dna_sequence_aligner 0.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (24) hide show
  1. data/.gitignore +8 -0
  2. data/History +10 -0
  3. data/LICENSE +22 -0
  4. data/README.rdoc +58 -0
  5. data/Rakefile +45 -0
  6. data/VERSION +1 -0
  7. data/bin/dna_sequence_aligner +61 -0
  8. data/bin/dna_translator.rb +59 -0
  9. data/lib/bio/alignment/dna_sequence.rb +313 -0
  10. data/older/align_all.rb +160 -0
  11. data/older/align_to_template.rb +143 -0
  12. data/reference/clustalw_opts.txt +73 -0
  13. data/script/fasta_compile_annotated.rb +19 -0
  14. data/spec/align_spec.rb +67 -0
  15. data/spec/spec_helper.rb +6 -0
  16. data/spec/testfiles/HA-mKSR1-KSRF1.txt +19 -0
  17. data/spec/testfiles/HA-mKSR1-KSRF2.txt +20 -0
  18. data/spec/testfiles/HA-mKSR1-KSRF3.txt +20 -0
  19. data/spec/testfiles/HA-mKSR1-KSRF4.txt +20 -0
  20. data/spec/testfiles/HA-mKSR1-KSRF5.txt +20 -0
  21. data/spec/testfiles/HA-mKSR1-OXL33.txt +20 -0
  22. data/spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta +77 -0
  23. data/spec/testfiles/testcase.fasta +55 -0
  24. metadata +99 -0
data/spec/spec_helper.rb ADDED
@@ -0,0 +1,6 @@
1
+ require 'rubygems'
2
+ require 'spec/more'
3
+
4
+ TESTFILES = File.expand_path(File.dirname(__FILE__) + '/testfiles')
5
+
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+ Bacon.summary_on_exit
data/spec/testfiles/HA-mKSR1-KSRF1.txt ADDED
@@ -0,0 +1,19 @@
1
+ >100122-36_G07_HA-mKSR1-KSRF1.ab1 950 [cut-JTP]
2
+ GNNNNNCCAGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAG
3
+ CCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGGTGACTGGCCTGGGAG
4
+ GGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGATGCTCGAGACAGT
5
+ AGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGC
6
+ CAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAG
7
+ ACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCGGACTCCTGTATCCCC
8
+ TTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATCAC
9
+ GCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAA
10
+ GGACACCCCCACCGCCAAGCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTC
11
+ CCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCTGGGAAACCGAAT
12
+ CGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGC
13
+ TGGTACGAAGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAG
14
+ TCATGGTTGTCACAGGTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGG
15
+ CGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAAGG
16
+ AAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGG
