Question

我正在解析一个大型EMBL文件（＆gt; 1G）并将其转换为gff文件。它有一些条目与传统的embl形成不匹配，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整个序列的一小部分，我想继续编写脚本，暂时忽略该异常。但perl脚本始终由异常停止。

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, &lt;GEN0> line 538764.
]

注意：我没有两次发布异常，它只是以这种方式发生，似乎只捕获了一个异常。

以下是导致问题的embl文件块。 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无法捕获低级别的Perl错误。还要检查$SIG{__DIE__}处理程序。如果一个骰子处理程序被写得不够熟练，它可能会死掉。例如，如果处理程序未检查$EXCEPTIONS_BEING_CAUGHT，则它可能来自处理程序exit。

但是看看你的输出，如果它打印出来：

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，它没有按照你说的那样做。您的eval 正在捕捉错误，或者您无法在前面使用"Oh no!"进行打印。它看起来像还在它自己做一些堆栈跟踪转储。

最后，看起来您的程序状态与数据有关，并且文件中的某些错误值会使其处于错误状态。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是否存在其他内容。看起来输入文件中的违规行是＃538,764。但我可能是错的。

注意：在评论中解决您的问题。如果Bioperl正在处理它发现的错误，而你只是想要浏览一系列记录，那么我的建议是你将eval 放在循环中 - {{{ 1}}或while循环。对于某些多线程应用程序，这是一个非常标准的形式。

for

如果可能，请记住将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; }放在要恢复处理的位置。

Perl如何捕获一次抛出的两个异常

1 个答案: