changed upper/lower case output in assemble_pairs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2151 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/out/assemble_pairs.out.1 b/bp_test/out/assemble_pairs.out.1
index 0c3a4128e71c0b5aa92dd27c17d4d9d1e2ef5535..f804cb79ea1d7699d5f1c6ac8f2296a8621ec445 100644 (file)
--- a/bp_test/out/assemble_pairs.out.1
+++ b/bp_test/out/assemble_pairs.out.1
@@ -1,33 +1,33 @@
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14862:1868 1:N:0:14:overlap=49:hamming=1
-SEQ: TGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATACCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAATTGTGAAGAAAAGTTAACGGTTAATAACCGTTAGCCTTGACGTTAACTTTAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGgaattactgggcgtaaagcgtgcgtaggcggtttattaagtcagatgtgAAAGCCCCGGGCTTAACCTGGGAACTGCATTTGAAACTGGTCAACTAGAGTATGGTAGAGGAAAGTGGAATTTCTGGTGTAGCGGTGAAATGCGTAGATATCAGAAGGAACATCAATGGCGAAGGCAGCTTTCTGGACCAATACTGACGCTGAGGTACGAAAGCGTGGGTAGCAAACAGG
+SEQ: tggggaatattggacaatgggggcaaccctgatccagcaataccgcgtgtgtgaagaaggcctgagggttgtaaagcactttcaattgtgaagaaaagttaacggttaataaccgttagccttgacgttaactttagaagaagcaccggctaactccgtgccagcagccgcggtaatacggagggtgcaagcgttaatcgGAATTACTGGGCGTAAAGCGTGCGTAGGCGGTTTATTAAGTCAGATGTGaaagccccgggcttaacctgggaactgcatttgaaactggtcaactagagtatggtagaggaaagtggaatttctggtgtagcggtgaaatgcgtagatatcagaaggaacatcaatggcgaaggcagctttctggaccaatactgacgctgaggtacgaaagcgtgggtagcaaacagg
 SEQ_LEN: 429
 SCORES: !??????BDDDDDDDDGGGGGGGHHIIIEHIHHFGGHFHHGHFHHDHEHEHHFAFFGFFHFHHFFHHHEFEEHHHHHHHHHHHHFFFHFHHHHHHHHHHHHGBDEGGGGGGGGGGGGGGGGEGEGGGGGCEGGGGECCECEEECGGG!ADGCGGGEGGEGGGGGEGCE8!2!DC!EEEGGC?!DGCCCEC:C?CCEGGGG??288<8B47>43,(195??=36)745<6.;:=?D?@6AB?@D8?@C=?AA;4'8D8?:::A?1*)=,,==EC==,,ACFCAAEBC=AEFCEBEDBDEEDED=EDD=?BFBFDFB!DFF@FFFHHHHHHHHHGGGDDHHHHFHDHIHHHHIIIIIHHFGCFFHHE!EEDFG?HIHGFGGFFFFF?CDCE?9FEHDHHGE;F;IHFFHFFFEEFDDDDDB!-!BB?????
 OVERLAP_LEN: 49
 HAMMING_DIST: 1
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14:overlap=96:hamming=2
-SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttggtggtgaaatcccagagcttaactctggaactgCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAATACCGATTGCGAAGGCAGCTTTCTGGATCATTACTGACGCTGAGGAACGAAAGCATGGGTAGCGAAGA