17
+ ACAGAGTCTGTCCCGTCAGATATCAACAACCCAGTGGACAGAGCAGCAGA
18
+ GCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTC
19
+ CAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCC
data/spec/testfiles/HA-mKSR1-KSRF2.txt ADDED
@@ -0,0 +1,20 @@
1
+ >100122-36_I07_HA-mKSR1-KSRF2.ab1 950
2
+ NNTNANCGCANGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGG
3
+ AGCAAGTCCCACGAGTCCCAGCTGGGAAACCGAATCGACGACGTCACCCC
4
+ GATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGAAGGGATA
5
+ TCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAG
6
+ GTGTGCAACGTGTGCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACA
7
+ CTGCAGGTTAAAATGCCATAACAAGTGCACAAAGGAAGCTCCCGCCTGCA
8
+ GGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCG
9
+ TCAGATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAAC
10
+ CCTTCCCAAGGCCCTGACAAAGAAGGAGCACCCTCCAGCCATGAACCTGG
11
+ ACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTCATCGCCG
12
+ GCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAA
13
+ CCCGTCACCTGGCCAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAG
14
+ CCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAGCCGACAGTACACGGCTC
15
+ GACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGGCTGA
16
+ GGAGCCTGAGGCTGGCAAGTCAGAGGCAGAGGATGACGAGGAGGATGAGG
17
+ TGGACGACCTCCCCAGCTCCCGCCGGCCCTGGAGGGGCCCCATCTCTCGA
18
+ AAGGCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCCCCTTTGA
19
+ ACAGGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGC
20
+ ACCGAGCCGTTGGCATGGCGAGGTGGNATTCGGCTGCTGGAGATGGANGN
data/spec/testfiles/HA-mKSR1-KSRF3.txt ADDED
@@ -0,0 +1,20 @@
1
+ >100122-36_K07_HA-mKSR1-KSRF3.ab1 950
2
+ NNNNNAGNCTGGGCANTCAGAGGCAGAGGANGACGAGGAGGATGAGGTGG
3
+ ACGACCTCCCCAGCTCCCGCCGGCCCTGGAGGGGCCCCATCTCTCGAAAG
4
+ GCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCCCCTTTGAACA
5
+ GGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGCACC
6
+ GAGGCCGTTGGCATGGCGAGGTGGCCATTCGGCTGCTGGAGATGGACGGC
7
+ CACAATCAGGACCACCTGAAGCTGTTCAAGAAAGAGGTGATGAACTACCG
8
+ GCAGACGCGGCATGAGAACGTGGTGCTCTTCATGGGGGCCTGCATGAACC
9
+ CACCTCACCTGGCCATTATCACCAGCTTCTGCAAGGGGCGGACATTGCAT
10
+ TCATTCGTGAGGGACCCCAAGACGTCTCTGGACATCAATAAGACTAGGCA
11
+ GATCGCCCAGGAGATCATCAAGGGCATGGGTTATCTTCATGCAAAAGGCA
12
+ TCGTGCACAAGGACCTCAAGTCCAAGAATGTCTTCTATGACAACGGCAAA
13
+ GTGGTCATCACAGACTTCGGGCTGTTTGGGATCTCGGGTGTGGTCCGAGA
14
+ GGAACGGCGCGAGAACCAACTGAAACTGTCACATGACTGGCTGTGCTACC
15
+ TGGCCCCCGAGATCGTACGAGAAATGATCCCAGGGCGGGACGAGGACCAG
16
+ CTGCCCTTCTCCAAAGCAGCCGATGTCTATGCATTCGGGACTGTGTGGTA
17
