[Bioperl-l] pir.pm => bug
Laure.Durufle at serono.com
Laure.Durufle at serono.com
Fri Jun 25 06:05:39 EDT 2004
Hi,
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
Gesundheit
Tsukuba 305-0005, Japan am Max-Planck-Instut f. Biochemie
Am Klopferspitz 18, D-82152 Martinsried,
FRG
This database may be redistributed without prior consent, provided that
this notice be given to each user and that the words "Derived from"
shall
precede this notice if the database has been altered by the
redistributor.
Copyright 2000, PIR-International.
*PIR is a registered mark of NBRF.
\\\
ENTRY A27187 #type complete
TITLE ubiquinol-cytochrome-c reductase (EC 1.10.2.2) cytochrome
c1
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
03-Jun-2002
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
crassa.
#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
FEATURE
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
C1H\
278-296 #domain transmembrane #status predicted #label TMM\
110,113 #binding_site heme (Cys) (covalent) #status
predicted\
114,234 #binding_site heme iron (His, Met) (axial ligands)
#status predicted
SUMMARY #length 332 #molecular-weight 36456 #checksum 1753
SEQUENCE
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
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.
=head1 DESCRIPTION
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
data.
=head1 FEEDBACK
=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
http://bugzilla.bioperl.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>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# 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) = @_;
$self->SUPER::_initialize(@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 = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
=cut
sub next_seq {
my ($self) = @_;
#local($/)= "\n";
my $line;
my ($desc,$seq,$id,$org,$date,$acc_string, at sec,$acc);
my ($annotation, %params, @features) = ( new
Bio::Annotation::Collection);
while(defined($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
book.");
$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'}}, $date;
}
#accession
if($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+(.*)/) {
$line=$1;
}
$seq = uc($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,
%params,
-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 $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects
=cut
#sub write_seq {
# my ($self, @seq) = @_;
# for my $seq (@seq) {
# $self->throw("Did not provide a valid Bio::PrimarySeqI object")
# unless defined $seq && ref($seq) &&
$seq->isa('Bio::PrimarySeqI');
# 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;
#}
1;
Laure Durufle
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