序列长度筛选求助！（已解决，再次谢谢b114213903）

56836430

有多条这样的序列，想根据它们的长度进行筛选，如小于100个氨基酸的删除
in.fasta
>lcl|Abi_c1818_g1_i1_m.11845 unnamed protein product
-------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------
------------------------PAVFSKGFNPQHVADGLYGRHLFVYSWPEGSLKQTLDLGSTGLIPLEVRFLHDPAKDTGYVACALSS
TLV----------------------------------------------------------------------------------------
-------------------------------------------------------------------------------------------
-------------------
>lcl|Abi_c315_g1_i1_m.67006 unnamed protein product
------------------------------------------------------------GP----------------------GY-----
-------------------------------ASPKEA---------MEGPREALIYVTAVYT------------GTGRGKPDYLATVDVDP
TSPTYSKVVHRLPVPHLGDELHHSGWNACSSCHGDASAQRRYLILPSLISGRIYAVDTAKDPRAPVLHKVVEPETILAKTGLGYPHTAHCL
ASGDILVSCLGDKDGNAEGNGFLLLDSDLNVKGR---------------------------------------------------WEKPGN
SPKFGYDFWYQPRHKTMISSSWGAPAAFTKGFNPQHVLDGLYGKHLFVYSWPDGTLKQTIDLGNEGLIPLEVRFLHEPSKDTGYVGCALSG
NMVRFFKTSDGSWDHEVVISVPRFKVQNWILPEMPGLITDLLISLDDRYLYFVNWLHGDVRQYNIEDPKKPVLVGQVWVGGLVRKGSKVIV
EKENGQQWQSDVSDVQGKYLRGGPQMIQLSLDGKRLYVTNSLFSAWDRQFY-PELIEKGSHILQIDCNTEKGGLSVNSNFFVDFETEPEGP
ALAHEMRYPGGDCTSDIWV

out.fasta

>lcl|Abi_c315_g1_i1_m.67006 unnamed protein product
------------------------------------------------------------GP----------------------GY-----
-------------------------------ASPKEA---------MEGPREALIYVTAVYT------------GTGRGKPDYLATVDVDP
TSPTYSKVVHRLPVPHLGDELHHSGWNACSSCHGDASAQRRYLILPSLISGRIYAVDTAKDPRAPVLHKVVEPETILAKTGLGYPHTAHCL
ASGDILVSCLGDKDGNAEGNGFLLLDSDLNVKGR---------------------------------------------------WEKPGN
SPKFGYDFWYQPRHKTMISSSWGAPAAFTKGFNPQHVLDGLYGKHLFVYSWPDGTLKQTIDLGNEGLIPLEVRFLHEPSKDTGYVGCALSG
NMVRFFKTSDGSWDHEVVISVPRFKVQNWILPEMPGLITDLLISLDDRYLYFVNWLHGDVRQYNIEDPKKPVLVGQVWVGGLVRKGSKVIV
EKENGQQWQSDVSDVQGKYLRGGPQMIQLSLDGKRLYVTNSLFSAWDRQFY-PELIEKGSHILQIDCNTEKGGLSVNSNFFVDFETEPEGP
ALAHEMRYPGGDCTSDIWV

从网上找到一个例子，但是这个例子中进行长度计算时，没有去除“-”，脚本如下：
#!/usr/bin/perl
use strict;

use Bio::SeqIO;


my ($infile, $outfile, $cut) = @ARGV;
my $o_seqi = Bio::SeqIO->new(-file => $infile, -format => 'fasta');
my $o_seqo = Bio::SeqIO->new(-file => ">$outfile",-format => 'fasta');
while (my $o_seq = $o_seqi->next_seq) {
next if ($o_seq->length < $cut);
$o_seqo->write_seq($o_seq);
}

请问怎么改进这个脚本，从而能实现目标？

b114213903

1. #!/usr/bin/perl
   
2. use strict;
   
3. use Bio::SeqIO;
   
4. 
   
5. my ($infile, $outfile, $cut) = @ARGV;
   
6. my $o_seqi = Bio::SeqIO->new(-file => $infile, -format => 'fasta');
   
7. my $o_seqo = Bio::SeqIO->new(-file => ">$outfile",-format => 'fasta');
   
8. while (my $o_seq = $o_seqi->next_seq) {
   
9.         (my $seq=$o_seq->seq())=~s/-//g;
   
10.         next if (length($seq) < $cut);
    
11.         $o_seqo->write_seq($o_seq);
    
12. }
    
13. $o_seqi->close();
    
14. $o_seqo->close();

复制代码

56836430

完美，谢谢！！！！！

b114213903 发表于 2015-10-10 12:51