+ TGAACTACAGGCAAGAGACTGGCCCTTTAAGCACCAGCCTGCTGAGGCCT
18
+ TGATCTGGCAGATTGGAAGTGGGGAAGGAGTACGGCGCGTCCTGCATCCG
19
+ TCAGCCTGGGGAAGGAGTCGGCGAGATCCTGTCTGCCTGCTGGGCTTTCG
20
+ ATCTGCAGGAGAGACCCAGCTTCAGCCTGCTGATGGACATGCTGGAGAAG
data/spec/testfiles/HA-mKSR1-KSRF4.txt ADDED
@@ -0,0 +1,20 @@
1
+ >100122-36_M07_HA-mKSR1-KSRF4.ab1 950
2
+ CNNNNNAAANAAANTTGTTCCGGGGGGGGGAGGAGAANGGCTCCCTTTCT
3
+ CAAACCACCAAATTTTTATGCTTTGGGGAGGGGGGGGAAAAAACAACGGG
4
+ AAAAAGAGGGCCTTTTAAACCCCCCCCCTGGTGAGGTTTTTTTGGGAAAA
5
+ ATGGAAGGGGGGGAGGGAGTGGGGCGCGCCCTGCCCCCCGTCCGCGGGGG
6
+ AAAGGAAGGGGGAAAGTTCTTGTGTGCGGGGGGGTTTTTCTTTCGGGAGA
7
+ AAACCCCCTCTTCCCCCCTGTTGAGGAACTTGGGGAAGGGGCTCCCAAAG
8
+ CTGACCGGGCGCTTCCCCCCCCGGGGGCTTTTTGGAAGGTGGGCTAATTT
9
+ AAACACCAAAAAATTCTCCCCCCTTTTAAAAGGGTTGGCCGGGGGCCCCG
10
+ GGGACCCGGGAAACCAAAAATTGTGGGGCGCCCCCCACCAGGGGGCCCGG
11
+ GGTTTCGGGGGGGGCAATTTCCCCCCCTCCCCCCCCAACCCCTCCCCGCC
12
+ CGTTTTAATAATTTTGGGGGAAAACCCCGTTAGAAATAGGGCGGGGGTGT
13
+ TTTTTTTTTTTTTTTTTTTCCCCCCATTTGGCCTTTTTGGGAAAGGGGGG
14
+ GGGCCGGAAAACGGGCCCTTTTTTTTTGGAAAATTTTCTGGGGGTTTTTC
15
+ CCCCTCTCCAAAAAGAAATGCAGGGTTTGTAAATTGTCATGAAAAAATCT
16
+ TTTCCTCTGAAATTTTTTTAAAAAAAAACAACTTCTGTAGCGACTTTTTG
17
+ CAGGCAGCGAAACCCCCCCCTGGCGACGGGTCCTTCTGCGGAAAAACCCA
18
+ TGTGTAAAAATACNCGGGAAAGCGCGGNACACCNNNTCGCATGTNNTGAT
19
+ TTGTATATTNNAGAAAAAAAGAAAGTGTCTCTCCTCGAGCTTATTAAAGA
20
+ GGGGNTANGGGATGCCNAGAGGCCCCCNNTGTANNGNNTCTGTCGGGGGN
data/spec/testfiles/HA-mKSR1-KSRF5.txt ADDED
@@ -0,0 +1,20 @@
1
+ >100122-36_O07_HA-mKSR1-KSRF5.ab1 950
2
+ GGTTTTNTNACTGGCTGTGCTACCTGGCCCCGAGATCGTACGAGAAATGA
3
+ TCCCAGGGCGGGACGAGGACCAGCTGCCCTTCTCCAAAGCAGCCGATGTC
4
+ TATGCATTCGGGACTGTGTGGTATGAACTACAGGCAAGAGACTGGCCCTT
5
+ TAAGCACCAGCCTGCTGAGGCCTTGATCTGGCAGATTGGAAGTGGGGAAG
6
+ GAGTACGGCGCGTCCTGGCATCCGTCAGCCTGGGGAAGGAAGTCGGCGAG
7
+ ATCCTGTCTGCCTGCTGGGCTTTCGATCTGCAGGAGAGACCCAGCTTCAG
8
+ CCTGCTGATGGACATGCTGGAGAGGCTGCCCAAGCTGAACCGGCGGCTCT
9
+ CCCACCCTGGGCACTTTTGGAAGTCGGCTGACATTAACAGCAGCAAAGTC
10
+ ATGCCCCGCTTTGAAAGGTTTGGCCTGGGGACCCTGGAGTCCGGTAATCC
11
+ AAAGATGTAGTGCGGCCGCCAGCACAGTGGCCATGGCATCTAGGGCGGCC
12
+ AATTCCGCCCTCNTTCCCCCCCCACCCTCTCCCTCCCCCCTGTAACGTTA
13
+ CTGGCCGAAGCCGCTTGGAATAAGGCCGGTGTGCGTTTGTCTATATGTTA
14
+ TTTTCCACCATATTGCCGTCTTTTGGCAATGTGAGGGCCCGGAAACCTGG
15
+ CCCTGTCTTCTTGACGAGCATTCCTAGGGGTCTTTCCCCTCTCGCCAAAG
16
+ GAATGCAAGGTCTGTTGAATGTCGTGAAGGAAGCAGTTCCTCTGGAAGCT
17
+ TCTTGAAGACAAACAACGTCTGTAGCGACCCTTTGCAGGCAGCGGAACCC
18
+ CCCACCTGGCGACAGGTGCCTCTGCGGCCAAAAGCCACGTGTATAAGATA
19
+ CACCTGCAAAGGCGGCACAACCCCAGTGCCACGTTGTGAGTTGGATAGTT
20
