worked on unit tests for sam.rb

[biopieces.git] / code_ruby / test / maasha / test_sam.rb

diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index 7410263976b2fc654930be0102b3a4b8f61d689a..e056b21012dda1de719e79079cf44dd8d9f2f03b 100755 (executable)
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -29,7 +29,7 @@ require 'maasha/sam'
 require 'pp'
 require 'stringio'
 
-SAM_TEST =
+SAM_DATA =
 %{@HD\tVN:1.3\tSO:coordinate
 @SQ\tSN:ref\tLN:45
 @CO\tMyComment
@@ -43,7 +43,7 @@ r001\t83\tref\t37\t30\t9M\t=\t7\t-39\tCAGCGCCAT\t*
 
 class SamTest < Test::Unit::TestCase
   def setup
-    @sam = Sam.new(StringIO.new(SAM_TEST))
+    @sam = Sam.new(StringIO.new(SAM_DATA))
   end
 
 #  def test_Sam_header_without_entry_returns_nil
@@ -52,13 +52,11 @@ class SamTest < Test::Unit::TestCase
 #  end
 
   def test_Sam_header_parse_with_missing_version_number_raises
-    sam = Sam.new(StringIO.new("@HD"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@HD")) }
   end
 
   def test_Sam_header_parse_with_bad_version_number_raises
-    sam = Sam.new(StringIO.new("@HD\tXN:1.3"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@HD\tXN:1.3")) }
   end
 
   def test_Sam_header_parse_with_ok_version_number_returns_correctly
@@ -67,8 +65,7 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_bad_sort_order_raises
-    sam = Sam.new(StringIO.new("@HD\tVN:1.3\tSO:fish"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@HD\tVN:1.3\tSO:fish")) }
   end
 
   def test_Sam_header_parse_with_ok_sort_order_returns_correctly
@@ -79,13 +76,11 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_missing_sequence_name_raises
-    sam = Sam.new(StringIO.new("@SQ"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@SQ")) }
   end
 
   def test_Sam_header_parse_with_bad_sequence_name_raises
-    sam = Sam.new(StringIO.new("@SQ\tSN:"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:")) }
   end
 
   def test_Sam_header_parse_with_ok_sequence_name_returns_correctly
@@ -94,18 +89,15 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_duplicate_sequence_name_raises
-    sam = Sam.new(StringIO.new("@SQ\tSN:ref\n@SQ\tSN:ref"))
-    assert_raise(SamError) { sam.header[:SQ][:SN][:ref] }
+    assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref\n@SQ\tSN:ref")) }
   end
 
   def test_Sam_header_parse_with_missing_sequence_length_raises
-    sam = Sam.new(StringIO.new("@SQ\tSN:ref"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref")) }
   end
 
   def test_Sam_header_parse_with_bad_sequence_length_raises
-    sam = Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:x"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:x")) }
   end
 
   def test_Sam_header_parse_with_ok_sequence_length_returns_correctly
@@ -114,23 +106,20 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_full_SQ_dont_raise
-    sam = Sam.new("@SQ\tSN:ref\tLN:45\tAS:ident\tM5:87e6b2aedf51b1f9c89becfab9267f41\tSP:E.coli\tUR:http://www.biopieces.org")
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\tAS:ident\tM5:87e6b2aedf51b1f9c89becfab9267f41\tSP:E.coli\tUR:http://www.biopieces.org"))
     assert_nothing_raised { sam.header }
   end
 
   def test_Sam_header_parse_with_bad_read_group_identifier_raises
-    sam = Sam.new(StringIO.new("@RG\tID:"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:")) }
   end
 
   def test_Sam_header_parse_with_missing_read_group_identifier_raises
-    sam = Sam.new(StringIO.new("@RG"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@RG")) }
   end
 
   def test_Sam_header_parse_with_duplicate_read_group_identifier_raises
-    sam = Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:123"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:123")) }
   end
 
   def test_Sam_header_parse_with_ok_read_group_identifier_dont_raise
@@ -139,8 +128,7 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_bad_flow_order_raises
-    sam = Sam.new(StringIO.new("@RG\tID:123\tFO:3"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tFO:3")) }
   end
 
