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標(biāo)題: [練習(xí)] 索引序列 [打印本頁]

作者: rubyish 時(shí)間: 2014-03-10 01:04
標(biāo)題: [練習(xí)] 索引序列
本帖最后由 rubyish 于 2014-03-09 23:34 編輯

有一組數(shù)據(jù)：
>1
GCGTGCGTAA
AAAATAAATCACCTTTCGGGCTAACTTTGCGGTCGAGAACTCATTACCCAAATCCTACAATCACAAATTTG
ACATACTTAGAATTAAAAAACCAAACCACACACAGAAACAAGGTTAAGATAAATGAACAAAGGAGAATGATTTAGTTAGTAACCTCAACATTAGAGAGCT
TTCCTTCGTTTAATACTTTGAAGATGGCAAAACCACCTGGCGTCTCAAACAGTATTAGCATTTTTACAAGCTCCTGAAAAGAAGAAAAAACAAGATTAAG
AGAAACCCTTGAATCAACTCAAAGTCACCAAACTTGCAAGTTAGTGTTTTACGAGCTAAAGCCATTAAGCTAGTACGAAACAATATTCAAGGTAAAACTT
TTTCCCTGTTTCGAAGTTTACAAATCAGAATAATAGTTAAGGCAGATACTCTGTTCAAATTCTTGAAAATCCGACAAAGAACAGAACTATACTTTGTCAA
AGTCTTAGAATTTTGGAAGCTTATTTGCCATAACAACGAAGAAAGAGAGGGCGAGAGAGATTCAGTACCTTAGAGGGTTAACGCACAACTACAGCTTTAG
AGAGAGCTAAAATCAGGAGCCGCGATTCTGCTAGGGTTTAAGATGGTTTTTA
>2
TAAAAAAAAAATAACATCATTATATAATATATAGAGTTTAAAACATCTCAAAAACAAATTCATCATATTTTGTGATTCGAAATTTTAAGAATGAACATAT
ATTAACTAATTGGCGAAAAATGCGTGGGTTCAACGTCCCGCAACGAATAAAATATTTTGACAATGATTCATAAACATATTATAAATAAGATCAACATTAA
TAAAATAAATAATTTTTTTTTGTGGATGGATTTGGTTTGGCAGGACGTTACTTAATAACAATTGTAAACTATAAAATAATTTACAAATTTT
ATATATATTAATTTAAAAAATGAATTGTCTACGCGGTGTACCGCATGTTAAAATTTAGTTTCTATATATTTTAGAAACAACTTTGAATTTATACTTTAAT
ATTGAATAAACAACACCAAACCCCCTATTATTCATGTTATCCATTTTTTGAAATAACAGAAAAATAGAAAATAATCATA
AGAAACCAAACAAAATATACACAACAAAAAATCAAATCATAAAGCTTTAAATACATATAAGTGAAAGATCAAATCATAAAACTATAAAGACATGAAGTAC
CTAAAACATAATATATGCTAAAAAGAAATTCAAAATACAAAATCTTCTACGTATTTGAATAATTCATCCAAACCTAAAACTGTATATCTGTTCACATATT
TGAATGAAAAATCAAATAAGCAAATCAAGCAAGAAATATTAATGATGTCTATGTGATTTTTTTTTTTGT
>3
TTAATCTGCTTTTTTTTTTTTTTTTTAATTTACTCATATTAGATTTAGCTTAATTTTGAGACTGTTAGCTTTCGGTGTGAACAAAAGAAATTTGTGAAAT
TTGATATTGTTGATACATTCTCTAGAAATTTTGGAAAGATTGTGTGTTTCTTTTCAAAATTCAAATATTAATAACGCACCAAAATATCTGAATAGAAAGA
ATAAATAATGCGCCAAAATATTGATATGATGAAAGGTTCCCGTCTCAATATGTTTTTAGACCCTAGGTAAAACTAAAT
TTACATATCCTTTTCACACGATTTTTTTTTTTTTTTTTTGACTCTTTTACTTAAAGGTTTTTTTAAAAAAATTTGCCATGCACCCTGGCAATGGCTTTTG
CCCCCACCTCCCCCACATTAAGCCAATCTTGTTGCATGGCCATCTCCCCTGACGAACACCATTAAAGATTCATCTATATGTGGTA
GCCACTGAGTAGACTTAATAGAGCATTAAATAAATGAAATTCGTGGATGCAAATTGTAGAAGAACTAGTATTTAACGGAGTGTTGCTTCATCACAAATTC

1: 想從每一條中挑選出GCGT**六個(gè)堿基（兩個(gè)星號(hào)代表GCGT后面兩個(gè)模糊匹配）的位置

2: Non-overlapping
>1
GCGTGCGTAA

1 GCGTGC 0

復(fù)制代碼

3: Overlapping

>1
GCGTGCGTAA

1 GCGTGC 0, GCGTAA 4

復(fù)制代碼

4: 結(jié)果應(yīng)該像這樣
when Overlapping:

1 GCGTGC 0, GCGTAA 4, GCGTCT 220
2 GCGTGG 121
3

復(fù)制代碼

when Non-overlapping

1 GCGTGC 0, GCGTCT 220
2 GCGTGG 121
3

復(fù)制代碼

作者: rubyish 時(shí)間: 2014-03-11 00:05
本帖最后由 rubyish 于 2014-04-24 19:04 編輯

dddddddddddd~~~

作者: klainogn 時(shí)間: 2015-07-26 19:42
本帖最后由 klainogn 于 2015-07-26 19:45 編輯

class String
   def srch(pattern, pos=0)
      if pos=self =~ pattern
         s=$&+" "+pos.to_s
         ext=$'.srch(pattern, pos+$&.length)
         if !ext.empty?
            s += ","+ext
         end
         return s
      else
         return ''
      end
   end
end
fd=File.open("a")
arr=fd.readlines
arr.each {|line|
rs= line.chomp.srch(/GCGT../)
p rs if !rs.empty?
}

"GCGTGC 0"
"GCGTCT 39"
[/code]

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