perl应用：DNA序列翻译（下）：从fasta格式中读取序列，然后输出蛋白质序列，以及fasta格式的介绍

use strict;  use warnings;      my $dna      ='';  my $protein  ='';  my @file_data=( );  my @filedata;  @filedata  = get_file_data();$dna       = extract_sequence_from_fasta_data(@filedata);  $protein   = dna2peptide($dna);  print_sequence($protein,25);    sub get_file_data{  # A subroutine to get data from a file given its filename#读取文件的子序列    my $dna_filename;my @filedata;    print "please input the Path just like this f:\\\\perl\\\\data.txt\n";       chomp($dna_filename=<STDIN>); open(DNAFILENAME,$dna_filename)||die("can not open the file!");    @filedata     = <DNAFILENAME>;  close DNAFILENAME;  return @filedata;#子函数的返回值一定要记住写}sub extract_sequence_from_fasta_data  {      #*******************************************************************      # A subroutine to extract FASTA sequence data from an array      # 得到其中的序列      # fasta格式介绍：      # 包括三个部分      # 1.第一行中以>开头的注释行，后面是名称和序列的来源      # 2.标准单字母符号的序列      # 3.*表示结尾      #*******************************************************************        my (@fasta_file_data) =@_;      my $sequence =' ';      foreach my $line (@fasta_file_data)      {          #这里忽略空白行          if ($line=~/^\s*$/)          {              next;          }          #忽略注释行          elsif($line=~/^\s*#/)          {              next;          }          #忽略fasta的第一行          elsif($line=~/^>/)          {              next;          }          else          {              $sequence .=$line;          }      }      $sequence=~s/\s//g;      return $sequence;  }    sub print_sequence  {      # A subroutine to format and print sequence data      my ($sequence, $length) = @_;      for (my $pos =0; $pos<length($sequence);$pos+=$length)      {          print substr($sequence,$pos,$length),"\n";      }  }           sub codon2aa     {           #第三种方法        #也就是运用哈希        #我们将所有的密码子作为hash的key，然后将代表的氨基酸作为hash的value        #然后进行匹配        # codon2aa         # A subroutine to translate a DNA 3-character codon to an amino acid         # Version 3, using hash lookup         my($codon) = @_;              $codon = uc $codon;#uc=uppercase;lc=lowercase                       #也就是大小写转换，uc表示将所有的小写 转换为大写                   #lc将所有的大写转换为小写              my(%genetic_code) = (                  'TCA' => 'S',    # Serine         'TCC' => 'S',    # Serine         'TCG' => 'S',    # Serine         'TCT' => 'S',    # Serine         'TTC' => 'F',    # Phenylalanine         'TTT' => 'F',    # Phenylalanine         'TTA' => 'L',    # Leucine         'TTG' => 'L',    # Leucine         'TAC' => 'Y',    # Tyrosine          'TAT' => 'Y',    # Tyrosine         'TAA' => '_',    # Stop         'TAG' => '_',    # Stop         'TGC' => 'C',    # Cysteine         'TGT' => 'C',    # Cysteine         'TGA' => '_',    # Stop         'TGG' => 'W',    # Tryptophan         'CTA' => 'L',    # Leucine         'CTC' => 'L',    # Leucine         'CTG' => 'L',    # Leucine         'CTT' => 'L',    # Leucine         'CCA' => 'P',    # Proline         'CCC' => 'P',    # Proline         'CCG' => 'P',    # Proline         'CCT' => 'P',    # Proline         'CAC' => 'H',    # Histidine         'CAT' => 'H',    # Histidine         'CAA' => 'Q',    # Glutamine         'CAG' => 'Q',    # Glutamine         'CGA' => 'R',    # Arginine         'CGC' => 'R',    # Arginine         'CGG' => 'R',    # Arginine         'CGT' => 'R',    # Arginine         'ATA' => 'I',    # Isoleucine         'ATC' => 'I',    # Isoleucine         'ATT' => 'I',    # Isoleucine         'ATG' => 'M',    # Methionine         'ACA' => 'T',    # Threonine         'ACC' => 'T',    # Threonine         'ACG' => 'T',    # Threonine         'ACT' => 'T',    # Threonine         'AAC' => 'N',    # Asparagine         'AAT' => 'N',    # Asparagine         'AAA' => 'K',    # Lysine         'AAG' => 'K',    # Lysine         'AGC' => 'S',    # Serine         'AGT' => 'S',    # Serine         'AGA' => 'R',    # Arginine         'AGG' => 'R',    # Arginine         'GTA' => 'V',    # Valine         'GTC' => 'V',    # Valine         'GTG' => 'V',    # Valine         'GTT' => 'V',    # Valine         'GCA' => 'A',    # Alanine         'GCC' => 'A',    # Alanine         'GCG' => 'A',    # Alanine         'GCT' => 'A',    # Alanine             'GAC' => 'D',    # Aspartic Acid         'GAT' => 'D',    # Aspartic Acid         'GAA' => 'E',    # Glutamic Acid         'GAG' => 'E',    # Glutamic Acid         'GGA' => 'G',    # Glycine         'GGC' => 'G',    # Glycine         'GGG' => 'G',    # Glycine         'GGT' => 'G',    # Glycine         );              if(exists $genetic_code{$codon})         {             return $genetic_code{$codon};         }        else        {                      print STDERR "Bad codon \"$codon\"!!\n";                 exit;         }     }       sub dna2peptide  {      my ($dna)=@_;      my $protein ='';      for (my $i=0; $i<(length($dna)-2);$i+=3)      {          $protein .=codon2aa(substr($dna,$i,3));      }      return $protein;#这个词错误找了一晚上，没有返回值，所以结果总是没有内容，以后要引以为戒，子程序一定要有返回值  }  

结果如下：

F:\>f:perl\a.plRWRR_GVLGALGRPPTGLQRRRRMGPAQ_EYAAWEA_LEAEVVVGAFATAWDAAEWSVQVRGSLAGVVRECAGSGDMEGDGSDPEPPDAGEDSKSENGENAPIYCICRKPDINCFMIGCDNCNEWFHGDCIRITEKMAKAIREWYCRECREKDPKLEIRYRHKKSRERDGNERDSSEPRDEGGGRKRPVPDPDLQRRAGSGTGVGAMLARGSASPHKSSPQPLVATPSQHHQQQQQQIKRSARMCGECEACRRTEDCGHCDFCRDMKKFGGPNKIRQKCRLRQCQLRARESYKYFPSSLSPVTPSESLPRPRRPLPTQQQPQPSQKLGRIREDEGAVASSTVKEPPEATATPEPLSDEDLF:\>