+ GTGGAAAGAGTCAAATGGCTCTCCCTCAAGCGTATTCAACAAGGGGCTGA
data/spec/testfiles/HA-mKSR1-OXL33.txt ADDED
@@ -0,0 +1,20 @@
1
+ >100122-36_E07_HA-mKSR1-OXL33.ab1 950
2
+ CNCNCNNGNNCNNCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCA
3
+ TCCTCTAGACTGCCGGATCCCAGTGTGGTGGTACGGGAATTATGTACCCA
4
+ TACGATGTTCCAGATTACGCTCTTATGGCCATGGAGGCCCGAATTCAAAT
5
+ GGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCG
6
+ GCGGCGGGGGCGCCGCGGCGGATGGGGGCGCAGGGGCCGCCGTCAGCCGG
7
+ GCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTCATCGATATCTCCATCGG
8
+ CAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACAC
9
+ AGCAGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAG
10
+ CAGCAGCAGAGCAAGCTTAGTGTGACCCCAAGCGACAGGACCGCCGAGCT
11
+ CAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAACGTGAGGC
12
+ CTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTG
13
+ GAGATGGACGAGGCCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAG
14
+ CACGGAGGAGTGCAGCCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGG
15
+ TGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACA
16
+ GATGCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCT
17
+ GGGCAGAGCGGGTGCCAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCG
18
+ CCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCG
19
+ GACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCT
20
+ GCACAGCTTCATCACGCCCCCTACCACACCCCAGCTACGACAGCACGCCA
data/spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta ADDED
@@ -0,0 +1,77 @@
1
+ >HA-mKSR1-pREX-CD2 NM_013571.2
2
+ # this is the leader found in the pRex vector
3
+ GCTTGGATACACGCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCATCCTCTAGACTGCC
4
+ # BamHI
5
+ GGATCC
6
+ CAGTGTGGTGGTAGGGAATTA
7
+ # this is the HA tag itself
8
+ ATGTACCCATACGATGTTCCAGATTACGCT
9
+ CTTATGGCCATGGAGGCCCGAATTC
10
+ # not sure how to account for these two A's but there they are
11
+ AA
12
+ # EXTRA BAGGAGE:
13
+ #GGTCGACCGAGATCTCTCGAGGTACC
14
+ # NotI cleavage site
15
+ #GCGGCCGC
16
+ #CAGCACAGTGGCCATGGCATCTAG
17
+ #This is the 5' UTR in mouse
18
+ #CTCGGGGCTTTCCTGCCGAGGCGCCCGTGTCCCCGGGCTCCTCGCCTCGGCCCCCAGCGGCCCCGATGCCGAGGC
19
+ #This is where translation actually begins:
20
+ ATGGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCGGCGGCGGGGGCGC
21
+ CGCGGCGGACGGGGGCGCAGGGGCCGCCGTCAGCCGGGCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTC
22
+ ATCGATATCTCCATCGGCAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACACAGC
23
+ AGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAGCAGCAGCAGAGCAAGCTTAGTGT
