linux perl的while循环中ctrl+c失效,bioperl模块中while循环问题

本帖最后由 hecm129 于 2014-06-05 19:03 编辑

我要找到位于染色体上某两个位点之间的全部基因序列，

loc.txt

1-1  chr1   192967435  195777777

1-2  chr3   10073404        10076403

1-3  chr1   27070214        27900131

...

data.fasta

>AC213524.3_FG003 seq=gene; coord=1:193514391..193515883:-1

ATGACTGTGTTGCATCATTCCCATTTGCCAACTGACACAAAGGTAGGTTGAGGAAGTATG

GCTAGACTATTTTGACAGCCAAGCAGGATAAGGAAGGAAAGAGGGAGAGTTTCTGCTACA

ACAGAAACATAGAAACAGCCTACTTCTGAATTCAAAAAAGAAAAACTCAACCGCACAATT

TTAATAGCTAACTATTATCTTTAAAAGTTTCAAACAGGGCTTAAGAATGAAAAAAAATAT

TATCATATAATCCATGATTGTGTATATATAAAAGTGAACGGATAATTTCTGAAGAAGTGA

TTCTGTCAATCAAGCTGATAACAGCTTTTTACTCATCCGTAGAGGCAGAGCGAAAGGGCT

GGTGGCCGCACACGAGCGTCAGCACCGCCGAGATCGCGGCCTTGTGCCGCGCGTCAGAGC

GAGTCACGCAGACGTGTAGCGGGCGGTGGTGCGCCTGCGGGCATCGCAGGTCTCTCATCG

TCTCGTTCACCTACCGCAAGCACCGACGGGGCGGGGAATCGCATGGTCGGTGTTCCACCC

ATCGCCCGGGGCGAACGGCTGGACGGGTGGGTCGGTGTTCCGGTGGCCGACCACCTGGCG

GGTCGCGCGATCGCAAGGGGCAGGCGCCTCTGTCTCGGCTCGGCCCAGTCACCATCTCTC

...

写如下程序:

#! usr/bin/perl -w

use strict;

use Bio::Perl;

open LOC,"loc.txt" or die "can't open file1";

open OUT,"> genes.obj" or die "can't open file2";

my (%genes);

my $seqin=Bio::SeqIO->new(-file=>"data.fasta",-format=>'fasta');

my $seqout=Bio::SeqIO->new(-file=>"> obj.fa",-format=>'fasta');

while(){

chomp;

my ($markers, $chr, $start, $end)=split/\s+/;

print "$markers, $chr, $start, $end\n";

while(my $seq=$seqin->next_seq){

my $id=$seq->display_id;

my $desc=$seq->desc;

if($desc=~/seq=gene; coord=(\d+):(\d+)..(\d+):.*/){

if(($chr==$1) &&( $start<=$2 ) &&($end>=$3)){

print  OUT "$id\t$1\t$2\t$3\t$start\t$end\n";

#                                print  "$1, $2, $3, $start, $end\n";

$seqout->write_seq($seq);

}

}

}

}

但运行的结果只能得到“1-1  chr1   192967435  195777777”的结果，从打印结果来看，while()能读出第二条位置及以后的位点信息，但是while(my $seq=$seqin->next_seq)循环在while()读出第二条位置时就不能再重新读入文件了 ，请假高手问题出现在哪儿了？有什么解决办法？