[Bioperl-l] pir.pm => bug

Laure.Durufle at serono.com Laure.Durufle at serono.com
Fri Jun 25 06:05:39 EDT 2004


I moved the package pir.pm / we give the file and with pir.pm we can parse
this file  pir*.dat :

like this format :

                P R O T E I N  S E Q U E N C E  D A T A B A S E
                             of PIR-International

                      Section 1. Fully Classified Entries
                         Release 79.01, April 04, 2004
                       20685 sequences, 8103841 residues

                       Protein Information Resource (PIR)*
                    National Biomedical Research Foundation
                          3900 Reservoir Road, N.W.,
                          Washington, DC  20007, USA

   Japan International Protein           Munich Information Center for
   Information Database (JIPID)             Protein Sequences (MIPS)
         Amakubo 1-16-1          GSF-Forschungszentrum f. Umwelt und
    Tsukuba 305-0005, Japan            am Max-Planck-Instut f. Biochemie
                                  Am Klopferspitz 18, D-82152 Martinsried,

   This database may be redistributed without prior consent, provided that
   this notice be given to each user and that the words "Derived from"
   precede this notice if the database has been altered by the

                       Copyright 2000, PIR-International.

                       *PIR is a registered mark of NBRF.
ENTRY           A27187  #type complete
TITLE           ubiquinol-cytochrome-c reductase (EC cytochrome
                precursor - Neurospora crassa
ALTERNATE_NAMES bc1 complex cytochrome c1; complex III cytochrome c1;
                cytochrome c1 heme protein
ORGANISM        #formal_name Neurospora crassa
DATE            05-Oct-1988 #sequence_revision 15-Oct-1994 #text_change
ACCESSIONS      A27187
REFERENCE       A27187
   #authors     Roemisch, J.; Tropschug, M.; Sebald, W.; Weiss, H.
   #journal     Eur. J. Biochem. (1987) 164:111-115
   #title       The primary structure of cytochrome c-1 from Neurospora
   #cross-references MUID:87161871; PMID:3030747
   #accession   A27187
      ##molecule_type mRNA
      ##residues 1-332 ##label ROE
      ##cross-references GB:X05235; NID:g3005; PIDN:CAA28860.1; PID:g3006
      ##note the authors translated the codon AGT for residue 316 as Arg
CLASSIFICATION  #superfamily cytochrome c1 heme protein; cytochrome c1 heme
                protein homology
KEYWORDS        chromoprotein; electron transfer; heme; iron;
                metalloprotein; mitochondrion; oxidative phosphorylation;
                oxidoreductase; respiratory chain; transmembrane protein
   1-70                #domain transit peptide (mitochondrion) #status
                       predicted #label TNP\
   71-332              #product cytochrome c1 #status predicted #label MAT\
   79-305              #domain cytochrome c1 heme protein homology #label
   278-296             #domain transmembrane #status predicted #label TMM\
   110,113             #binding_site heme (Cys) (covalent) #status
   114,234             #binding_site heme iron (His, Met) (axial ligands)
                       #status predicted
SUMMARY         #length 332  #molecular-weight 36456  #checksum 1753
                 5        10        15        20        25        30
       1 M L A R T C L R S T R T F A S A K N G A F K F A K R S A S T
      31 Q S S G A A A E S P L R L N I A A A A A T A V A A G S I A W
      61 Y Y H L Y G F A S A M T P A E E G L H A T K Y P W V H E Q W
      91 L K T F D H Q A L R R G F Q V Y R E V C A S C H S L S R V P
     121 Y R A L V G T I L T V D E A K A L A E E N E Y D T E P N D Q
     151 G E I E K R P G K L S D Y L P D P Y K N D E A A R F A N N G
     181 A L P P D L S L I V K A R H G G C D Y I F S L L T G Y P D E
     211 P P A G A S V G A G L N F N P Y F P G T G I A M A R V L Y D
     241 G L V D Y E D G T P A S T S Q M A K D V V E F L N W A A E P
     271 E M D D R K R M G M K V L V V T S V L F A L S V Y V K R Y K
     301 W A W L K S R K I V Y D P P K S P P P A T N L A L P Q Q R A
     331 K S

the package is that :
# $Id: pir.pm,v 1.4 2004/06/25 09:51:14 ldurufle Exp $
# BioPerl module for Bio::SeqIO::PIR
# Cared for by Aaron Mackey <amackey at virginia.edu>
# Copyright Aaron Mackey
# You may distribute this module under the same terms as perl itself
# _history
# October 18, 1999  Largely rewritten by Lincoln Stein

# POD documentation - main docs before the code

=head1 NAME

Bio::SeqIO::pir - PIR sequence input/output stream


Do not use this module directly.  Use it via the Bio::SeqIO class.