+SEQ: tagggaatcttgcacaatggaggaaactctgatgcagcgatgccgcgtgagtgaagaaggcctttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacgAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTGccatcaaaactttttagctagagtatgatagaggaaagcagaatttctagtgtagaggtgaaattcgtagatattagaaagaataccgattgcgaaggcagctttctggatcattactgacgctgaggaacgaaagcatgggtagcgaaga
 SEQ_LEN: 402
 SCORES: !???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHHEDDEGHHHCEHE?EFHFGHFHFHIHIIIHCECEHHHIFHIIIHGHFHHHHHHEEFFFFFEEFFFEFFFEEEEEFFFFFFFCEFBEEDEFFFFFFEFEFFEEFFFFDDDDA?EEEFFB@C?8B=:7785;660@?@FEB?7B;?2BBA?CED@@@B?=5@DEFD??;8@E0@BEC788>@?95*4-:=7BEB8B7BB2@B?8&+98>2CDBB>A=AEECCEEEEDB=FFEFEEEDEFFFBFFFFF?.HFDBDD?FFHFHFFFHFFFHHGGGGCBFAHHIHFHHHGCGGIIIHHHGE5!HFBDE@E@DGHHHFFFHIHHFFGFDC0?E?FHEHEHIIHHFHIHFHFFFFFFDDBDBADD?BB??!
 OVERLAP_LEN: 96
 HAMMING_DIST: 2
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14:overlap=96:hamming=0
-SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACgaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttggtggtgaaatcccagagcttaactctggaactGCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAATACCGATTGCGAAGGCAGCTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAAG
+SEQ: tagggaatcttgcacaatggaggaaactctgatgcagcgatgccgcgtgagtgaagaaggcctttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTgccatcaaaactttttagctagagtatgatagaggaaagcagaatttctagtgtagaggtgaaattcgtagatattagaaagaataccgattgcgaaggcagctttctggatcattactgacactgaggaacgaaagcatgggtagcgaag
 SEQ_LEN: 401
 SCORES: ?????BBBBBDDBDDBFFFFFFECHFHFHFHGHHFGD?!CFHHHHHH!DEEFFFFDFFHF@FHHHIFHEEHHHIIHHHIHIHHHDEHHHHFEEFFF?FEEEEFEEFFEE:!CEEFEFFFBEEEEEDEFE::AE:?AECEFEF?A!;D88;CEEEC@@668CCBC??C;8?+02>CEA>CB@;;?8@B@CCDE@D@?5@B>ABB:2::1>CDB=/@>BB@<19=4?6:7@A6@=?36875:8?A=DBDC@ACC;EEEEEEDEEDD;=DFB?FFDFFFB?C=FFFF?HHFDD@.DCFHHFHHHGFHHFHHGECBFFFEF?CHFGEA??HHHIHHHFC!E@DDEDDFHHHDHGGFBE?C=FF?CC?=F?CHFA9C0GBHFFHF;HFFF?FFBBBBB?BB?B??!
 OVERLAP_LEN: 96
 HAMMING_DIST: 0
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14:overlap=96:hamming=1
-SEQ: AGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACgaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttgatggtgaaatcccaaggctcaaccttggaactGCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGTGGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAACATCAAAAGCGAAGGCAACTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAAGAGG
