序列長(zhǎng)度篩選求助�。ㄒ呀鉀Q，再次謝謝b114213903）

56836430

有多條這樣的序列，想根據(jù)它們的長(zhǎng)度進(jìn)行篩選，如小于100個(gè)氨基酸的刪除
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

從網(wǎng)上找到一個(gè)例子，但是這個(gè)例子中進(jìn)行長(zhǎng)度計(jì)算時(shí)，沒有去除“-”，腳本如下：
#!/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);
}

請(qǐng)問怎么改進(jìn)這個(gè)腳本，從而能實(shí)現(xiàn)目標(biāo)？

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();

復(fù)制代碼

56836430

完美，謝謝�。。。�！

b114213903 發(fā)表于 2015-10-10 12:51