[练习] 索引序列

rubyish

有一组数据：
>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: 想从每一条中挑选出GCGT**六个碱基（两个星号代表GCGT后面两个模糊匹配）的位置

2: Non-overlapping
>1
GCGTGCGTAA

1. 1       GCGTGC 0

复制代码

3: Overlapping

>1
GCGTGCGTAA

1. 1       GCGTGC 0, GCGTAA 4

复制代码

4: 结果应该像这样
when Overlapping:

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

复制代码

when Non-overlapping

1. 1       GCGTGC 0, GCGTCT 220
   
2. 2       GCGTGG 121
   
3. 3
   

复制代码

rubyish

dddddddddddd~~~

klainogn

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]