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大家好，我在使用 Perl 模块时遇到问题，因为我正在使用此模块从包含多组信息的平面文件中检索某些特定行，正如我在代码中提到的那样。（这是 Bio::Parse 的示例代码::SwissProt.pm）。但问题是，每当我们使用这段代码时，它的 Refs 语句都会出现问题。它在第 345 行尝试修改只读值时出错。c:/wamp/bin/perl/site/lib/bio/parse/swissprot.pm输入文件如下所示

输入文件（平面文件）

ID   P72354_STAAU            Unreviewed;       575 AA.
AC   P72354;
DT   01-FEB-1997, integrated into UniProtKB/TrEMBL.
DT   01-FEB-1997, sequence version 1.
DT   29-MAY-2013, entry version 79.
DE   SubName: Full=ATP-binding cassette transporter A;
GN   Name=abcA;
OS   Staphylococcus aureus.
OC   Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcus.
OX   NCBI_TaxID=1280;
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=NCTC 8325;
RX   PubMed=8878592;
RA   Henze U.U., Berger-Bachi B.;
RT   "Penicillin-binding protein 4 overproduction increases beta-lactam
RT   resistance in Staphylococcus aureus.";
RL   Antimicrob. Agents Chemother. 40:2121-2125(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=NCTC 8325;
RX   PubMed=9158759;
RA   Henze U.U., Roos M., Berger-Bachi B.;
RT   "Effects of penicillin-binding protein 4 overproduction in
RT   Staphylococcus aureus.";
RL   Microb. Drug Resist. 2:193-199(1996).
 CC   -!- SIMILARITY: Belongs to the ABC transporter superfamily.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; X91786; CAA62898.1; -; Genomic_DNA.
DR   ProteinModelPortal; P72354; -.
DR   SMR; P72354; 335-571.
DR   GO; GO:0016021; C:integral to membrane; IEA:InterPro.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0042626; F:ATPase activity
DR   GO; GO:0006200; P:ATP catabolic process; IEA:GOC.
DR   InterPro; IPR003593; AAA+_ATPase.
DR   InterPro; IPR003439; ABC_transporter-like.
DR   InterPro; IPR017871; ABC_transporter_CS.
DR   InterPro; IPR017940; ABC_transporter_type1.
DR   InterPro; IPR001140; ABC_transptr_TM_dom.
DR   InterPro; IPR011527; ABC_transptrTM_dom_typ1.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   Pfam; PF00664; ABC_membrane; 1.
DR   Pfam; PF00005; ABC_tran; 1.
DR   SMART; SM00382; AAA; 1.
DR   SUPFAM; SSF90123; ABC_TM_1; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   PROSITE; PS50929; ABC_TM1F; 1.
DR   PROSITE; PS00211; ABC_TRANSPORTER_1; 1.
DR   PROSITE; PS50893; ABC_TRANSPORTER_2; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Nucleotide-binding.
SQ   SEQUENCE   575 AA;  64028 MW;  F7E30A85971719B9 CRC64;
     MKRENPLFFL FKKLSWPVGL IVAAITISSL GSLSGLLVPL FTGRIVDKFS VSHINWNLIA
     LFGGIFVINA LLSGLGLYLL SKIGEKIIYA IRSVLWEHII QLKMPFFDKN ESGQLMSRLT
     DDTKVINEFI SQKLPNLLPS IVTLVGSLIM LFILDWKMTL LTFITIPIFV LIMIPLGRIM
     QKISTSTQSE IANFSGLLGR VLTEMRLVKI SNTERLELDN AHKNLNEIYK LGLKQAKIAA
     VVQPISGIVM LLTIAIILGF GALEIATGAI TAGTLIAMIF YVIQLSMPLI NLSTLVTDYK
     KAVGASSRIY EIMQEPIEPT EALEDSENVL IDDGVLSFEH VDFKYDVKKI LDDVSFQIPQ
     GQVSAFVGPS GSGKSTIFNL IERMYEIESG DIKYGLESVY DIPLSKWRRK IGYVMQSNSM
     MSGTIRDNIL YGINRHVSDE ELINYAKLAN CHDFIMQFDE GYDTLVGERG LKLSGGQRQR
     IDIARSFVKN PDILLLDEAT ANLDSESELK IQEALETLME GRTTIVIANR LSTIKKAGQI
     IFLDKGQVTG KGTHSELMAS HAKYKNFVVS QKLTD
//