+SEQ: agggaatcttgcacaatgggggaaaccctgatgcagcgatgccgcgtgagtgaagaaggcccttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGATGGTGAAATCCCAAGGCTCAACCTTGGAACTgccatcaaaactttttagctagagtatgatagaggaaagtggaatttctagtgtagaggtgaaattcgtagatattagaaagaacatcaaaagcgaaggcaactttctggatcattactgacactgaggaacgaaagcatgggtagcgaagagg
 SEQ_LEN: 403
 SCORES: !???B-!-?!BBBBBFFF;!CEEECC;EFFH=EGBE=CEFHD@CDCE!+!5C=FBAEADHFEHHHHHHECCG=CD=CCF=DC=DDACEE5:DEEEECBECEC3?3;?B:@CEEECEEC?CC????E?CAAAE?ACEEEEEEEE????A;)::ABCEB8CA669967)2955CA@=FEB=??<2:>?@6@7B7>449*<<9<957:9D;AD88;60?CEB2@8:;:B?>@749-663=<2-6<>46>A=64.EFEEEEDDEFBDDFFFFFFHHHHFFCC.?HFFCFHFDFDDFFGBBHHHHFGDHHGGBHIHHIIHHHDGHHHFECHHIIHFHGEA+HHFC@EHIIHHGFEGHHFGDHGDDC0?GGFGC90A0DBFFIIHFHFFFFFBBBBBDBB??BB?????
 OVERLAP_LEN: 96
 HAMMING_DIST: 1
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13072:2276 1:N:0:14:overlap=9:hamming=0
-SEQ: GGGAATTTTGCGCAATGGGCGAAAGCCTGACGCAGCAACGCCGCGGGATCGAAGAAGCTCTGCGGAGTGTAAAGATCTGTCATAAGGGAAGAATAACGAGTATTCTAACAAAATATTCGTCTGACGGTACCTTATAAGAAAGCCACGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAGGGGGGCAAGCGTTATCCGGAATCATTGGGCGTAAAGGGGTCGTATGAGGactgatcagTTGGAATTAAAAGACCGCGGCTTAACCGGGGGAACGGTTTCAATACTGTCAGTCTTGAGTGAGGTAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACATCAAAGGCGAAGGCAGCTTACTGGGCCTATACTGACGCTGAGGAACGAAAGCGTGGGGAGCAAAC
+SEQ: gggaattttgcgcaatgggcgaaagcctgacgcagcaacgccgcgggatcgaagaagctctgcggagtgtaaagatctgtcataagggaagaataacgagtattctaacaaaatattcgtctgacggtaccttataagaaagccacggctaacttcgtgccagcagccgcggtaatacgaggggggcaagcgttatccggaatcattgggcgtaaaggggtcgtatgaggACTGATCAGttggaattaaaagaccgcggcttaaccgggggaacggtttcaatactgtcagtcttgagtgaggtagaggtaagcggaattcctggtgtagcggtgaaatgcgtagatatcaggaggaacatcaaaggcgaaggcagcttactgggcctatactgacgctgaggaacgaaagcgtggggagcaaac
 SEQ_LEN: 425
 SCORES: ?????B?BB!-5@BC9CFFB!+C!C!E?@B=!,!5!FE,!77!CE)!!:CD=@DEFHDDBCFFEE8:=@,BD=,3;BEEEE?;BCCECCCE?B;?B3:AA88?:**:CAAA88:::::??8*)AC).8?)*:???:0?CEAAE8**4;8;AA:??:8:??8?EE:AC?;42.)4?*::8).'''..'.8C8A)8AAE:A;?'0:?CAEE?8''4A8?*8'0)''8*0*/:2?.?32;816666..//((6/'(.'''6(6;64-2'8(6///-'96;/(;8@;*78*;@@@@9**0*88;@0*2*9@3*D199;99DDD99D@EDECCDDDDDEEDD9EDDDDEEEDDEC!DE@AC5A=CCAE!5C9+E=@DB@DFFC=C+EEEA9.A999EC7@7-C!A/ECAAEEEEEEC@@@@@-5-!!!!!
 OVERLAP_LEN: 9

