如何找序列中的包含关系！

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

1^# choose2005 发表于 2008-05-23 15:28

如何找序列中的包含关系！

我有这样一个文件：
里面有一系列的序列：
如：
AAAAAAAAAGATTGAG             SEQ.1893836.16.1
AAAAAAAAAGATTGAGACGAATT       SEQ.1549482.23.1
AAAAAAAAAGATTGAGCCGAA          SEQ.2553655.21.1
AAAAAAAAAGATTGAGCCGAAA       SEQ.2706125.22.3
AAAAAAAAAGATTGAGCCGAAT       SEQ.1372232.22.9
AAAAAAAAAGATTGAGCCGAATA       SEQ.1365232.23.4
AAAAAAAAAGATTGAGCCGAGTTA             SEQ.889399.24.1
AAAAAAAAAGATTGAGCCGCAAAA             SEQ.1263859.24.1
AAAAAAAAAGATTGAGTCGAATA       SEQ.970919.23.1
AAAAAAAAAGATTGTCACAACT       SEQ.142122.22.1
AAAAAAAAAGATTTGCGAAAACT       SEQ.785497.23.1
AAAAAAAAAGCAAAGAACAAAAAG             SEQ.926879.24.1
AAAAAAAAAGCTCTTCAGGAGGG       SEQ.50491.23.1
AAAAAAAAAGTGATACTTCTTGTT             SEQ.1347612.24.1
AAAAAAAAATAAAAAACAAGA          SEQ.1258876.21.1
AAAAAAAAATAAAGCAAGAA          SEQ.2556803.20.1
AAAAAAAAATACGAACCGTTCTTT             SEQ.1157920.24.1
AAAAAAAAATAGCGTGGGAATGAG             SEQ.1457720.24.1
AAAAAAAAATAGGAAAAAA          SEQ.1060112.19.1
AAAAAAAAATAGGCTTATCAACCA             SEQ.1528036.24.1
AAAAAAAAATCATCATACAGGGT       SEQ.556325.23.1
AAAAAAAAATCGACGGCTAGATA       SEQ.1452090.23.1
AAAAAAAAATGCAGTCTTGTCAA       SEQ.2525543.23.1
AAAAAAAAATGCATTGATCAT          SEQ.1264660.21.1
AAAAAAAAATGTTCTCATGGTT       SEQ.2274085.22.1
AAAAAAAAATTAAACGGGCCGTGC             SEQ.880386.24.1
AAAAAAAAATTCGATATAGA          SEQ.2571452.20.1
AAAAAAAACACCGAGCTATCGGCT             SEQ.1882674.24.1
AAAAAAAACACTCAGGATTCAGGA             SEQ.2492497.24.1
AAAAAAAACACTCTGCAACAGATG             SEQ.1064.24.1
AAAAAAAACACTTTCGGCGCCAAC             SEQ.1954907.24.1
AAAAAAAACATGTAGTCTT          SEQ.2131152.19.1
AAAAAAAACCCGACTCGGGCACACA             SEQ.1023067.25.1
AAAAAAAACCGGACAAATCA          SEQ.2385057.20.1
AAAAAAAACCGGTCCGTTTGGATC             SEQ.1419987.24.1
AAAAAAAACCGTTTAGATACATGT             SEQ.1275097.24.1
AAAAAAAACCTACTTGAGCTACGC             SEQ.2530317.24.1
AAAAAAAACGCCTTCAGCAGGGCC             SEQ.1595165.24.1
AAAAAAAACGTCTAATACATGTAA             SEQ.1756499.24.1
AAAAAAAACGTCTAGATACATAGA             SEQ.155114.24.1
AAAAAAAACGTCTAGATACATGTA             SEQ.316197.24.1
AAAAAAAACGTGGGATGCTA          SEQ.1811897.20.1
AAAAAAAACGTTTAGATACATGTA             SEQ.901852.24.1
AAAAAAAACGTTTGGCAATCGAAA             SEQ.2696829.24.1
AAAAAAAACTAAAAATAAAAGA       SEQ.2667333.22.1
AAAAAAAACTCGGTCGCAGGCCTG             SEQ.1867874.24.1
AAAAAAAACTGCTCCAACGGCATA             SEQ.1044149.24.2
AAAAAAAAGACACACGAGGTTGGT             SEQ.1133483.24.1
AAAAAAAAGATACATTATCAT          SEQ.1951462.21.1
AAAAAAAAGATCAGAGAT             SEQ.2455401.18.1
AAAAAAAAGATTGAGCCGAA          SEQ.626739.20.4
AAAAAAAAGATTGAGCCGAAACT       SEQ.854926.23.1
AAAAAAAAGATTGAGCCGAAAG       SEQ.1664333.22.1
AAAAAAAAGATTGAGCCGAAT          SEQ.2647549.21.4
AAAAAAAAGATTGAGCCGAATA       SEQ.822665.22.3
AAAAAAAAGCACAACTCGGCTGCT             SEQ.73260.24.1
AAAAAAAAGCTGTGCCCTAGCTGG             SEQ.375077.24.1
AAAAAAAAGGAACAGTGACATATT             SEQ.226404.24.1
AAAAAAAAGGACAAATGCAGTGCA             SEQ.1071214.24.1
AAAAAAAAGGTATGTAGTGTGCCT             SEQ.2467414.24.1
AAAAAAAAGTAAAAAAAAAAAA       SEQ.1895978.22.1
