perl 引号

一串儿葡萄皮

部分文件
>Srcc10g063050.1.1 Receptor-like kinase    Try_threonine protein kinase
MKTKHKLTPRPFTPTPSPTHIMGILLICFIFSITNSFVIAQDDAVPAKSFPVFTPEDNFL
IDCGATSSITLPGNKAFQPDQNTAKYLSYTGKDIQACASDKINVPSTLYVNAKIFTTEAI
YTFHASTSGLHWIRLHFFPFKYEEYDLK
">Solyc11g072930.1.1 LRR receptor-like serine_threonine-protein kinase, RLP"
MASSYFLLLVLVLSVFSVSADVFVSLDCGSSEAYTDHETSIDWLGDVDYVANGESHVVPS
NNSISHVSALEVRGLDSTMYSHVDDNSSDPPRITALYLSKFNLSGSLPDFSSMDAL
ETIDLSNNNLDGPIPDFFGTLPNLKELNLANNKFSGPVPASLSNKNGLTLDTSGNSDLCS
SSEESCQNNDSSSPGNDQPTTGSTNNNKKKKKKKNNLPIILGTTISAFLLLWAIVGIFAI
LHYKNKRAATSLINPGQASGGSTPFVDRVQMSEKIEKNPEVTAHDHENSTNV
">Solyc12g00890.1.1 Kinesin  IPR001752  Kinesin, motor region"
ESVINGRDLLGFSLTSPDLVICTGSPDIPARNYGDSPEFLKGCSISLENGI
KGSEEVQAATKLFTDWQGSKDDDLCAPADFELPSPPVEENSSELSVPIVSINVGSTDCIS
SESGIQFSEDKYFCGGNVLSTDTRIEESICASVYQTARVGNFSYHFNNLSAGFYLVDLHF
VEVVLTDGSTGDFSENSPQRNSLEVNGDIKAAGKLQLANVSREK

MMMIX

一串儿葡萄皮 发表于 2015-08-12 11:09
while(<W>){
   chomp;
    my$i='"\w+"';
        $i=~s/\"//g;

}

你这就是个空循环, 除了把 W 读了一遍之外, 啥用都没有.

另外, 你把 my $i 写成 my$i 自己看着不糟心么? 多输入个空格是能累着你咋滴?

BTW again, 这都不是代码风格问题, 你这完全是审美观病变坏死的征兆!!!

MMMIX

一串儿葡萄皮 发表于 2015-08-12 11:09
#!/usr/bin/perl    -w
use warnings;

这两句完全就是不求甚解的范例: -w 和 use warnings; 的功能是重复的.

b114213903

回复 10# 一串儿葡萄皮


    我已经在二楼给你提醒过了，ID行有引号的，不是标准的FASTA格式，BioPerl模块不能识别！

1. >Srcc10g063050.1.1 Receptor-like kinase    Try_threonine protein kinase
   
2. MKTKHKLTPRPFTPTPSPTHIMGILLICFIFSITNSFVIAQDDAVPAKSFPVFTPEDNFL
   
3. IDCGATSSITLPGNKAFQPDQNTAKYLSYTGKDIQACASDKINVPSTLYVNAKIFTTEAI
   
4. YTFHASTSGLHWIRLHFFPFKYEEYDLK
   
5. ">Solyc11g072930.1.1 LRR receptor-like serine_threonine-protein kinase, RLP"
   
6. MASSYFLLLVLVLSVFSVSADVFVSLDCGSSEAYTDHETSIDWLGDVDYVANGESHVVPS
   
7. NNSISHVSALEVRGLDSTMYSHVDDNSSDPPRITALYLSKFNLSGSLPDFSSMDAL
   
8. ETIDLSNNNLDGPIPDFFGTLPNLKELNLANNKFSGPVPASLSNKNGLTLDTSGNSDLCS
   
9. SSEESCQNNDSSSPGNDQPTTGSTNNNKKKKKKKNNLPIILGTTISAFLLLWAIVGIFAI
   
10. LHYKNKRAATSLINPGQASGGSTPFVDRVQMSEKIEKNPEVTAHDHENSTNV
    
11. ">Solyc12g00890.1.1 Kinesin  IPR001752  Kinesin, motor region"
    
