Question

大神们，本人新手，求一个perl程序，谢谢

序列信息如下：

>ENSG00000179088
TGGTGGTTTGCTGCATCTATCATCCCATCACCTAGGTATTAAGCCGAGCATGCATTAGCTATTTTTCCTA
ATGCCCTCCCTCCCCCAACCCCACCCCCCAACAGGCCCCAGTGCATATTGTTTCCCTCCCTGTGTCCATG
TATTCTCATTGTTCAGCTTCCATTTATAAGTGAGAACATGCAGTGTTTCTGTTTTCTGTTCTAGTGTTAG
TTTGCTGAGGATAATGGCTTCCAGCTCCATCCATGTACCTGCAAAGGCCATGATCTTGTTCCTTTTTATG
GCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTTATCCAGTCTATCATTGATGGGCATTTGG
GTGGAGTTAGACTTTTAAATATTCCATACATAAGTGAGATCATGCAGTGTTTGTCCTTCTGTGACTGGTT
TATTTAACCTAATGTCCTCTAGGCTCATCCATATTGTCACAAGTGGGGAGATTTTCTTCCTTTTTTGTCT
>ENSG00000178828
CTCTCTTTCTTCTTTTTTTTTTTTGAGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGAAGTGGCGCT
GTCTCTGCTCACTGCAACCTCTGCCTCACAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTG
GGACTATGGGCGCGTGCCACCACACCCGGCTAATTTTTTTTATTTTGTTTTAGTAGAGACGGGATTTCAC
CATGTTAGCCAGGATGGTATCGATCTCCAGACCTAGTGATCCGCCTGCCTCGGCCTCCCAAAATGTTGGA
ATTATAGGCGTGAGCCACCGTGCCCAGCCTTTTCTTTCTTTTAAAATCTGTTTGCACCACAAAAGAATGA
GCTCTACAGGGATGGGGATCTTTGTTTATTTTGCCTGACACGTGATAGGTACTCAAGGATTATTTGCTGA
AATTGATGAAGAGTTCTCATTTCTGTAGTGAAAACAGCAGCTGTAGGAATGGTAACAGAGTAGACAAAGG
GCATTTTCAGGTGTTTTTGGTGTGCAAAGCTGCACCTCTGTGATATTGTTGGGGTTAAGAGAGCACTGGG
TATCCATAGCCACTAGCAGTACAGTCTTGGGCCAGTCACTTACCATTTTGGGGCTTGCTACCTTATCTAT

要把>ENSG00000179088下的序列提取出来并把所有序列变换成一行，然后从中提取第38位到89位之间的序列。谢谢

Answer 1

#!/usr/bin/perl -w
use strict;
die "perl $0 <seq_file.fa>\n" unless(@ARGV == 1);
open IN,$ARGV[0];
$/=">";
<IN>;
$/="\n";
while(<IN>){
chomp $_;
my $seqName = $_;
$/=">";
my $seq = <IN>;
chomp $seq;
$/ = "\n";
if($seqName =~/ENSG00000179088/){
$seq =~s/[\r\n]//g;
my $result = substr($seq,37,52);
print "提取的子序列为:\n$result\n";
}
}
close IN;

使用的时候，将假设将脚本存为 picseq.pl
然后序列所在fa文件为 test.fa
运行的时候再命令行输入 picseq.pl test.fa
回车即可。
如果有疑问，可以随时追问，希望能够帮到你

Answer 2

$/=">";
<>;
while(<>){

chomp;
@tmp=split/\n/,$_,2;
if ($tmp[0] eq ENSG00000179088){
$tmp[1]=~s/\s+//g;
print ">$tmp[0]\n$tmp[1]\n"；
$seq=substr($tmp[1],37,52)；
print "$seq\n";
}
}