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1 # $Id: LargeSeq.pm,v 1.11 2002/10/22 07:38:40 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Seq::LargeSeq
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4 #
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5 # Cared for by Ewan Birney, Jason Stajich
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6 #
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7 # Copyright Ewan Birney, Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp
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16
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17 =head1 SYNOPSIS
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18
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19 # normal primary seq usage
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20
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21 =head1 DESCRIPTION
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22
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23 This object stores a sequence as a series of files in a temporary
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24 directory. The aim is to allow someone the ability to store very large
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25 sequences (eg, E<gt> 100MBases) in a file system without running out of memory
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26 (eg, on a 64 MB real memory machine!).
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27
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28 Of course, to actually make use of this functionality, the programs
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29 which use this object B<must> not call $primary_seq-E<gt>seq otherwise the
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30 entire sequence will come out into memory and probably paste your
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31 machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only
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32 90 characters to be brought into real memory.
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33
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34 =head1 FEEDBACK
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35
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36 =head2 Mailing Lists
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37
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38 User feedback is an integral part of the evolution of this
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39 and other Bioperl modules. Send your comments and suggestions preferably
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40 to one of the Bioperl mailing lists.
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41 Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://www.bioperl.org/MailList.html - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 the bugs and their resolution.
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50 Bug reports can be submitted via email or the web:
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51
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52 bioperl-bugs@bio.perl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Ewan Birney
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56
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57 Email birney@ebi.ac.uk
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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62
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63 =cut
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64
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65
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66 # Let the code begin...
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67
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68
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69 package Bio::Seq::LargeSeq;
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70 use vars qw($AUTOLOAD @ISA);
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71 use strict;
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72
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73 # Object preamble - inherits from Bio::Root::Objecttest 8,
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74
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75 use Bio::Seq::LargePrimarySeq;
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76 use Bio::Seq;
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77
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78 @ISA = qw(Bio::Seq);
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79
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80
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81 sub new {
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82 my ($class, @args) = @_;
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83 my $self = $class->SUPER::new(@args);
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84
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85 my ($pseq) = $self->_rearrange([qw(PRIMARYSEQ)], @args);
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86
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87 if( ! defined $pseq ) {
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88 $pseq = new Bio::Seq::LargePrimarySeq(@args);
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89 }
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90 $self->primary_seq($pseq);
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91
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92 return $self;
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93 }
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94
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95
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96 =head2 trunc
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97
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98 Title : trunc
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99 Usage : $subseq = $myseq->trunc(10,100);
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100 Function: Provides a truncation of a sequence,
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101
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102 Example :
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103 Returns : a fresh Bio::SeqI object
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104 Args :
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105
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106 =cut
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107
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108 sub trunc {
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109 my ($self, $s, $e) = @_;
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110 return new Bio::Seq::LargeSeq(
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111 '-display_id' => $self->display_id,
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112 '-accession_number' => $self->accession_number,
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113 '-desc' => $self->desc,
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114 '-alphabet' => $self->alphabet,
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115 -primaryseq =>
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116 $self->primary_seq->trunc($s,$e));
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117
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118 }
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119
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120 =head2 Bio::Seq::LargePrimarySeq methods
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121
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122 =cut
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123
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124 =head2 add_sequence_as_string
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125
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126 Title : add_sequence_as_string
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127 Usage : $seq->add_sequence_as_string("CATGAT");
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128 Function: Appends additional residues to an existing LargePrimarySeq object.
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129 This allows one to build up a large sequence without storing
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130 entire object in memory.
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131 Returns : Current length of sequence
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132 Args : string to append
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133
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134 =cut
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135
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136 sub add_sequence_as_string {
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137 my ($self,$str) = @_;
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138 return $self->primary_seq->add_sequence_as_string($str);
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139 }
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140
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141 1;
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