Perl如何捕獲一次拋出兩個異常

Question

我正在解析一個大的EMBL文件（> 1G）並將其轉換爲gff文件。它有一些條目與傳統的embl格式不匹配，從而導致bioperl模塊拋出異常。我的問題是，因爲有錯誤的條目只是整個序列的一小部分，我想繼續使用該腳本，現在就忽略該異常。但是perl腳本總是被異常停止。

我是一個Linux下的操作系統和與Perl版本5.8.8

我的Perl腳本

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. 
] 

注意的錯誤：我沒有貼例外兩次，它只是以這種方式發生，只有一個例外似乎被捕獲。

這是embl文件的塊造成的問題。 mRNA條目導致第一個異常，CDS導致第二個異常。

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沒有捕獲到低級的Perl錯誤。同時檢查一個$SIG{__DIE__}處理程序。如果一個模具處理程序是不熟練的，它可能會死亡。例如，如果處理程序不檢查$EXCEPTIONS_BEING_CAUGHT，則它可能來自處理程序的exit。

但是就看你的輸出，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. ] 

然後，它沒有這樣做，你說什麼它正在做。您的eval是捕獲錯誤，否則您將無法在前面打印"Oh no!"。它看起來像也自己做一些堆棧跟蹤轉儲是所有。

最後，它看起來像你的程序狀態是依賴於數據的，你的文件中的一些錯誤值可能會使它處於錯誤的狀態。無論出於何種原因，它無法創建BIO::Seq對象，並將其傳遞給某個函數，該函數檢查參數isa是否有其他值。它看起來像輸入文件中的有問題的行是＃538,764。但我可能是錯的。

注意：解決您的問題在評論。如果Bioperl正在處理它發現的錯誤，並且您只想記錄一系列記錄，那麼我建議您將eval放在的循環中 - while或for循環。對於一些多線程應用程序，這是一個非常標準的表單。

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; 
} 

記得把eval在您想要恢復處理，如果可能的話的地方。