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旋转小马

生物信息中，这是一fastq文档，每四行是一个循环，现在我要看每个循环的第二行的碱基“A”或者“T”是否连续超过40个以上（包括40个），如果是的话，把这整个循环去掉，最后输出一个文件，用perl怎样实现？
@HWI-D00318:33:H166PADXX:2:1101:1337:2089 1:N:0:TAGCTT
AAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
CCCFFADFHHHHHJJJJJJJHFDDDDDDDDDDDDDDDDDDBDBDDDDDDDDDBDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:1493:2146 1:N:0:TAGCTT
CAGATACACAGGAGTATTCAAAACCCTGGCAAGTATTGATGACAAACCGTCCCGTTTCGAAATTTTGATACCATTGGTACAAACTTTAGTTCGCGACAAT
+
CCCFFFFFHHHHHJGIJJJJJJJJJJJJJJJJJHIJJJJJJJJJJJJIIGIJJJJIJIJJJJHHHHHFFFFFFFEEEAEEDDDDDDDDDDDEDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:1515:2150 1:N:0:TAGCTT
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
CCCFFFFFHHHHHJJJHFDDDDDDD8BDD@BDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDBDDDDDDDDBBDDDDBDDDDDDDDDDDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:1798:2219 1:N:0:TAGCTT
CCTAAAGCCTAAGAGAGCAGGACTCAGGCTGGAGGCCTCTGCCTGGCCAGGATGAGGCTGAGGGCTTGGGGCAAAATTACTACCTGTCCTGATACCTGCA
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJGIJJJJJJJIHHHDFFFDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:2167:2087 1:N:0:TAGCTT
GCTGGGATGGGCCTCCAACTCCTCTGACAGGGCCTGCTAATCCAGCAGGAGCCTGGGGAATAGGTACACCTGCTGGCACTCCTCTGCCAGCTGCTCTTCC
+
CCCFFFFFHHHGHJJJJJJJJJIJJJJJJJIJJJJJJJJJJJJJJJJJJJGHJJIJJJJHHHHHBCFFFFEEEEEDDDDDDDDDDCDDDDDDDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:2072:2182 1:N:0:TAGCTT
ATGCTGAGCTATCAGGTGTTCAGCCACAGTGGAGTTCTCCCCACTGCCTGTTGCTGTCATCCGGGCCACGTGGTCTACACCGATCCGTTCAGCTTCCTCA
+
CCCFFFFFHHHHHJJJGHIIJJJJJJJJJHIIHIJJJJJJJJJJJIJJJJIJJIJJHIJJJJJJJJHFFFCDDCEDDDDDDDDDDDDDDDDDDDDDDDDD
@HWI-D00318:33:H166PADXX:2:1101:2852:2107 1:N:0:TAGCTT
ATTTTTTTCTTTTTTTTTTTTTTTTACTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
@@@DDDDDHHHHHIIIIIIIIIE',((-(5>5<?B339BBBBBBBBBBBB5@BBBBBBBB7@BBBBBB8BB9@@BBBBBB>BB5@BBBBBBBBBBBBBBB
@HWI-D00318:33:H166PADXX:2:1101:4032:2050 1:N:0:TAGCTT
GATAATATCCGGGTAGGCGCAATCACTTTCGTCTACTCCGTTACAAAGCGAGGCTGGGTATTTCCCGGCCTTTCTGTTATCCGAAATCCACTGAAAGCAC
+
CCCFFFFFHHHHHBGHIJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJIJJJJHFFFDDACDEEFEDDDDDDDDDDDEDDEDDDDDDDDDDDDDDDDDDDD

pitonas

1. #!/usr/bin/perl -w
   
2. 
   
3. my ( $in, $out ) = ( 'data.txt', 'save.txt' );
   
4. open my $I, '<', $in  or die "$in\t$!";
   
5. open my $S, '>', $out or die "$out\t$!";
   
6. 
   
7. while (<$I>) {
   
8.     my $line = <$I>;
   
9.     if ( $line =~ /A{40,}/ or $line =~ /T{40,}/ ) { <$I>, <$I> }
   
10.     else { print $S $_, $line, <$I> . <$I> }
    
11. }
    
12. 
    
