fasta格式文件转换为 反向互补链
1 #!/usr/bin/env perl 2 3 use strict; 4 use warnings; 5 6 local $/ =">"; 7 while(<>){ 8 chomp; 9 my $lineSepPos = index($_," 10 "); 11 my $header = substr($_,0,$lineSepPos); 12 if($header){ 13 print(">", $header,"(reverse-complemented) 14 "); 15 my $sequence = reverse(substr($_,$lineSepPos)); 16 # see http://shootout.alioth.debian.org/u32/performance.php?test=revcomp#about 17 # for ambiguity codes and translation 18 $sequence =~ tr/ACGTUMRWSYKVHDBNacgtumrwsykvhdbn 19 /TGCAAKYWSRMBDHVNtgcaakywsrmbdhvn/d; 20 for(my $pos = 0; $pos < length($sequence);$pos += 60){ 21 print(substr($sequence, $pos, 60)," 22 "); 23 } 24 } 25 }
数值60代表每行输出60个碱基。（感谢原作者）
执行命令：perl fasta_re.perl srr.fasta > srr_re.fasta
如若执行不了，记得查看pl文件是否有可执行权限。
