각기 다른 유기체에서 시퀀스 길이 가져 오기-genbank 파일

다른 유기체 유형을 포함하는 genbank 파일에서 최대, 최소 및 평균 길이를 얻고 싶습니다. 모든 유기체에 대해 이것을 얻고 싶습니다.

예:

Organism: Homo sapiens
average length = 160 
shortest length = 20 | id of shortest seq
longest length = 500 | id of longest seq

Organism: Caenorhabditis elegans
average length = 140 
shortest length = 40 | id of shortest seq
longest length = 300 | id of longest seq

길이는 알아 냈지만 유기체별로 구분할 수 없습니다

use strict;
use warnings;

print "enter file path: ";
my $filename = <>;
chomp ($filename);
open(IN, $filename) or die "\n error opening file \n;/\n";

$/ = "//";

my %organisms ;
while (my $block = <IN>)  {
    next if $block =~ /^\s*\n\s*$/;
    my ($definition , $sequence) = split "ORIGIN", $block; 

    my $accession; 
    $definition =~ m/(ACCESSION.+[0-9])/x
        ? $accession = $1
        : die "No ACCESSION";

    my $organism;
    $definition =~ m/(ORGANISM\s+.+\n)/x
        ? $organism = $1
        : die "No ORGANISM";


    $sequence =~ s/[\d\n\s\t\/]//g;
    $organisms{ $sequence } = [ $organism, $accession ];
    }

my $sum = 0;
foreach my $sequence( keys %organisms) {

    my $current_len = length($sequence);
         $sum += $current_len;
};
my $number_seqs = scalar keys %organisms;
my $average = ($sum / $number_seqs);
print "average length = $average \n";

my @sorted_keys = sort { length $a  <=>  length $b } keys %organisms ;
my $shortest = $sorted_keys[0];
my $longest  = $sorted_keys[-1];
my $short = length $shortest;
my $long = length $longest;
my $short_id = $organisms{$shortest}->[1];
my $long_id = $organisms{$longest}->[1];
my $short_type = $organisms{$shortest}->[0];
my $long_type = $organisms{$longest}->[0];

print "shortest length = $short | $short_id | $short_type\n";
print "longest length = $long | $long_id | $long_type\n";


exit;

각 유기체의 길이를 인쇄하려면 어느 부분을 변경해야합니까?

입력 예 :

LOCUS       NM_001112            40 bp    mRNA    linear   PRI 20-AP
DEFINITION  Homo sapiens transcript variant 5, mRNA.
ACCESSION   NM_001112
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
ORIGIN      
        1 actgggcggc ccttagaccc
       //
LOCUS       NM_854               212 bp    mRNA    linear   PRI 20-AP
DEFINITION  Homo sapiens transcript variant 1, mRNA.
ACCESSION   NM_854
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
ORIGIN      
        1 gggcaaaag aagcaggtca cacagcctgt ttcctgtttt caaacgggga acttagaaag

//
LOCUS       AW057463                 469 bp    mRNA    linear   EST 29-SE
DEFINITION  ca03d09.x1 C elegans fem3 Q23 S1 Caenorhabditis elegans cDNA 3'
ACCESSION   AW057463
VERSION     AW057463.1  GI:5933102
DBLINK      BioSample: LIBEST_002392
KEYWORDS    EST.
SOURCE      Caenorhabditis elegans
  ORGANISM  Caenorhabditis elegans
ORIGIN      
        1 ttttactcaa aactatctat ccaagttaat cagtagtgtt agttctagtt aagttattaa
       61 ggcgcacggt ctgtctcctt gcttcttctc tttgtatccc ctttctcctt tttcaaaact
      121 tcactttcat caataattgg ttctttagaa tacagttttc caatttccac gtactctctt
      181 ctcttccgat ccttgtcaaa ctttttcttc gggagctcat cttctggaac tactttcaca
//
LOCUS       AW04463                 259 bp    mRNA    linear   EST 14-SE
DEFINITION  ca02d86.x1 C elegans fem6 S12 Q3 Caenorhabditis elegans cDNA 3'
ACCESSION   AW04463
VERSION     AW04463.1  GI:90872
DBLINK      BioSample: LIBEST_004372
KEYWORDS    EST.
SOURCE      Caenorhabditis elegans
  ORGANISM  Caenorhabditis elegans
ORIGIN      
      241 tttttcgatg gaaccaaacg ggaacgagtt ggcttttcca ccaaaagatt agcgtactcc
      301 gaactgtatt tccccttctt tttcttttca agaggaacat tttctcgttg agtatcatcg
      361 tcctccaaac tttgttgagt agtcatggac tgggtccgag agaattcaac ggtaggcatg
      421 gaacctttgc tcttgtcgtc gtttgccttt ggtgcctttc ccttttgaa
//