AAAAAAAAGTAAATTACAGATAAC             SEQ.2427386.24.1
AAAAAAAAGTCAATTCGTTCGA       SEQ.2234367.22.1
AAAAAAAAGTCACATCCGA          SEQ.2424071.19.1
AAAAAAAAGTGTCTAGATACACGT             SEQ.2033632.24.1
AAAAAAAAGTGTCTCTTGGGGACT             SEQ.2382025.24.1
AAAAAAAAGTTTAGATACATGTAAT             SEQ.1263057.25.1
AAAAAAAATATGGAACATAGGGAGT             SEQ.1391063.25.1
AAAAAAAATATGTGGAAA             SEQ.2506062.18.1
AAAAAAAATCCAGATGTTGATGA       SEQ.360584.23.1
AAAAAAAATCCTTTAGGAACG          SEQ.2306220.21.1
AAAAAAAATCGTCCATTGTACC       SEQ.184068.22.1
AAAAAAAATCTAGATGTTGGTCAG             SEQ.2464218.24.1
AAAAAAAATCTGGATTCGTGATTT             SEQ.1703616.24.1
AAAAAAAATGACATGTGAGTCCAA             SEQ.492275.24.1
AAAAAAAATGATCGGTATCGGTCG             SEQ.1784908.24.1
AAAAAAAATGCATTGAAAAA          SEQ.1196651.20.1
AAAAAAAATGCATTGATCA          SEQ.226298.19.1
AAAAAAAATGCATTGATCATA          SEQ.1992480.21.1
AAAAAAAATGGACAAGATTTAAAT             SEQ.2627544.24.1
AAAAAAAATTAACCAAATCGCATG             SEQ.1340145.24.1
AAAAAAAATTCTATCCATTCGGAT             SEQ.564597.24.1
AAAAAAAATTCTGCGATGAGAAGT             SEQ.515474.24.1
CAAGGTCTGAAATCCTTAGTA          SEQ.1147435.21.1
CAAGGTCTTCATGCCGGCTTA          SEQ.263499.21.1
CAAGGTGAACAGCCTCT             SEQ.110162.17.6
CAAGGTGAACAGCCTCTG             SEQ.842849.18.5
CAAGGTGAACAGCCTCTGCTGT       SEQ.841302.22.1
CAAGGTGAACAGCCTCTGG          SEQ.1427456.19.2
CAAGGTGAACAGCCTCTGGC          SEQ.295890.20.30
CAAGGTGAACAGCCTCTGGCC          SEQ.1155377.21.9
CAAGGTGAACAGCCTCTGGCCA       SEQ.247839.22.14
CAAGGTGAACAGCCTCTGGCCAA       SEQ.2085008.23.5
CAAGGTGAACAGCCTCTGGCCAAT             SEQ.1241836.24.2
CAAGGTGAACAGCCTCTGGCCAATG             SEQ.150863.25.2
CAAGGTGAACAGCCTCTGGCCACTC             SEQ.2289679.25.1
CAAGGTGAACAGCCTCTGGCCCA       SEQ.197175.23.1
CAAGGTGAACAGCCTCTGGCCTGT             SEQ.1487567.24.1
CAAGGTGAACAGCCTGGCCA          SEQ.642268.20.1
CAAGGTGAACAGCTCTGG             SEQ.1372063.18.1
CAAGGTGAACAGTCTCTGGC          SEQ.305520.20.1
CAAGGTGAACGGCCTTGGC          SEQ.370621.19.1
CAAGGTGAAGAAATTCAAC          SEQ.1298817.19.1
CAAGGTGACAACAGTAAC             SEQ.12876.18.1
CAAGGTGACAACAGTAACCTG          SEQ.895208.21.19
CAAGGTGACAACAGTAACCTGCC       SEQ.1890248.23.1
CAAGGTGACACAAGTAACCTGCCG             SEQ.79758.24.1
CAAGGTGACAGCAGTAACCTG          SEQ.910509.21.1
CAAGGTGACCCTGCTTTTTCAGGGA             SEQ.1499918.25.1
CAAGGTGAGCAGCCTCTGGCCAA       SEQ.2571296.23.1
CAAGGTGAGGGCGCCCCTGCAGGC             SEQ.228694.24.1
CAAGGTGAGGGCGGCCCGGCCGGT             SEQ.1871447.24.1
CAAGGTGAGTTTACCCACCTCGGC             SEQ.1872162.24.1
CAAGGTGATCGTCCCAATACCA       SEQ.220011.22.1
CAAGGTGATGAAGGAAATTT          SEQ.2523909.20.1
CAAGGTGCACTACTCACTGCACGA             SEQ.1680725.24.4
CAAGGTGCGGGGCCTTCCTGTGGA             SEQ.172187.24.1
CAAGGTGCTAAGACAGGTGCTTT       SEQ.245869.23.1
CAAGGTGGACACAGGACACAG          SEQ.2626465.21.1
CAAGGTGGACAGCCTCTGGC          SEQ.1929138.20.1
CAAGGTGGACGCATTTTTGCTAA       SEQ.635404.23.1
CAAGGTGGCCAGCGAGTGCT          SEQ.170744.20.1
CAAGGTGGCTGCGTCCAAGCGGG       SEQ.542762.23.1
CAAGGTGGGACTATTCCCAA          SEQ.763696.20.1
CAAGGTGGTAACTACACCAGGGT       SEQ.1202265.23.1
CAAGGTGGTACGCTGAACGCACCG             SEQ.661635.24.1
。。。。。