12. ESVINGRDLLGFSLTSPDLVICTGSPDIPARNYGDSPEFLKGCSISLENGI
    
13. KGSEEVQAATKLFTDWQGSKDDDLCAPADFELPSPPVEENSSELSVPIVSINVGSTDCIS
    
14. SESGIQFSEDKYFCGGNVLSTDTRIEESICASVYQTARVGNFSYHFNNLSAGFYLVDLHF
    
15. VEVVLTDGSTGDFSENSPQRNSLEVNGDIKAAGKLQLANVSREK

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这些示例数据，就用BioPerl的Bio::SeqIO模块来读只能识别第一个序列！

1. #!/usr/bin/perl
   
2. use strict;
   
3. use Bio::SeqIO;
   
4. use Bio::Seq;
   
5. 
   
6. my $fasta=shift @ARGV;
   
7. (my $Out=$fasta)=~s/(\.[^\.]+)$/_out$1/;
   
8. 
   
9. open (IN,"<$fasta") or die "Open $fasta failed!\n";
   
10. my $Out=Bio::SeqIO->new(-file=>">$Out",-format=>'fasta');
    
11. 
    
12. my ($flag,$seq,$id,$desc)=();
    
13. while(my $line=<IN>){
    
14.         chomp($line);
    
15.         if($line=~/\>/){
    
16.                 if($flag){
    
17.                         print "$id\t$desc\n$seq\n";
    
18.                         my $SEQ_OBJ=Bio::Seq->new(-seq=>$seq,-id=>$id,-desc=>$desc,-alphabet=>'protein');
    
19.                         $Out->write_seq($SEQ_OBJ);
    
20.                 }
    
21.                 $line=~s/[\"\>]//g;
    
22.                 ($id,$desc)=split (/\s+/,$line,2);
    
23.                 $seq=undef;
    
24.                 $flag=1;
    
25.         }else{
    
26.                 $seq.=$line;
    
27.         }
    
28. }
    
29. print "$id\t$desc\n$seq\n";
    
30. my $SEQ_OBJ=Bio::Seq->new(-seq=>$seq,-id=>$id,-desc=>$desc,-alphabet=>'protein');
    
31. $Out->write_seq($SEQ_OBJ);
    
32. 
    
33. $Out->close();

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一串儿葡萄皮

受教了，这里果然是个好地方，谢谢回复 12# MMMIX


   

一串儿葡萄皮

(my $Out=$fasta)=~s/(\.[^\.]+)$/_out$1/;这一句怎么理解？O(∩_∩)O谢谢









回复 14# b114213903


   

MMMIX

一串儿葡萄皮 发表于 2015-08-12 15:20
(my $Out=$fasta)=~s/(\.[^\.]+)$/_out$1/;

等价于:

1. 
   
2. my $Out = $fasta;
   
3. $Out =~ s/(\.[^\.]+)$/_out$1/;
   

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一串儿葡萄皮

1. 2
   
2. my ($flag,$seq,$id)=();
   
3. 
   
4. --------------------- WARNING ---------------------
   
5. MSG: sequence '1' doesn't validate, mismatch is  ($,,$,,$,),();
   
6. ---------------------------------------------------
   
7. 
   
8. ------------- EXCEPTION -------------
   
9. MSG: Attempting to set the sequence '1' to [my ($flag,$seq,$id)=();] which does not look healthy
   
10. STACK Bio::PrimarySeq::seq /usr/lib64/perl5/vendor_perl/5.16.0/Bio/PrimarySeq.pm:285
    
11. STACK Bio::PrimarySeq::new /usr/lib64/perl5/vendor_perl/5.16.0/Bio/PrimarySeq.pm:239
    
12. STACK Bio::Seq::new /usr/lib64/perl5/vendor_perl/5.16.0/Bio/Seq.pm:497
    
13. STACK toplevel delete_qw-A.pl:18
    
14. -------------------------------------
    

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回复 14# b114213903

有这样的报错？
   

b114213903

我这运行正常，不知道什么原因

104359176

文件替换要考虑特殊情况，这种情况加一个位置限定符就好了：

1. /^\<"|"$/

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特别声明引号出现在开始尖括号的后面和行末。