   def test_Sam_header_parse_with_ok_flow_order_dont_raise
@@ -151,8 +139,7 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_bad_platform_raises
-    sam = Sam.new(StringIO.new("@RG\tID:123\tPL:maersk"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tPL:maersk")) }
   end
 
   def test_Sam_header_parse_with_ok_platform_dont_raise
@@ -161,23 +148,19 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_header_parse_with_bad_program_identifier_raises
-    sam = Sam.new(StringIO.new("@PG\tID:"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:")) }
   end
 
   def test_Sam_header_parse_with_missing_program_identifier_raises
-    sam = Sam.new(StringIO.new("@PG"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@PG")) }
   end
 
   def test_Sam_header_parse_with_duplicate_program_identifier_raises
-    sam = Sam.new(StringIO.new("@PG\tID:123\n@PG\tID:123"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:123\n@PG\tID:123")) }
   end
 
   def test_Sam_header_parse_with_bad_comment_raises
-    sam = Sam.new(StringIO.new("@CO\t"))
-    assert_raise(SamError) { sam.header }
+    assert_raise(SamError) { Sam.new(StringIO.new("@CO\t")) }
   end 
 
   def test_Sam_header_parse_with_ok_comment_dont_raise
@@ -196,160 +179,173 @@ class SamTest < Test::Unit::TestCase
   end
 
   def test_Sam_each_with_ok_field_count_dont_raise
-    sam = Sam.new(SAM_TEST)
+    sam = Sam.new(StringIO.new(SAM_DATA))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_qname_raises
-    sam = Sam.new(" \t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new(" \t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_qname_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised(SamError) { sam.each }
   end
 
   def test_Sam_each_with_bad_flag_raises
-    sam = Sam.new("*\t-1\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t-1\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
 
-    sam = Sam.new("*\t65536\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t65536\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_flag_dont_raise
-    sam = Sam.new("*\t0\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t0\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t65535\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t65535\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_rname_raises
-    sam = Sam.new("*\t*\t \t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t \t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_rname_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_pos_raises
-    sam = Sam.new("*\t*\t*\t-1\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t-1\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
 
-    sam = Sam.new("*\t*\t*\t536870912\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t536870912\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_pos_dont_raise
-    sam = Sam.new("*\t*\t*\t0\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t0\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t536870911\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t536870911\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_mapq_raises
-    sam = Sam.new("*\t*\t*\t*\t-1\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t-1\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t256\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t256\t*\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_mapq_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t0\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t0\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t255\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t255\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_cigar_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t24\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24\t*\t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_cigar_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t24M2I3D\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24M2I3D\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_rnext_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t \t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t \t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_rnext_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t=\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t=\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t!\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t!\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_pnext_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t-1\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t-1\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t536870912\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t536870912\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_pnext_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t0\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t0\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t536870911\t*\t*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t536870911\t*\t*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_tlen_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t-536870912\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t-536870912\t*\t*\n"))
     assert_raise(SamError) { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t536870912\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t536870912\t*\t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_tlen_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t-536870911\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t-536870911\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t536870911\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t536870911\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_seq_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t \t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t \t*\n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_seq_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
     assert_nothing_raised { sam.each }
 
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\tATCGatcg=.\t*\n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\tATCGatcg=.\t*\n"))
     assert_nothing_raised { sam.each }
   end
 
   def test_Sam_each_with_bad_qual_raises
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t \n")
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t \n"))
     assert_raise(SamError) { sam.each }
   end
 
   def test_Sam_each_with_ok_qual_dont_raise
-    sam = Sam.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t@\n")
-    assert_nothing_raised(SamError) { sam.each }
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t@\n"))
+    assert_nothing_raised { sam.each }
+  end
+
+  def test_Sam_each_with_rname_missing_from_header_raises
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\tMIS\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
+    assert_raise(SamError) { sam.each }
+  end
+
+  def test_Sam_each_wtih_rname_present_in_header_dont_raise
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\tref\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
+    assert_nothing_raised { sam.each }
+
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
+    assert_nothing_raised { sam.each }
   end
 end