我想找出像这样的所有group;

CGGGGCATGACGTCACGATGATG
CGGGGCATGACGTCACGAT
   GGGCATGACGTCACG
            ATGACGTCACGATGAT
            ATGACGTCACGATGATG

即包含关系，该怎么来想这个问题呢？
我sort了一下，这能找出
CGGGGCATGACGTCACGATGATG
CGGGGCATGACGTCACGAT
or
CGGGGCATGACGTCACGATGATG
            ATGACGTCACGATGATG
但是这种的
CGGGGCATGACGTCACGATGATG
      GCATGACGTCACG
就找不出来了

谢谢！

cobrawgl

UID: 21059
帖子: 1
积分: 2
在线时间: 10 分钟

2^# cobrawgl 发表于 2008-05-23 15:49

#!/usr/bin/perl

#!/usr/bin/perl

use strict;
use warnings;

my @string;

while (<DATA>) {
chomp;
push @string, (split)[0];
}

@string = sort {length($b) <=> length($a)} @string;

for my $tpl (0 .. $#string-1) {
print "$tpl [$string[$tpl]] Have:\n";
for ($tpl+1 .. $#string) {
      print "\t$_ $string[$_]\n" if $string[$tpl] =~ m/$string[$_]/;
}
}

__DATA__
AAAAAAAAAGATTGAG             SEQ.1893836.16.1
AAAAAAAAAGATTGAGACGAATT       SEQ.1549482.23.1
AAAAAAAAAGATTGAGCCGAA          SEQ.2553655.21.1
AAAAAAAAAGATTGAGCCGAAA       SEQ.2706125.22.3
AAAAAAAAAGATTGAGCCGAAT       SEQ.1372232.22.9
AAAAAAAAAGATTGAGCCGAATA       SEQ.1365232.23.4
AAAAAAAAAGATTGAGCCGAGTTA             SEQ.889399.24.1
AAAAAAAAAGATTGAGCCGCAAAA             SEQ.1263859.24.1
AAAAAAAAAGATTGAGTCGAATA       SEQ.970919.23.1
AAAAAAAAAGATTGTCACAACT       SEQ.142122.22.1
AAAAAAAAAGATTTGCGAAAACT       SEQ.785497.23.1
AAAAAAAAAGCAAAGAACAAAAAG             SEQ.926879.24.1
AAAAAAAAAGCTCTTCAGGAGGG       SEQ.50491.23.1
AAAAAAAAAGTGATACTTCTTGTT             SEQ.1347612.24.1
AAAAAAAAATAAAAAACAAGA          SEQ.1258876.21.1
AAAAAAAAATAAAGCAAGAA          SEQ.2556803.20.1
AAAAAAAAATACGAACCGTTCTTT             SEQ.1157920.24.1
AAAAAAAAATAGCGTGGGAATGAG             SEQ.1457720.24.1
AAAAAAAAATAGGAAAAAA          SEQ.1060112.19.1
AAAAAAAAATAGGCTTATCAACCA             SEQ.1528036.24.1
AAAAAAAAATCATCATACAGGGT       SEQ.556325.23.1
AAAAAAAAATCGACGGCTAGATA       SEQ.1452090.23.1
AAAAAAAAATGCAGTCTTGTCAA       SEQ.2525543.23.1
AAAAAAAAATGCATTGATCAT          SEQ.1264660.21.1
AAAAAAAAATGTTCTCATGGTT       SEQ.2274085.22.1
AAAAAAAAATTAAACGGGCCGTGC             SEQ.880386.24.1
AAAAAAAAATTCGATATAGA          SEQ.2571452.20.1
AAAAAAAACACCGAGCTATCGGCT             SEQ.1882674.24.1
AAAAAAAACACTCAGGATTCAGGA             SEQ.2492497.24.1
AAAAAAAACACTCTGCAACAGATG             SEQ.1064.24.1
AAAAAAAACACTTTCGGCGCCAAC             SEQ.1954907.24.1
AAAAAAAACATGTAGTCTT          SEQ.2131152.19.1
