Perl如何捕获一次抛出两个异常

Question

我正在解析一个大的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，从而导致bioperl模块抛出异常。我的问题是，因为有错误的条目只是整个序列的一小部分，我想继续使用该脚本，现在就忽略该异常。但是perl脚本总是被异常停止。

我是一个Linux下的操作系统和与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

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. 
] 

注意的错误：我没有贴例外两次，它只是以这种方式发生，只有一个例外似乎被捕获。

这是embl文件的块造成的问题。 mRNA条目导致第一个异常，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没有捕获到低级的Perl错误。同时检查一个$SIG{__DIE__}处理程序。如果一个模具处理程序是不熟练的，它可能会死亡。例如，如果处理程序不检查$EXCEPTIONS_BEING_CAUGHT，则它可能来自处理程序的exit。

但是就看你的输出，如果它打印此：

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. ] 

然后，它没有这样做，你说什么它正在做。您的eval是捕获错误，否则您将无法在前面打印"Oh no!"。它看起来像也自己做一些堆栈跟踪转储是所有。

最后，它看起来像你的程序状态是依赖于数据的，你的文件中的一些错误值可能会使它处于错误的状态。无论出于何种原因，它无法创建BIO::Seq对象，并将其传递给某个函数，该函数检查参数isa是否有其他值。它看起来像输入文件中的有问题的行是＃538,764。但我可能是错的。

注意：解决您的问题在评论。如果Bioperl正在处理它发现的错误，并且您只想记录一系列记录，那么我建议您将eval放在的循环中 - while或for循环。对于一些多线程应用程序，这是一个非常标准的表单。

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; 
} 

记得把eval在您想要恢复处理，如果可能的话的地方。