13. print 'finish';

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旋转小马

结果不大对呢，就是在第二行中，若出现连续的“A”或“T”达到40或以上的时候，这一个循环去掉的，这里好像没实现！回复 2# pitonas


   

mcshell

期望的结果什么？ LZ贴出来{:3_204:}

旋转小马

我这要是能得出结果就不求助大家了，上面的文档4行一循环，如果在每个循环中的第二行中，若“A”或“T”连续出现40次以上（包括40次），那么就把这一个循环去掉，最后输出剩下的文档就可以了！回复 4# mcshell


   

pitonas

这是实现, 8个循环 -> 5个循环 save.txt

1. @HWI-D00318:33:H166PADXX:2:1101:1493:2146 1:N:0:TAGCTT
   
2. CAGATACACAGGAGTATTCAAAACCCTGGCAAGTATTGATGACAAACCGTCCCGTTTCGAAATTTTGATACCATTGGTACAAACTTTAGTTCGCGACAAT
   
3. +
   
4. CCCFFFFFHHHHHJGIJJJJJJJJJJJJJJJJJHIJJJJJJJJJJJJIIGIJJJJIJIJJJJHHHHHFFFFFFFEEEAEEDDDDDDDDDDDEDDDDDDDD
   
5. @HWI-D00318:33:H166PADXX:2:1101:1798:2219 1:N:0:TAGCTT
   
6. CCTAAAGCCTAAGAGAGCAGGACTCAGGCTGGAGGCCTCTGCCTGGCCAGGATGAGGCTGAGGGCTTGGGGCAAAATTACTACCTGTCCTGATACCTGCA
   
7. +
   
8. CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJGIJJJJJJJIHHHDFFFDDDDDDDDDDDDDEDDDDDDDDDDDDDDDDDD
   
9. @HWI-D00318:33:H166PADXX:2:1101:2167:2087 1:N:0:TAGCTT
   
10. GCTGGGATGGGCCTCCAACTCCTCTGACAGGGCCTGCTAATCCAGCAGGAGCCTGGGGAATAGGTACACCTGCTGGCACTCCTCTGCCAGCTGCTCTTCC
    
11. +
    
12. CCCFFFFFHHHGHJJJJJJJJJIJJJJJJJIJJJJJJJJJJJJJJJJJJJGHJJIJJJJHHHHHBCFFFFEEEEEDDDDDDDDDDCDDDDDDDDDDDDDD
    
13. @HWI-D00318:33:H166PADXX:2:1101:2072:2182 1:N:0:TAGCTT
    
14. ATGCTGAGCTATCAGGTGTTCAGCCACAGTGGAGTTCTCCCCACTGCCTGTTGCTGTCATCCGGGCCACGTGGTCTACACCGATCCGTTCAGCTTCCTCA
    
15. +
    
16. CCCFFFFFHHHHHJJJGHIIJJJJJJJJJHIIHIJJJJJJJJJJJIJJJJIJJIJJHIJJJJJJJJHFFFCDDCEDDDDDDDDDDDDDDDDDDDDDDDDD
    
17. @HWI-D00318:33:H166PADXX:2:1101:4032:2050 1:N:0:TAGCTT
    
18. GATAATATCCGGGTAGGCGCAATCACTTTCGTCTACTCCGTTACAAAGCGAGGCTGGGTATTTCCCGGCCTTTCTGTTATCCGAAATCCACTGAAAGCAC
    
19. +
    
20. CCCFFFFFHHHHHBGHIJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJIJJJJHFFFDDACDEEFEDDDDDDDDDDDEDDEDDDDDDDDDDDDDDDDDDDD
    

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pitonas

代码LZ贴出来

旋转小马

纳尼？？？我怎么没得到这结果！！！回复 6# pitonas


   

旋转小马

  1 #!/usr/bin/perl -w
  2 use strict;
  3 use PerlIO::gzip;
  4 open IN,"1Asel_L2_I010.R1.clean.fastq.gz"or die"Can not open IN.\n";
  5 open OUT,">R1.gz"or die"Can not open endfile.\n";  
  9 while (<IN>){
10         my $line = <IN>;
11         if($line =~/A{40}/ or $line =~/T{40}/){
12         <IN>;
13         <IN>;
14         }else{
15         print OUT $_, $line, <IN> . <IN> }
16 }
17         print 'finish';回复 7# pitonas


   

pitonas

please read doc how to use PerlIO::gzip
http://search.cpan.org/~nwclark/PerlIO-gzip-0.18/gzip.pm