AAAAAAAACCCGACTCGGGCACACA             SEQ.1023067.25.1
AAAAAAAACCGGACAAATCA          SEQ.2385057.20.1
AAAAAAAACCGGTCCGTTTGGATC             SEQ.1419987.24.1
AAAAAAAACCGTTTAGATACATGT             SEQ.1275097.24.1
AAAAAAAACCTACTTGAGCTACGC             SEQ.2530317.24.1
AAAAAAAACGCCTTCAGCAGGGCC             SEQ.1595165.24.1
AAAAAAAACGTCTAATACATGTAA             SEQ.1756499.24.1
AAAAAAAACGTCTAGATACATAGA             SEQ.155114.24.1
AAAAAAAACGTCTAGATACATGTA             SEQ.316197.24.1
AAAAAAAACGTGGGATGCTA          SEQ.1811897.20.1
AAAAAAAACGTTTAGATACATGTA             SEQ.901852.24.1
AAAAAAAACGTTTGGCAATCGAAA             SEQ.2696829.24.1
AAAAAAAACTAAAAATAAAAGA       SEQ.2667333.22.1
AAAAAAAACTCGGTCGCAGGCCTG             SEQ.1867874.24.1
AAAAAAAACTGCTCCAACGGCATA             SEQ.1044149.24.2
AAAAAAAAGACACACGAGGTTGGT             SEQ.1133483.24.1
AAAAAAAAGATACATTATCAT          SEQ.1951462.21.1
AAAAAAAAGATCAGAGAT             SEQ.2455401.18.1
AAAAAAAAGATTGAGCCGAA          SEQ.626739.20.4
AAAAAAAAGATTGAGCCGAAACT       SEQ.854926.23.1
AAAAAAAAGATTGAGCCGAAAG       SEQ.1664333.22.1
AAAAAAAAGATTGAGCCGAAT          SEQ.2647549.21.4
AAAAAAAAGATTGAGCCGAATA       SEQ.822665.22.3
AAAAAAAAGCACAACTCGGCTGCT             SEQ.73260.24.1
AAAAAAAAGCTGTGCCCTAGCTGG             SEQ.375077.24.1
AAAAAAAAGGAACAGTGACATATT             SEQ.226404.24.1
AAAAAAAAGGACAAATGCAGTGCA             SEQ.1071214.24.1
AAAAAAAAGGTATGTAGTGTGCCT             SEQ.2467414.24.1
AAAAAAAAGTAAAAAAAAAAAA       SEQ.1895978.22.1
AAAAAAAAGTAAATTACAGATAAC             SEQ.2427386.24.1
AAAAAAAAGTCAATTCGTTCGA       SEQ.2234367.22.1
AAAAAAAAGTCACATCCGA          SEQ.2424071.19.1
AAAAAAAAGTGTCTAGATACACGT             SEQ.2033632.24.1
AAAAAAAAGTGTCTCTTGGGGACT             SEQ.2382025.24.1
AAAAAAAAGTTTAGATACATGTAAT             SEQ.1263057.25.1
AAAAAAAATATGGAACATAGGGAGT             SEQ.1391063.25.1
AAAAAAAATATGTGGAAA             SEQ.2506062.18.1
AAAAAAAATCCAGATGTTGATGA       SEQ.360584.23.1
AAAAAAAATCCTTTAGGAACG          SEQ.2306220.21.1
AAAAAAAATCGTCCATTGTACC       SEQ.184068.22.1
AAAAAAAATCTAGATGTTGGTCAG             SEQ.2464218.24.1
AAAAAAAATCTGGATTCGTGATTT             SEQ.1703616.24.1
AAAAAAAATGACATGTGAGTCCAA             SEQ.492275.24.1
AAAAAAAATGATCGGTATCGGTCG             SEQ.1784908.24.1
AAAAAAAATGCATTGAAAAA          SEQ.1196651.20.1
AAAAAAAATGCATTGATCA          SEQ.226298.19.1