24
+ GACCCCAAGCGACAGGACCGCCGAGCTCAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAAC
25
+ GTGAGGCCTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTGGAGATGGACGAGG
26
+ CCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAGCCGCCTACAGCAAGCCCT
27
+ TACCTGCCTTCGGAAGGTGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGAT
28
+ GCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGCCAGCACTC
29
+ AGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGG
30
+ CCTCTCGGACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATC
31
+ ACGCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAAGGACACCCCCACCGCCAA
32
+ GCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCT
33
+ GGGAAACCGAATCGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGA
34
+ AGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGT
35
+ GCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAA
36
+ GGAAGCTCCCGCCTGCAGGATCACCTTCCTCCCACTGGCCAGGCTTCGGAGGACAGAGTCTGTCCCGTCA
37
+ GATATCAACAACCCAGTGGACAGAGCAGCAGAGCCCCATTTTGGAACCCTTCCCAAGGCCCTGACAAAGA
38
+ AGGAGCACCCTCCAGCCATGAACCTGGACTCCAGCAGCAACCCATCCTCCACCACGTCCTCCACACCCTC
39
+ ATCGCCGGCACCTTTCCTGACCTCATCTAATCCCTCCAGTGCCACCACGCCTCCCAACCCGTCACCTGGC
40
+ CAGCGGGACAGCAGGTTCAGCTTCCCAGACATTTCAGCCTGTTCTCAGGCAGCCCCGCTGTCCAGCACAG
41
+ CCGACAGTACACGGCTCGACGACCAGCCCAAAACAGATGTGCTAGGTGTTCACGAAGCAGAGGCTGAGGA
42
+ GCCTGAGGCTGGCAAGTCAGAGGCAGAGGATGACGAGGAGGATGAGGTGGACGACCTCCCCAGCTCCCGC
43
+ CGGCCCTGGAGGGGCCCCATCTCTCGAAAGGCCAGCCAGACCAGCGTTTACCTGCAAGAGTGGGACATCC
44
+ CCTTTGAACAGGTGGAACTGGGCGAGCCCATTGGACAGGGTCGCTGGGGCCGGGTGCACCGAGGCCGTTG
45
+ GCATGGCGAGGTGGCCATTCGGCTGCTGGAGATGGACGGCCACAATCAGGACCACCTGAAGCTGTTCAAG
46
+ AAAGAGGTGATGAACTACCGGCAGACGCGGCATGAGAACGTGGTGCTCTTCATGGGGGCCTGCATGAACC
47
+ CACCTCACCTGGCCATTATCACCAGCTTCTGCAAGGGGCGGACATTGCATTCATTCGTGAGGGACCCCAA
48
+ GACGTCTCTGGACATCAATAAGACTAGGCAGATCGCCCAGGAGATCATCAAGGGCATGGGTTATCTTCAT
49
+ GCAAAAGGCATCGTGCACAAGGACCTCAAGTCCAAGAATGTCTTCTATGACAACGGCAAAGTGGTCATCA
50
+ CAGACTTCGGGCTGTTTGGGATCTCGGGTGTGGTCCGAGAGGAACGGCGCGAGAACCAACTGAAACTGTC
51
+ ACATGACTGGCTGTGCTACCTGGCCCCCGAGATCGTACGAGAAATGATCCCGGGGCGGGACGAGGACCAG
52
+ CTGCCCTTCTCCAAAGCAGCCGATGTCTATGCATTCGGGACTGTGTGGTATGAACTACAGGCAAGAGACT
53
+ GGCCCTTTAAGCACCAGCCTGCTGAGGCCTTGATCTGGCAGATTGGAAGTGGGGAAGGAGTACGGCGCGT
54
+ CCTGGCATCCGTCAGCCTGGGGAAGGAAGTCGGCGAGATCCTGTCTGCCTGCTGGGCTTTCGATCTGCAG
55
+ GAGAGACCCAGCTTCAGCCTGCTGATGGACATGCTGGAGAGGCTGCCCAAGCTGAACCGGCGGCTCTCCC
56
+ ACCCTGGGCACTTTTGGAAGTCGGCTGACATTAACAGCAGCAAAGTCATGCCCCGCTTTGAAAGGTTTGG
57
