,,,N703,AGGCAGAA,S517,GCGTAAGA,,
+BWH001lib2,,,,N705,GGACTCCT,S517,GCGTAAGA,,
+NEGCSF3lib2,,,,N706,TAGGCATG,S502,CTCTCTAT,,
+NS_guide2_2,,,,172,CCTACCAT,417,CGGTTCTT,,
+C044_rs9283753,,,,44,CTGCGGAT,34,TCTTTCCC,,
+C045_rs9283753,,,,45,TCGGAATG,34,TCTTTCCC,,
+C066_rs9283753,,,,46,TCTGCAAG,34,TCTTTCCC,,
+C067_rs9283753,,,,47,AACTTGAC,34,TCTTTCCC,,
+
+C081_rs9283753,,,,66,TTGAGCCT,34,TCTTTCCC,,
+C082_rs9283753,,,,67,GGTCCAGA,34,TCTTTCCC,,
+NA12872_rs9283753,,,,68,CCAGTTAG,34,TCTTTCCC,,
+NA12812_rs9283753,,,,69,CAATAGTC,34,TCTTTCCC,,
+

test/unit/test_illumina.py

@@ -66,6 +66,12 @@ def test_tabfile(self):
         self.assertEqual(samples.num_indexes(), 2)
         self.assertEqual(len(samples.get_rows()), 24)
 
+    def test_blank_line_in_tabular_section(self):
+        inDir = util.file.get_test_input_path(self)
+        samples = illumina.SampleSheet(os.path.join(inDir, 'SampleSheet-with-blanklines.csv'))
+        self.assertEqual(samples.num_indexes(), 2)
+        self.assertEqual(len(samples.get_rows()), 12)
+
 
 class TestRunInfo(TestCaseWithTmp):