AAAAAAAATGCATTGATCATA          SEQ.1992480.21.1
AAAAAAAATGGACAAGATTTAAAT             SEQ.2627544.24.1
AAAAAAAATTAACCAAATCGCATG             SEQ.1340145.24.1
AAAAAAAATTCTATCCATTCGGAT             SEQ.564597.24.1
AAAAAAAATTCTGCGATGAGAAGT             SEQ.515474.24.1
CAAGGTCTGAAATCCTTAGTA          SEQ.1147435.21.1
CAAGGTCTTCATGCCGGCTTA          SEQ.263499.21.1
CAAGGTGAACAGCCTCT             SEQ.110162.17.6
CAAGGTGAACAGCCTCTG             SEQ.842849.18.5
CAAGGTGAACAGCCTCTGCTGT       SEQ.841302.22.1
CAAGGTGAACAGCCTCTGG          SEQ.1427456.19.2
CAAGGTGAACAGCCTCTGGC          SEQ.295890.20.30
CAAGGTGAACAGCCTCTGGCC          SEQ.1155377.21.9
CAAGGTGAACAGCCTCTGGCCA       SEQ.247839.22.14
CAAGGTGAACAGCCTCTGGCCAA       SEQ.2085008.23.5
CAAGGTGAACAGCCTCTGGCCAAT             SEQ.1241836.24.2
CAAGGTGAACAGCCTCTGGCCAATG             SEQ.150863.25.2
CAAGGTGAACAGCCTCTGGCCACTC             SEQ.2289679.25.1
CAAGGTGAACAGCCTCTGGCCCA       SEQ.197175.23.1
CAAGGTGAACAGCCTCTGGCCTGT             SEQ.1487567.24.1
CAAGGTGAACAGCCTGGCCA          SEQ.642268.20.1
CAAGGTGAACAGCTCTGG             SEQ.1372063.18.1
CAAGGTGAACAGTCTCTGGC          SEQ.305520.20.1
CAAGGTGAACGGCCTTGGC          SEQ.370621.19.1
CAAGGTGAAGAAATTCAAC          SEQ.1298817.19.1
CAAGGTGACAACAGTAAC             SEQ.12876.18.1
CAAGGTGACAACAGTAACCTG          SEQ.895208.21.19
CAAGGTGACAACAGTAACCTGCC       SEQ.1890248.23.1
CAAGGTGACACAAGTAACCTGCCG             SEQ.79758.24.1
CAAGGTGACAGCAGTAACCTG          SEQ.910509.21.1
CAAGGTGACCCTGCTTTTTCAGGGA             SEQ.1499918.25.1
CAAGGTGAGCAGCCTCTGGCCAA       SEQ.2571296.23.1
CAAGGTGAGGGCGCCCCTGCAGGC             SEQ.228694.24.1
CAAGGTGAGGGCGGCCCGGCCGGT             SEQ.1871447.24.1
CAAGGTGAGTTTACCCACCTCGGC             SEQ.1872162.24.1
CAAGGTGATCGTCCCAATACCA       SEQ.220011.22.1
CAAGGTGATGAAGGAAATTT          SEQ.2523909.20.1
CAAGGTGCACTACTCACTGCACGA             SEQ.1680725.24.4
CAAGGTGCGGGGCCTTCCTGTGGA             SEQ.172187.24.1
CAAGGTGCTAAGACAGGTGCTTT       SEQ.245869.23.1
CAAGGTGGACACAGGACACAG          SEQ.2626465.21.1
CAAGGTGGACAGCCTCTGGC          SEQ.1929138.20.1
CAAGGTGGACGCATTTTTGCTAA       SEQ.635404.23.1
CAAGGTGGCCAGCGAGTGCT          SEQ.170744.20.1
CAAGGTGGCTGCGTCCAAGCGGG       SEQ.542762.23.1
CAAGGTGGGACTATTCCCAA          SEQ.763696.20.1
CAAGGTGGTAACTACACCAGGGT       SEQ.1202265.23.1
CAAGGTGGTACGCTGAACGCACCG             SEQ.661635.24.1

