perl脚本将embl格式文件转换成fasta及gff3格式

 最近找基因组注释的时候发现一个基因组只上传了embl格式，为了下游分析想把它分成fasta和gff3，但是该embl格式有一点奇怪，常用的转格式软件转不成功，那就自己写个脚本好了。
 该embl文件大概长这样：

ID   XXX; XXX; linear; other RNA; XXX; XXX; 177118352 BP.
XX
AC   XXX; 
XX
AC * _scaf_1
XX
PR   Project:PRJEB51672;
XX
DT   04-NOV-2022 (Rel. 133, Created)
XX
DE   XXX
XX
KW   .
XX
OS   Poa pratensis
XX
OC   cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina;
OC   Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida;
OC   Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae;
OC   BOP clade; Pooideae; Poodae; Poeae; Poeae Chloroplast Group 2 (Poeae type);
OC   Poodinae; Poinae; Poa.
XX
RN   [1]
RP   1-177118352
RG   XXX
RT   ;
RL   Submitted (04-NOV-2022) to the INSDC.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..177118352
FT                   /mol_type="other RNA"
FT                   /organism="Poa pratensis"
FT   gene            complement(11455981..11457619)
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462"
FT                   /note="source:PanAnd"
FT   mRNA            complement(11455981..11457619)
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462_T001"
FT                   /note="source:PanAnd"
FT   exon            complement(11455981..11457619)
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462_T001.exon.1"
FT                   /note="source:PanAnd"
FT   3'UTR           complement(11455981..11456845)
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462_T001.three_prime_utr.4"
FT                   /note="source:PanAnd"
FT   CDS             complement(11456846..11457412)
FT                   /codon_start=1
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462_P001"
FT                   /note="source:PanAnd"
FT                   /transl_table=1
FT   5'UTR           complement(11457413..11457619)
FT                   /locus_tag="PPR_LOCUS256280"
FT                   /note="ID:Ppr00001aa254462_T001.five_prime_utr.3"
FT                   /note="source:PanAnd"
FT   gene            complement(11455981..11461780)
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461"
FT                   /note="source:PanAnd"
FT   mRNA            complement(join(11455981..11456778,11461090..11461780))
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_T001"
FT                   /note="source:PanAnd"
FT   exon            complement(11455981..11456778)
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_T001.exon.1"
FT                   /note="source:PanAnd"
FT   exon            complement(11461090..11461780)
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_T001.exon.2"
FT                   /note="source:PanAnd"
FT   3'UTR           complement(join(11455981..11456778,11461090..11461145))
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_T001.three_prime_utr.5"
FT                   /note="ID:Ppr00001aa254461_T001.three_prime_utr.6"
FT                   /note="source:PanAnd"
FT   CDS             complement(11461146..11461712)
FT                   /codon_start=1
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_P001"
FT                   /note="source:PanAnd"
FT                   /transl_table=1
FT   5'UTR           complement(11461713..11461780)
FT                   /locus_tag="PPR_LOCUS256281"
FT                   /note="ID:Ppr00001aa254461_T001.five_prime_utr.4"
FT                   /note="source:PanAnd"
//

 好多东西暂时没用，比如UTR之类的，就先不提取了。

#注释过几天再补！
#!/usr/bin/perl
use strict; use warnings; use Getopt::Std;

my $usage = "embl2other.pl -e <embl file> -g <output gff3 file> or -f <output fasta file>";

my %opt;
getopts('e:g:f:', \%opt);

my $AC;

#如果需要转成fasta
if($opt{
   f}){
   
    my $SQ;

	#创建或覆盖目标文件
	open(FASTA,">","$opt{f}");
	print "";
	close(FASTA);

	#打开文件
	open(FASTA,">>","$opt{f}");
	open(EMBL,"$opt{e}") or die $!;
	while(<EMBL>){
   
		#提取AC，即染色体/contig编号，源文件中有两个AC，抛弃内容只有XXX的一个，再存入文件
	    if(m/^AC/){
   
		    next if (split(/\s+/))[1] eq "XXX;";
		    $AC = (split(/\s+/))[2];
		    print FASTA ">".$AC."\n";
		}

		#从SQ行到\\行之间提取序列并存入目标文件
		if(m/^SQ/ .. m/^\/\//){
   
			next if (m/^SQ/);
			next if (m/^\/\//);
			s/[^A-Z]//g;
			$SQ = $_;
			print FASTA $SQ."\n";
		}
	}
	#关闭文件
	close(FASTA);
	close(EMBL)