diff --git a/bp_test/out/assemble_pairs.out.2 b/bp_test/out/assemble_pairs.out.2
index af608609268c1fdf4fb9e674ddbcbb7dc55f3736..1bf0ec54c1b533dd035944f89d9d5299212bb12b 100644 (file)
--- a/bp_test/out/assemble_pairs.out.2
+++ b/bp_test/out/assemble_pairs.out.2
@@ -1,19 +1,19 @@
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:13906:2139 1:N:0:14:overlap=96:hamming=2
-SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttggtggtgaaatcccagagcttaactctggaactgCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAATACCGATTGCGAAGGCAGCTTTCTGGATCATTACTGACGCTGAGGAACGAAAGCATGGGTAGCGAAGA
+SEQ: tagggaatcttgcacaatggaggaaactctgatgcagcgatgccgcgtgagtgaagaaggcctttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacgAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTGccatcaaaactttttagctagagtatgatagaggaaagcagaatttctagtgtagaggtgaaattcgtagatattagaaagaataccgattgcgaaggcagctttctggatcattactgacgctgaggaacgaaagcatgggtagcgaaga
 SEQ_LEN: 402
 SCORES: !???9?BBBDBDDBDDFFFFFFHHHIFHFHHIHHFHHHHEDDEGHHHCEHE?EFHFGHFHFHIHIIIHCECEHHHIFHIIIHGHFHHHHHHEEFFFFFEEFFFEFFFEEEEEFFFFFFFCEFBEEDEFFFFFFEFEFFEEFFFFDDDDA?EEEFFB@C?8B=:7785;660@?@FEB?7B;?2BBA?CED@@@B?=5@DEFD??;8@E0@BEC788>@?95*4-:=7BEB8B7BB2@B?8&+98>2CDBB>A=AEECCEEEEDB=FFEFEEEDEFFFBFFFFF?.HFDBDD?FFHFHFFFHFFFHHGGGGCBFAHHIHFHHHGCGGIIIHHHGE5!HFBDE@E@DGHHHFFFHIHHFFGFDC0?E?FHEHEHIIHHFHIHFHFFFFFFDDBDBADD?BB??!
 OVERLAP_LEN: 96
 HAMMING_DIST: 2
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:14865:2158 1:N:0:14:overlap=96:hamming=0
-SEQ: TAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCTTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACgaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttggtggtgaaatcccagagcttaactctggaactGCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAATACCGATTGCGAAGGCAGCTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAAG
+SEQ: tagggaatcttgcacaatggaggaaactctgatgcagcgatgccgcgtgagtgaagaaggcctttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAATCCCAGAGCTTAACTCTGGAACTgccatcaaaactttttagctagagtatgatagaggaaagcagaatttctagtgtagaggtgaaattcgtagatattagaaagaataccgattgcgaaggcagctttctggatcattactgacactgaggaacgaaagcatgggtagcgaag
 SEQ_LEN: 401
 SCORES: ?????BBBBBDDBDDBFFFFFFECHFHFHFHGHHFGD?!CFHHHHHH!DEEFFFFDFFHF@FHHHIFHEEHHHIIHHHIHIHHHDEHHHHFEEFFF?FEEEEFEEFFEE:!CEEFEFFFBEEEEEDEFE::AE:?AECEFEF?A!;D88;CEEEC@@668CCBC??C;8?+02>CEA>CB@;;?8@B@CCDE@D@?5@B>ABB:2::1>CDB=/@>BB@<19=4?6:7@A6@=?36875:8?A=DBDC@ACC;EEEEEEDEEDD;=DFB?FFDFFFB?C=FFFF?HHFDD@.DCFHHFHHHGFHHFHHGECBFFFEF?CHFGEA??HHHIHHHFC!E@DDEDDFHHHDHGGFBE?C=FF?CC?=F?CHFA9C0GBHFFHF;HFFF?FFBBBBB?BB?B??!
 OVERLAP_LEN: 96
 HAMMING_DIST: 0
 ---
 SEQ_NAME: M01168:16:000000000-A1R9L:1:1101:17246:2253 1:N:0:14:overlap=96:hamming=1
-SEQ: AGGGAATCTTGCACAATGGGGGAAACCCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACgaagggacctagcgtagttcggaattactgggcttaaagagttcgtaggtggttaaaaaagttgatggtgaaatcccaaggctcaaccttggaactGCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGTGGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAACATCAAAAGCGAAGGCAACTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAAGAGG
+SEQ: agggaatcttgcacaatgggggaaaccctgatgcagcgatgccgcgtgagtgaagaaggcccttgggttgtaaagctctttcgtcggggaagaaaatgactgtacccgaataagaaggtccggctaacttcgtgccagcagccgcggtaatacGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGATGGTGAAATCCCAAGGCTCAACCTTGGAACTgccatcaaaactttttagctagagtatgatagaggaaagtggaatttctagtgtagaggtgaaattcgtagatattagaaagaacatcaaaagcgaaggcaactttctggatcattactgacactgaggaacgaaagcatgggtagcgaagagg
 SEQ_LEN: 403
 SCORES: !???B-!-?!BBBBBFFF;!CEEECC;EFFH=EGBE=CEFHD@CDCE!+!5C=FBAEADHFEHHHHHHECCG=CD=CCF=DC=DDACEE5:DEEEECBECEC3?3;?B:@CEEECEEC?CC????E?CAAAE?ACEEEEEEEE????A;)::ABCEB8CA669967)2955CA@=FEB=??<2:>?@6@7B7>449*<<9<957:9D;AD88;60?CEB2@8:;:B?>@749-663=<2-6<>46>A=64.EFEEEEDDEFBDDFFFFFFHHHHFFCC.?HFFCFHFDFDDFFGBBHHHHFGDHHGGBHIHHIIHHHDGHHHFECHHIIHFHGEA+HHFC@EHIIHHGFEGHHFGDHGDDC0?GGFGC90A0DBFFIIHFHFFFFFBBBBBDBB??BB?????
 OVERLAP_LEN: 96

diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm
index eb8beac9522706d66c92afe41ee4e08ff54011a0..d689f9c6fc2682f2a03db14517e49c890085e413 100644 (file)
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -505,6 +505,8 @@ sub biopiece2bed
 
     if ( exists $bp_record->{ "SCORE" } ) {
         $bed_entry[ score ] = $bp_record->{ "SCORE" };
+    } elsif ( exists $bp_record->{ "BIT_SCORE" } ) {
+        $bed_entry[ score ] = $bp_record->{ "BIT_SCORE" };
     } else {
         return wantarray ? @bed_entry : \@bed_entry;
     }

diff --git a/code_ruby/lib/maasha/seq/assemble.rb b/code_ruby/lib/maasha/seq/assemble.rb
index 7b02d03a61a827782a802ade399ebd5c378105cb..016322727cf15eb824f9e3f0518cca9b2ecb0241 100644 (file)
--- a/code_ruby/lib/maasha/seq/assemble.rb
+++ b/code_ruby/lib/maasha/seq/assemble.rb
@@ -64,8 +64,9 @@ class Assemble
           entry_overlap = @entry1[-1 * overlap .. -1]
         end
 
-        entry_left.seq.upcase!
-        entry_right.seq.upcase!
+        entry_left.seq.downcase!
+        entry_overlap.seq.upcase!
+        entry_right.seq.downcase!
         entry_merged          = entry_left + entry_overlap + entry_right
         entry_merged.seq_name = @entry1.seq_name + ":overlap=#{overlap}:hamming=#{hamming_dist}"
 

diff --git a/code_ruby/test/maasha/seq/test_assemble.rb b/code_ruby/test/maasha/seq/test_assemble.rb
index e4901b4d2e6a66710e9fb4c5bcf52898fab990f3..b5ddb7d706c03b3b4ea633149b8e55f7741785e6 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_assemble.rb
+++ b/code_ruby/test/maasha/seq/test_assemble.rb
@@ -12,19 +12,19 @@ class TestAssemble < Test::Unit::TestCase
   end
 
   test "Assemble.pair with overlap returns the correctly" do
-    assert_equal("ATCgATC", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
-    assert_equal("ATcgAT",  Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
-    assert_equal("AtcgA",   Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
-    assert_equal("atcg",    Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
+    assert_equal("atcGatc", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc")).seq)
+    assert_equal("atCGat",  Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat")).seq)
+    assert_equal("aTCGa",   Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga")).seq)
+    assert_equal("ATCG",    Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg")).seq)
   end
 
   test "Assemble.pair with overlap and overlap_min returns correctly" do
     assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "gatc"), :overlap_min => 2))
-    assert_equal("ATcgAT", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
+    assert_equal("atCGat", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "cgat"), :overlap_min => 2).seq)
   end
 
   test "Assemble.pair with overlap and overlap_max returns correctly" do
-    assert_equal("AtcgA", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
+    assert_equal("aTCGa", Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "tcga"), :overlap_max => 3).seq)
     assert_nil(Assemble.pair(Seq.new("test1", "atcg"), Seq.new("test2", "atcg"), :overlap_max => 3))
   end
 
@@ -35,7 +35,7 @@ class TestAssemble < Test::Unit::TestCase
   end
 
   test "Assemble.pair with mismatch returns the highest scoring" do
-    assert_equal("atcga", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
-    assert_equal("attga", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)
+    assert_equal("ATCGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "IIIII"), Seq.new("t2", "attga", :dna, "55555"), :mismatches_max => 20).seq)
+    assert_equal("ATTGA", Assemble.pair(Seq.new("t1", "atcga", :dna, "55555"), Seq.new("t2", "attga", :dna, "IIIII"), :mismatches_max => 20).seq)
   end
 end