cobrawgl

UID: 21059
帖子: 1
积分: 2
在线时间: 10 分钟

3^# cobrawgl 发表于 2008-05-23 16:05

把打印结果美化了一下

#!/usr/bin/perl

use strict;
use warnings;

my @string;

while (<DATA>) {
chomp;
push @string, (split)[0];
}

@string = sort {length($b) <=> length($a)} @string;

for my $tpl (0 .. $#string-1) {
my @result = ();
for ($tpl+1 .. $#string) {
      push @result, $string[$_] if $string[$tpl] =~ m/$string[$_]/;
}
if (@result) {
      print "[$string[$tpl]] Have:\n";
print "\t$_\n" for @result;
}
}

__DATA__
AAAAAAAAAGATTGAG             SEQ.1893836.16.1
AAAAAAAAAGATTGAGACGAATT       SEQ.1549482.23.1
AAAAAAAAAGATTGAGCCGAA          SEQ.2553655.21.1
AAAAAAAAAGATTGAGCCGAAA       SEQ.2706125.22.3
AAAAAAAAAGATTGAGCCGAAT       SEQ.1372232.22.9
AAAAAAAAAGATTGAGCCGAATA       SEQ.1365232.23.4
AAAAAAAAAGATTGAGCCGAGTTA             SEQ.889399.24.1
AAAAAAAAAGATTGAGCCGCAAAA             SEQ.1263859.24.1
AAAAAAAAAGATTGAGTCGAATA       SEQ.970919.23.1

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

4^# choose2005 发表于 2008-05-23 17:07

我想把这样的一块输出来怎么弄呢



如我的序列是这样的
ACCGTTTAGATACATGT             SEQ.1275097.24.1
CGGGGCATGACGTCACGATGATG          SEQ.197109.23.1
AAAAAAAACCTACTTGAGCTACGC             SEQ.2530317.24.1
AAAAAAAACGCCTTCAGCAGGGCC       SEQ.1945375.23.1
CGGGGCATGACGTCACGAT             SEQ.1595165.24.1
AAAAAAAACGTCTAATACATGTAA          SEQ.1971895.23.1
CGGGGCATGACGTCACGATGATG          SEQ.1756499.24.1
ATGACGTCACGATGAT                         SEQ.5697175.23.1
GGGCATGACGTCACG                      SEQ.197174.23.2
CAAGGTGAACAGCCTCTGGCCCA       SEQ.197175.23.1
CAAGGTGAACAGCCTCTGGCCTGT             SEQ.1487567.24.1

我想得到这样的结果：
CGGGGCATGACGTCACGATGATG
CGGGGCATGACGTCACGAT
   GGGCATGACGTCACG
            ATGACGTCACGATGAT
            ATGACGTCACGATGATG
怎么输出呢

