Perl如何捕获一次抛出的两个异常

Question

我正在解析一个大型 EMBL 文件 (>1G) 并将其转换为 gff 文件。它有一些条目与传统的 embl 格式不匹配，因此导致 bioperl 模块抛出异常。我的问题是因为有错误的条目只是总序列的一小部分，我想继续脚本，暂时忽略异常。但是 perl 脚本总是被异常停止。

我在 linux 操作系统下使用 perl 版本 5.8.8

我的 perl 脚本

use strict;
use Bio::SeqIO;
use Bio::Tools::GFF;
use warnings;
use Try::Tiny;

open (E ,">","emblError.txt");

if (@ARGV != 1) {    die "USAGE: embl2gff.pl   > outputfile.\n"; }

my $in = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'EMBL');
eval {
   while (my $seq = $in->next_seq) {
      for my $feat ($seq->top_SeqFeatures) {
          my $gffio = Bio::Tools::GFF->new(-gff_version => 3);
          print $feat->gff_string($gffio)."\n";
        }
    }
};
if ($@) {
    warn "Oh no! [$@]\n";
}

我得到的错误

Name "main::E" used only once: possible typo at embl2GFF3.pl line 7.

--------------------- WARNING ---------------------
MSG: exception while parsing location line [join(9174..9343,14214..14303)complement(9268..9363),complement(9140..9198),complement(8965..9034),complement(8751..8884),complement(8419..8535),complement(8232..8337),complement(7952..8149),complement(7256..7332),complement(7051..7175),complement(6769..6877),complement(6601..6659),complement(4690..6530))] in reading EMBL/GenBank/SwissProt, ignoring feature mRNA (seqid=XcouVSXmac70forkSpecies.Scaffold1050.final):
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bad operator 1: had multiple locations 2, should be SplitLocationI
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472
STACK: Bio::Factory::FTLocationFactory::from_string /usr/lib/perl5/site_perl/5.8.8/Bio/Factory/FTLocationFactory.pm:210
STACK: Bio::Factory::FTLocationFactory::from_string /usr/lib/perl5/site_perl/5.8.8/Bio/Factory/FTLocationFactory.pm:204
STACK: Bio::SeqIO::FTHelper::_generic_seqfeature /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/FTHelper.pm:133
STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/embl.pm:403
STACK: embl2GFF3.pl:14
-----------------------------------------------------------

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: exception while parsing location line [join(14219..14303,14368..14513)complement(9140..9198),complement(8965..9034),complement(8751..8884),complement(8419..8535),complement(8232..8337),complement(7952..8149),complement(7256..7332),complement(7051..7175),complement(6769..6877),complement(6601..6659),complement(6461..6530))] in reading EMBL/GenBank/SwissProt, ignoring feature CDS (seqid=XcouVSXmac70forkSpecies.Scaffold1050.final):
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bad operator 1: had multiple locations 2, should be SplitLocationI
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472
STACK: Bio::Factory::FTLocationFactory::from_string /usr/lib/perl5/site_perl/5.8.8/Bio/Factory/FTLocationFactory.pm:210
STACK: Bio::Factory::FTLocationFactory::from_string /usr/lib/perl5/site_perl/5.8.8/Bio/Factory/FTLocationFactory.pm:204
STACK: Bio::SeqIO::FTHelper::_generic_seqfeature /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/FTHelper.pm:133
STACK: Bio::SeqIO::embl::next_seq /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/embl.pm:403
STACK: embl2GFF3.pl:14
-----------------------------------------------------------

---------------------------------------------------
Oh no! [Can't call method "isa" on an undefined value at /usr/lib/perl5/site_perl/5.8.8/Bio/Seq.pm line 1142, <GEN0> line 538764.
]

注意：我没有两次发布异常，它只是以这种方式发生，似乎只有一个异常被捕获。

这是导致问题的 embl 文件块。 mRNA 进入导致第一个异常，CDS 导致第二个异常。

FT   mRNA            join(9174..9343,14214..14303)
FT                   complement(9268..9363),complement(9140..9198),
FT                   complement(8965..9034),complement(8751..8884),
FT                   complement(8419..8535),complement(8232..8337),
FT                   complement(7952..8149),complement(7256..7332),
FT                   complement(7051..7175),complement(6769..6877),
FT                   complement(6601..6659),complement(4690..6530))
FT                   /gene="ENSXMAG00000014948"
FT                   /note="transcript_id=ENSXMAT00000015030"
FT   CDS             join(14219..14303,14368..14513)
FT                   complement(9140..9198),complement(8965..9034),
FT                   complement(8751..8884),complement(8419..8535),
FT                   complement(8232..8337),complement(7952..8149),
FT                   complement(7256..7332),complement(7051..7175),
FT                   complement(6769..6877),complement(6601..6659),
FT                   complement(6461..6530))
FT                   /gene="ENSXMAG00000014948"
FT                   /protein_id="ENSXMAP00000015010"
FT                   /note="transcript_id=ENSXMAT00000015030"
FT                   /db_xref="HGNC_transcript_name:ENO3-201"

Answer 1

eval 不会捕获低级 Perl 错误。还要检查$SIG{__DIE__} 处理程序。如果一个 die-handler 写得不熟练，它可能就死了。例如，如果处理程序不检查$EXCEPTIONS_BEING_CAUGHT，它可能会来自模具处理程序的exit。

但只要看看你的输出，如果它打印了这个：

Oh no! [Can't call method "isa" on an undefined value at 
/usr/lib/perl5/site_perl/5.8.8/Bio/Seq.pm line 1142, line 538764. ]

那么，它并没有按照你所说的那样做。您的eval 发现了错误，否则您将无法在前面加上"Oh no!" 打印它。看起来它也自己做了一些堆栈跟踪转储。

最后，您的程序状态看起来是依赖于数据的，并且您的文件中的一些错误值可能会将其置于错误状态。无论出于何种原因，它都无法创建 BIO::Seq 对象并将其传递给某个函数，该函数检查参数 isa 是否存在。看起来您输入文件中的违规行是#538,764。但我可能是错的。

注意：解决您在 cmets 中的问题。如果 Bioperl 正在处理它发现的错误，而您只想浏览一系列记录，那么我的建议是您将 eval inside 放在循环中——while 或for 循环。对于某些多线程应用程序来说，这是一种非常标准的形式。

 while ( 1 ) {
     eval { $me->spin(); 1; } or say "WARNING: $@";
     # unless we are officially done, just get ready to
     # handle somebody causing an exception in our thread.
     last if $me->done; 
 }

如果可能，请记住将eval 放在要恢复处理的位置。