+ CCTGGGGACCCTGGAGTCCGGTAATCCAAAGATGTAGCCAGCCCTGCACGTTCATGCAGAGAGTGTCTTC
58
+ CTTTCGAAAACATGATCACGAAACATGCAGACCACCACCTCAAGGAATCAGAAGCATTGCATCCCAAGCT
59
+ GCGGACTGGGAGCGTGTCTCCTCCCTAAAGGACGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCG
60
+ TCACCAAGGTGTGTGGAGCTCAGGATCGCAGCCATACACGCAACTCCAGATGATACCACTACCGCCAGTG
61
+ TTTACACAGAGGTTTCTGCCTGGCAAGCTTGGTATTTTACAGTAGGTGAAGATCATTCTGCAGAAGGGTG
62
+ CTGGCACAGTGGAGCAGCACGGATGTCCCCAGCCCCCGTTCTGGAAGACCCTACAGCTGTGAGAGGCCCA
63
+ GGGTTGAGCCAGATGAAAGAAAAGCTGCGTGGGTGTGGGCTGTACCCGGAAAAGGGCAGGTGGCAGGAGG
64
+ TTTGCCTTGGCCTGTGCTTGGGCCGAGAACCACACTAAGGAGCAGCAGCCTGAGTTAGGAATCTATCTGG
65
+ ATTACGGGGATCAGAGTTCCTGGAGAGTGGACTCAGTTTCTGCTCTGATCCAGGCCTGTTGTGCTTTTTT
66
+ TTTTTCCCCCTTAAAAAAAAAAAAGTACAGACAGAATCTCAGCGGCTTCTAGACTGATCTGATGGATCTT
67
+ AGCCCGGCTTCTACTGCGGGGGGGAGGGGGGGAGGGATAGCCACATATCTGTGGAGACACCCACTTCTTT
68
+ ATCTGAGGCCTCCAGGTAGGCACAAAGGCTGTGGAACTCAGCCTCTATCATCAGACACCCCCCCCCAATG
69
+ CCTCATTGACCCCCTTCCCCCAGAGCCAAGGGCTAGCCCATCGGGTGTGTGTACAGTAAGTTCTTGGTGA
70
+ AGGAGAACAGGGACGTTGGCAGAAGCAGTTTGCAGTGGCCCTAGCATCTTAAAACCCATTGTCTGTCACA
71
+ CCAGAAGGTTCTAGACCTACCACCACTTCCCTTCCCCATCTCATGGAAACCTTTTAGCCCATTCTGACCC
72
+ CTGTGTGTGCTCTGAGCTCAGATCGGGTTATGAGACCGCCCAGGCACATCAGTCAGGGAGGCTCTGATGT
73
+ GAGCCGCAGACCTCTGTGTTCATTCCTATGAGCTGGAGGGGCTGGACTGGGTGGGGTCAGATGTGCTTGG
74
+ CAGGAACTGTCAGCTGCTGAGCAGGGTGGTCCCTGAGCGGAGGATAAGCAGCATCAGACTCCACAACCAG
75
+ AGGAAGAAAGAAATGGGGATGGAGCGGAGACCCACGGGCTGAGTCCCGCTGTGGAGTGGCCTTGCAGCTC
76
+ CCTCTCAGTTAAAACTCCCAGTAAAGCCACAGTTCTCCGAGCACCCAAGTCTGCTCCAGCCGTCTCTTAA
77
+ AACAGGCCACTCTCTGAGAAGGAATTC
data/spec/testfiles/testcase.fasta ADDED
@@ -0,0 +1,55 @@
1
+ >HA-mKSR1-pREX-CD2 NM_013571.2
2
+ # this is the leader found in the pRex vector
3
+ GCTTGGATACACGCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCATCCTCTAGACTGCC
4
+ # BamHI
5
+ GGATCC
6
+ CAGTGTGGTGGTAGGGAATTA
7
+ # this is the HA tag itself
8
+ ATGTACCCATACGATGTTCCAGATTACGCT
9
+ CTTATGGCCATGGAGGCCCGAATTC
10
+ # not sure how to account for these two A's but there they are
11
+ AA
12
+ # EXTRA BAGGAGE:
13
+ #GGTCGACCGAGATCTCTCGAGGTACC
14
+ # NotI cleavage site
15
+ #GCGGCCGC
16
+ #CAGCACAGTGGCCATGGCATCTAG
17
+ #This is the 5' UTR in mouse
18
+ #CTCGGGGCTTTCCTGCCGAGGCGCCCGTGTCCCCGGGCTCCTCGCCTCGGCCCCCAGCGGCCCCGATGCCGAGGC
19
+ #This is where translation actually begins:
20
+ ATGGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCGGCGGCGGGGGCGC
21
+ CGCGGCGGACGGGGGCGCAGGGGCCGCCGTCAGCCGGGCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTC
22
+ ATCGATATCTCCATCGGCAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACACAGC
23
+ AGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAGCAGCAGCAGAGCAAGCTTAGTGT
24
+ GACCCCAAGCGACAGGACCGCCGAGCTCAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAAC
25
+ GTGAGGCCTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTGGAGATGGACGAGG
26
+ CCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAGCACGGAGGAGTGCAGCCGCCTACAGCAAGCCCT
27
+ TACCTGCCTTCGGAAGGTGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACAGAT
28
+ GCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCTGGGCAGAGCGGGTGCCAGCACTC
29
+ AGGGACCCCGTTCCATCTCCGTGTCCGCCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGG
30
+ CCTCTCGGACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCTGCACAGCTTCATC
31
+ ACGCCCCCTACCACACCCCAGCTACGACGGCACGCCAAGCTGAAGCCACCAAGGACACCCCCACCGCCAA
32
+ GCCGCAAGGTCTTCCAGCTGCTCCCCAGCTTCCCCACACTCACACGGAGCAAGTCCCACGAGTCCCAGCT
33
+ GGGAAACCGAATCGACGACGTCACCCCGATGAAGTTTGAACTCCCTCATGGATCCCCACAGCTGGTACGA
34
+ AGGGATATCGGGCTCTCGGTGACGCACAGGTTCTCCACAAAGTCATGGTTGTCACAGGTGTGCAACGTGT
35
+ GCCAGAAGAGCATGATTTTTGGCGTGAAGTGCAAACACTGCAGGTTAAAATGCCATAACAAGTGCACAAA
36
+ >100122-36_E07_HA-mKSR1-OXL33.ab1 950
37
+ CNCNCNNGNNCNNCCGCCCACGTGAAGGCTGCCGACCCCGGGGGTGGACCA
38
+ TCCTCTAGACTGCCGGATCCCAGTGTGGTGGTACGGGAATTATGTACCCA
39
+ TACGATGTTCCAGATTACGCTCTTATGGCCATGGAGGCCCGAATTCAAAT
40
+ GGATAGAGCGGCGTTGCGCGCGGCAGCGATGGGCGAGAAAAAGGAGGGCG
41
+ GCGGCGGGGGCGCCGCGGCGGATGGGGGCGCAGGGGCCGCCGTCAGCCGG
42
+ GCGCTGCAGCAGTGCGGCCAGCTGCAGAAGCTCATCGATATCTCCATCGG
43
+ CAGTCTGCGCGGGCTGCGCACCAAGTGCTCAGTGTCTAACGACCTCACAC
44
+ AGCAGGAGATCCGGACCCTAGAGGCAAAGCTGGTGAAATACATTTGCAAG
45
+ CAGCAGCAGAGCAAGCTTAGTGTGACCCCAAGCGACAGGACCGACCGAGCT
46
+ CAACAGCTACCCACGCTTCAGTGACTGGCTGTACATCTTCAACGTGAGGC
47
+ CTGAGGTGGTGCAGGAGATCCCCCAAGAGCTCACACTGGATGCTCTGCTG
48
+ GAGATGGACGAGGCCAAAGCCAAGGAGATGCTGCGGCGCTGGGGGGCCAG
49
+ CACGGAGGAGTGCAGCCGCCTACAGCAAGCCCTTACCTGCCTTCGGAAGG
50
+ TGACTGGCCTGGGAGGGGAGCACAAAATGGACTCAGGTTGGAGTTCAACA
51
+ GATGCTCGAGACAGTAGCTTGGGGCCTCCCATGGACATGCTTTCCTCGCT
52
+ GGGCAGAGCGGGTGCCAGCACTCAGGGACCCCGTTCCATCTCCGTGTCCG
53
+ CCCTGCCTGCCTCAGACTCTCCGGTCCCCGGCCTCAGTGAGGGCCTCTCG
54
+ GACTCCTGTATCCCCTTGCACACCAGCGGCCGGCTGACCCCCCGGGCCCT
55
+ GCACAGCTTCATCACGCCCCCTACCACACCCCAGCTACGACAGCACGCCA
metadata ADDED
@@ -0,0 +1,99 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: dna_sequence_aligner
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.0.2
5
+ platform: ruby
6
+ authors:
7
+ - John T. Prince