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

5^# choose2005 发表于 2008-05-23 17:11

即这样的中间包含关系也要一块输出
CGGGGCATGACGTCACGATGATG
ATGACGTCACGATGAT

cobrawgl

UID: 21059
帖子: 1
积分: 2
在线时间: 10 分钟

6^# cobrawgl 发表于 2008-05-23 18:38

用 index()

if (@result) {
         print "$string[$tpl]\n";
            for (@result) {
      print ' 'x(index $string[$tpl], $_);
print "$_\n";
}
print "\n";
      }

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

7^# choose2005 发表于 2008-05-23 20:02

这样的话你会重复输出结果，如：
AAAAAAAAAAAAGGGGGGGGGGGG
AAAAAAAAAAAAGGGGGGGGG
AAAAAAAAAAAAGGGGG
      AAAAAAAAGGGGG

你输出的结果会是：

AAAAAAAAAAAAGGGGGGGGGGGG
AAAAAAAAAAAAGGGGGGGGG
AAAAAAAAAAAAGGGGG
      AAAAAAAAGGGGG

AAAAAAAAAAAAGGGGGGGGG
AAAAAAAAAAAAGGGGG
      AAAAAAAAGGGGG

AAAAAAAAAAAAGGGGG
      AAAAAAAAGGGGG

而我只想输出第一个结果即：
AAAAAAAAAAAAGGGGGGGGGGGG
AAAAAAAAAAAAGGGGGGGGG
AAAAAAAAAAAAGGGGG
      AAAAAAAAGGGGG

cobrawgl

UID: 21059
帖子: 1
积分: 2
在线时间: 10 分钟

8^# cobrawgl 发表于 2008-05-23 20:11

那就加个 flag 吧

#!/usr/bin/perl

use strict;
use warnings;

my @string;

while (<DATA>) {
chomp;
      push @string, (split)[0];
}

@string = sort {length($b) <=> length($a)} @string;

my @flag;                <----------------
$flag[$_] = 0 for (0 .. $#string);    <-------------

for my $tpl (0 .. $#string-1) {
      my @result = ();
      for ($tpl+1 .. $#string) {
next if $flag[$_];  <---------------
         if ($string[$tpl] =~ m/$string[$_]/) {
      push @result, $string[$_];
$flag[$_] = 1;  <--------------
}
      }
      if (@result) {
            print "$string[$tpl]\n";
            for (@result) {
                     print ' 'x(index $string[$tpl], $_);
                     print "$_\n";
}
print "\n";
      }
}

__DATA__
ACCGTTTAGATACATGT             SEQ.1275097.24.1
CGGGGCATGACGTCACGATGATG          SEQ.197109.23.1
AAAAAAAACCTACTTGAGCTACGC             SEQ.2530317.24.1
AAAAAAAACGCCTTCAGCAGGGCC       SEQ.1945375.23.1
CGGGGCATGACGTCACGAT             SEQ.1595165.24.1
AAAAAAAACGTCTAATACATGTAA          SEQ.1971895.23.1
CGGGGCATGACGTCACGATGATG          SEQ.1756499.24.1
ATGACGTCACGATGAT                         SEQ.5697175.23.1
GGGCATGACGTCACG                      SEQ.197174.23.2
CAAGGTGAACAGCCTCTGGCCCA       SEQ.197175.23.1
CAAGGTGAACAGCCTCTGGCCTGT             SEQ.1487567.24.1

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

9^# choose2005 发表于 2008-05-23 20:46

谢谢！

choose2005

UID: 11866
帖子: 37
积分: 85
在线时间: 2 小时

10^# choose2005 发表于 2008-05-23 21:00

我觉得这样效率会更高些
for my $tpl (0 .. $#string-1) {
      my @result = ();
      next if $flag[$_]; ####<---------------
      for ($tpl+1 .. $#string) {

         if ($string[$tpl] =~ m/$string[$_]/) {
                        push @result, $string[$_];
                              $flag[$_] = 1;  <--------------
                     }
      }
      if (@result) {
            print "$string[$tpl]\n";
            for (@result) {
                     print ' 'x(index $string[$tpl], $_);
                     print "$_\n";
            }
            print "\n";
      }
}