This object can transform Bio::Seq objects to and from pir flat
file databases.

Note: This does not completely preserve the PIR format - quality
information about sequence is currently discarded since bioperl
does not have a mechanism for handling these encodings in sequence


=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l at bioperl.org                 - General discussion
  http://www.bioperl.org/MailList.shtml - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.
 Bug reports can be submitted via email or the web:

  bioperl-bugs at bio.perl.org

=head1 AUTHORS

Aaron Mackey E<lt>amackey at virginia.eduE<gt>
Lincoln Stein E<lt>lstein at cshl.orgE<gt>
Jason Stajich E<lt>jason at bioperl.orgE<gt>


The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _


# Let the code begin...

package Bio::SeqIO::pir;
use vars qw(@ISA);
use strict;

use Bio::SeqIO;
use Bio::Seq::SeqFactory;
use Bio::Species;
use Bio::Annotation::Collection;

@ISA = qw(Bio::SeqIO);

sub _initialize {
  my($self, at args) = @_;
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
                        (-verbose => $self->verbose(),
                         -type => 'Bio::Seq::RichSeq'));

=head2 next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    : NONE


sub next_seq {
    my ($self) = @_;
    #local($/)= "\n";
    my $line;
    my ($desc,$seq,$id,$org,$date,$acc_string, at sec,$acc);
    my ($annotation, %params, @features) = ( new

    while(defined($line = $self->_readline())) {
      last if index($line,'ENTRY       ') == 0;
    return undef if( !defined $line ); # end of file

    $line =~ /^ENTRY\s+(\S+)\s+/ ||
        $self->throw("Pir stream with bad ENTRY line. Not Pir in my
    $id = $1;
    $params{'-display_id'} = $id;

    until(defined ($line) && ($line =~ /^SEQUENCE/) ) {

    # Description line(s)
      if ($line=~/^TITLE\s+(.*)/) {
      $desc = $1;
      # organism line(s)
      if ($line=~/^ORGANISM\s+\#formal_name\s+(.*)/) {
      $org = $1;
      my @class =($org);
      my $make = Bio::Species->new();
      $make->classification(\@class,"FORCE"); # no name validation please
      $params{'-species'}= $make;
      # date line
      if($line=~/^DATE\s+(\d\d-\w\w\w-\d\d\d\d).*/) {
      $date = $1;
      $date =~ s/\;//;
      $date =~ s/\s+$//;
      push @{$params{'-dates'}}, $date;
      if($line=~/^ACCESSIONS\s+(.*)/) {
      $seq = "";
      $acc_string =$1;
      $acc_string =~ s/\;\s*/ /g;
      ($acc, at sec) = split " ",$acc_string;

      $line = $self->_readline();

    my ($seqc,$seqn) = ("","");
    my $nb=0;
    while( defined ($line = $self->_readline) ) {
      if ($line=~/^\/\/\//) {last};
      if ($line=~/^\s+\d+\s+\d+/) {next};
      if ($line=~/^\s+\d+(.*)/) {
      $seq   = uc($line);
      $seqc .= $seq;

    # P - indicates complete protein
    # F - indicates protein fragment
    # not sure how to stuff these into a Bio object
    # suitable for writing out.
    $seqc =~ s/\*//g;
    $seqc =~ s/[\(\)\.\/\=\,]//g;
    $seqc =~ s/\s+//g;        # get rid of whitespace
    $params{'-seq_version'} = '';

    my ($alphabet) = ('protein');
    # TODO - not processing SFS data
    my $entry = $self->sequence_factory->create
      (-verbose  => $self->verbose,
       -seq        => $seqc,
       -primary_id => $id,
       -id         => $id,
       -desc       => $desc,
       -alphabet    => $alphabet,
       -accession_number => $acc,
       -secondardy_accessions => \@sec,

   return $entry;

=head2 write_seq

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Array of Bio::PrimarySeqI objects


#sub write_seq {
#    my ($self, @seq) = @_;
#    for my $seq (@seq) {
#     $self->throw("Did not provide a valid Bio::PrimarySeqI object")
#         unless defined $seq && ref($seq) &&
#     my $str = $seq->seq();
#     return unless $self->_print(">".$seq->id(),
#                           "\n", $seq->desc(), "\n",
#                           $str, "*\n");
#    }

#    $self->flush if $self->_flush_on_write && defined $self->_fh;
#    return 1;


Laure Durufle

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