BioPerl Sequence Object -- test code... Testing Seq.pm output formats ----------------------- Creating new object from sample.tfa... Dumping contents of object.. ID : sample Type :Dna Monomer :1 Origin :UnknownOrigin Seq :aaaacctatggggtgggctctcaagctgagaccctgtgtgcacagccctctggctggtggcagtggagacgggatnnnatgacaagcctgggggacatgaccccagagaaggaacgggaacaggatgagtgagaggaggttctaaattatccattagcacaggctgccagtggtccttgcataaatgtatagagcacacaggtggggggaaagggagagagagaagaagccagggtataa Format :7 Numbering:1 Desc :Sample Bio::Seq sequence Descffmt :7 Names - none = none Isolate = 5 Location = /usr2/users/dag/bioperl/sample.tfa Tissue = Xenopus CloneID = DB1 Testing default GCG layout... Sample Bio::Seq sequence sample Length: 240 Tue Feb 11 20:48:01 EST 1997 Type: N Check: 5371 .. 1 aaaacctatg gggtgggctc tcaagctgag accctgtgtg cacagccctc 51 tggctggtgg cagtggagac gggatnnnat gacaagcctg ggggacatga 101 ccccagagaa ggaacgggaa caggatgagt gagaggaggt tctaaattat 151 ccattagcac aggctgccag tggtccttgc ataaatgtat agagcacaca 201 ggtgggggga aagggagaga gagaagaagc cagggtataa About to call out_GCG() directly with named parameters... This is a user submitted header New ID (doublespaced) Length: 240 DATE GOES HERE Type: N Check: 1291 .. 1 AAAACCTATG GGGTGGGCTC TCAAGCTGAG ACCCTGTGTG CACAGCCCTC 51 TGGCTGGTGG CAGTGGAGAC GGGATNNNAT GACAAGCCTG GGGGACATGA 101 CCCCAGAGAA GGAACGGGAA CAGGATGAGT GAGAGGAGGT TCTAAATTAT 151 CCATTAGCAC AGGCTGCCAG TGGTCCTTGC ATAAATGTAT AGAGCACACA 201 GGTGGGGGGA AAGGGAGAGA GAGAAGAAGC CAGGGTATAA Testing default Primer format: *seq: sample # Sample Bio::Seq sequence # sample aaaacctatg gggtgggctc tcaagctgag accctgtgtg cacagccctc tggctggtgg cagtggagac gggatnnnat gacaagcctg ggggacatga ccccagagaa ggaacgggaa caggatgagt gagaggaggt tctaaattat ccattagcac aggctgccag tggtccttgc ataaatgtat agagcacaca ggtgggggga aagggagaga gagaagaagc cagggtataa Testing GenBank format with named parameters: LOCUS sample 240 Dna Tue Feb 11 20:48:01 EST 1997 DEFINITION This is a new definition ACCESSION xxx0000 ORIGIN UnknownOrigin 1 AAAACCTATG GGGTGGGCTC TCAAGCTGAG ACCCTGTGTG CACAGCCCTC 51 TGGCTGGTGG CAGTGGAGAC GGGATNNNAT GACAAGCCTG GGGGACATGA 101 CCCCAGAGAA GGAACGGGAA CAGGATGAGT GAGAGGAGGT TCTAAATTAT 151 CCATTAGCAC AGGCTGCCAG TGGTCCTTGC ATAAATGTAT AGAGCACACA 201 GGTGGGGGGA AAGGGAGAGA GAGAAGAAGC CAGGGTATAA // Testing GenBank default layout format: LOCUS sample 240 Dna Tue Feb 11 20:48:01 EST 1997 DEFINITION Sample Bio::Seq sequence ORIGIN UnknownOrigin 1 aaaacctatg gggtgggctc tcaagctgag accctgtgtg cacagccctc 51 tggctggtgg cagtggagac gggatnnnat gacaagcctg ggggacatga 101 ccccagagaa ggaacgggaa caggatgagt gagaggaggt tctaaattat 151 ccattagcac aggctgccag tggtccttgc ataaatgtat agagcacaca 201 ggtgggggga aagggagaga gagaagaagc cagggtataa // Testing PIR default layout format: ENTRY sample TITLE Sample Bio::Seq sequence DATE Tue Feb 11 20:48:01 EST 1997 SEQUENCE 5 10 15 20 25 30 1 a a a a c c t a t g g g g t g g g c t c t c a a g c t g a g 31 a c c c t g t g t g c a c a g c c c t c t g g c t g g t g g 61 c a g t g g a g a c g g g a t n n n a t g a c a a g c c t g 91 g g g g a c a t g a c c c c a g a g a a g g a a c g g g a a 121 c a g g a t g a g t g a g a g g a g g t t c t a a a t t a t 151 c c a t t a g c a c a g g c t g c c a g t g g t c c t t g c 181 a t a a a t g t a t a g a g c a c a c a g g t g g g g g g a 211 a a g g g a g a g a g a g a a g a a g c c a g g g t a t a a /// Testing PIR format w/ named parameters: ENTRY This is MY ENTRY TITLE MY CLONE ACCESSION some number goes here DATE April 1 2020 REFERENCE reference goes here SEQUENCE 5 10 15 20 25 30 1 a a a a c c t a t g g g g t g g g c t c t c a a g c t g a g 31 a c c c t g t g t g c a c a g c c c t c t g g c t g g t g g 61 c a g t g g a g a c g g g a t n n n a t g a c a a g c c t g 91 g g g g a c a t g a c c c c a g a g a a g g a a c g g g a a 121 c a g g a t g a g t g a g a g g a g g t t c t a a a t t a t 151 c c a t t a g c a c a g g c t g c c a g t g g t c c t t g c 181 a t a a a t g t a t a g a g c a c a c a g g t g g g g g g a 211 a a g g g a g a g a g a g a a g a a g c c a g g g t a t a a ///