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+
12
+ date: 2010-02-12 00:00:00 -07:00
13
+ default_executable:
14
+ dependencies:
15
+ - !ruby/object:Gem::Dependency
16
+ name: bio
17
+ type: :runtime
18
+ version_requirement:
19
+ version_requirements: !ruby/object:Gem::Requirement
20
+ requirements:
21
+ - - ">="
22
+ - !ruby/object:Gem::Version
23
+ version: "0"
24
+ version:
25
+ - !ruby/object:Gem::Dependency
26
+ name: spec-more
27
+ type: :development
28
+ version_requirement:
29
+ version_requirements: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - ">="
32
+ - !ruby/object:Gem::Version
33
+ version: "0"
34
+ version:
35
+ description: does high pairwise alignment of sequencing reads with a template using bioruby and clustalw. gives template-centric output.
36
+ email: jtprince@gmail.com
37
+ executables:
38
+ - dna_sequence_aligner
39
+ - dna_translator.rb
40
+ extensions: []
41
+
42
+ extra_rdoc_files:
43
+ - LICENSE
44
+ - README.rdoc
45
+ files:
46
+ - .gitignore
47
+ - History
48
+ - LICENSE
49
+ - README.rdoc
50
+ - Rakefile
51
+ - VERSION
52
+ - bin/dna_sequence_aligner
53
+ - bin/dna_translator.rb
54
+ - lib/bio/alignment/dna_sequence.rb
55
+ - older/align_all.rb
56
+ - older/align_to_template.rb
57
+ - reference/clustalw_opts.txt
58
+ - script/fasta_compile_annotated.rb
59
+ - spec/align_spec.rb
60
+ - spec/spec_helper.rb
61
+ - spec/testfiles/HA-mKSR1-KSRF1.txt
62
+ - spec/testfiles/HA-mKSR1-KSRF2.txt
63
+ - spec/testfiles/HA-mKSR1-KSRF3.txt
64
+ - spec/testfiles/HA-mKSR1-KSRF4.txt
65
+ - spec/testfiles/HA-mKSR1-KSRF5.txt
66
+ - spec/testfiles/HA-mKSR1-OXL33.txt
67
+ - spec/testfiles/KSR1_mouse_NM_013571_in_HA_pREX.ANNOTATED.fasta
68
+ - spec/testfiles/testcase.fasta
69
+ has_rdoc: true
70
+ homepage: http://jtprince.github.com/dna_sequence_aligner
71
+ licenses: []
72
+
73
+ post_install_message:
74
+ rdoc_options:
75
+ - --charset=UTF-8
76
+ require_paths:
77
+ - lib
78
+ required_ruby_version: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ">="
81
+ - !ruby/object:Gem::Version
82
+ version: "0"
83
+ version:
84
+ required_rubygems_version: !ruby/object:Gem::Requirement
85
+ requirements:
86
+ - - ">="
87
+ - !ruby/object:Gem::Version
88
+ version: "0"
89
+ version:
90
+ requirements: []
91
+
92
+ rubyforge_project:
93
+ rubygems_version: 1.3.5
94
+ signing_key:
95
+ specification_version: 3
96
+ summary: does high pairwise alignment of sequencing reads with a template
97
+ test_files:
98
+ - spec/align_spec.rb
99
+ - spec/spec_helper.rb