脚本部分 C:/wamp/bin/perl/bin/perl.exe 

use strict;
use warnings;
use Data::Dumper;
use SWISS::Entry;
use Bio::Parse::SwissProt;
my $sp = Bio::Parse::SwissProt->new(FILE =>"me.txt")or die $!;

# Read in all the entries and fill %entries
my $entry_name =  $sp->entry_name( );
print "$entry_name\n";
my $seq_len = $sp->seq_len( );
print "$seq_len\n";
$refs = $sw->refs();
$refs = $sw->refs(TITLE => 1, AUTH => 1);
for my $i (0..$#{$refs}) {
    print "@{$refs->[$i]}\n";

输出应该像

[1]
  NUCLEOTIDE SEQUENCE.
  STRAIN=NCTC 8325;
  PubMed=8878592;
  Henze U.U., Berger-Bachi B.;
  "Penicillin-binding protein 4 overproduction increases beta-lactam
  resistance in Staphylococcus aureus.";
  Antimicrob. Agents Chemother. 40:2121-2125(1996).
[2]
  NUCLEOTIDE SEQUENCE.
  STRAIN=NCTC 8325;
  PubMed=9158759;
  Henze U.U., Roos M., Berger-Bachi B.;
  "Effects of penicillin-binding protein 4 overproduction in
  Staphylococcus aureus.";
  Microb. Drug Resist. 2:193-199(1996).
</code></pre>
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1 回答 1

1

在互联网上进行一些搜索后，您似乎正在使用SWISS::EntrySwissknife软件包，并且您（或某人）似乎从 sourceforgeBio::Parse::SwissProt下载了一个独立项目（不是 BioPerl 的一部分）。我对这些项目中的任何一个都不熟悉，但是您可以通过简单地使用BioPerl 获得所需的信息。这是获取参考的示例：Bio::SeqIO

#!usr/bin/env perl

use strict;
use warnings;
use Bio::SeqIO;

my $usage = "perl $0 swiss-file\n";
my $infile = shift or die $usage;

my $io = Bio::SeqIO->new(-file => $infile, -format => 'swiss');
my $seqio = $io->next_seq;
my $anno_collection = $seqio->annotation;

for my $key ( $anno_collection->get_all_annotation_keys ) {
    my @annotations = $anno_collection->get_Annotations($key);
    for my $value ( @annotations ) {
        if ($value->tagname eq "reference") {
            my $hash_ref = $value->hash_tree;
            for my $key (keys %{$hash_ref}) {
                print $key,": ",$hash_ref->{$key},"\n" if defined $hash_ref->{$key};
            }
        }
    }
}

运行它会提供您想要的信息：

authors: Henze U.U., Berger-Bachi B.
location: Antimicrob. Agents Chemother. 40:2121-2125(1996).
title: "Penicillin-binding protein 4 overproduction increases beta-lactam resistance in Staphylococcus aureus."
pubmed: 8878592
authors: Henze U.U., Roos M., Berger-Bachi B.
location: Microb. Drug Resist. 2:193-199(1996).
title: "Effects of penicillin-binding protein 4 overproduction in Staphylococcus aureus."
pubmed: 9158759

BioPerl Feature Annotation HOWTO对解析这些类型的文件很有帮助。如果您想获取条目然后解析它们，您可以使用Bio::DB::Swissprot并在上面的示例中添加几行代码。我知道这不是您特定问题的答案，但它是一个解决方案，您会发现很多人可以帮助您使用 BioPerl。

于 2013-07-05T17:20:40.843 回答