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1 #-----------------------------------------------------------------------------
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2 # PACKAGE : Bio::SeqIO::raw
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3 # AUTHOR : Ewan Birney <birney@ebi.ac.uk>
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4 # CREATED : Feb 16 1999
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5 # REVISION: $Id: raw.pm,v 1.15.2.1 2003/02/05 21:55:21 jason Exp $
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6 #
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7 # Copyright (c) 1997-9 bioperl, Ewan Birney. All Rights Reserved.
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8 # This module is free software; you can redistribute it and/or
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9 # modify it under the same terms as Perl itself.
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10 #
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11 # _History_
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12 #
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13 # Ewan Birney <birney@ebi.ac.uk> developed the SeqIO
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14 # schema and the first prototype modules.
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15 #
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16 # This code is based on his Bio::SeqIO::Fasta module with
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17 # the necessary minor tweaks necessary to get it to read
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18 # and write raw formatted sequences made by
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19 # chris dagdigian <dag@sonsorol.org>
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20 #
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21 # October 18, 1999 Largely rewritten by Lincoln Stein
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22 #
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23 # Copyright Ewan Birney
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24 #
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25 # You may distribute this module under the same terms as perl itself
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26
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27 # POD documentation - main docs before the code
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28
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29 =head1 NAME
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30
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31 Bio::SeqIO::raw - raw sequence file input/output stream
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32
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33 =head1 SYNOPSIS
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34
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35 Do not use this module directly. Use it via the L<Bio::SeqIO> class.
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36
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37 =head1 DESCRIPTION
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38
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39 This object can transform Bio::Seq objects to and from raw flat
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40 file databases.
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41
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42
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43 =head1 FEEDBACK
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44
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45 =head2 Mailing Lists
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46
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47 User feedback is an integral part of the evolution of this
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48 and other Bioperl modules. Send your comments and suggestions preferably
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49 to one of the Bioperl mailing lists.
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50 Your participation is much appreciated.
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51
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52 bioperl-l@bioperl.org - General discussion
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53 http://www.bioperl.org/MailList.shtml - About the mailing lists
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54
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55 =head2 Reporting Bugs
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56
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57 Report bugs to the Bioperl bug tracking system to help us keep track
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58 the bugs and their resolution.
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59 Bug reports can be submitted via email or the web:
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60
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61 bioperl-bugs@bio.perl.org
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62 http://bugzilla.bioperl.org/
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63
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64 =head1 AUTHORS
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65
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66 Ewan Birney E<lt>birney@ebi.ac.ukE<gt>
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67 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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68
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69 =head1 CONTRIBUTORS
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70
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71 Jason Stajich E<lt>jason@bioperl.org<gt>
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72
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73 =head1 APPENDIX
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74
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75 The rest of the documentation details each of the object methods.
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76 Internal methods are usually preceded with a _
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77
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78 =cut
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79
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80
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81 # Let the code begin...
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82
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83 package Bio::SeqIO::raw;
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84 use strict;
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85 use vars qw(@ISA);
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86
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87 use Bio::SeqIO;
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88 use Bio::Seq::SeqFactory;
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89
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90 @ISA = qw(Bio::SeqIO);
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91
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92 sub _initialize {
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93 my($self,@args) = @_;
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94 $self->SUPER::_initialize(@args);
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95 if( ! defined $self->sequence_factory ) {
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96 $self->sequence_factory(new Bio::Seq::SeqFactory
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97 (-verbose => $self->verbose(),
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98 -type => 'Bio::Seq'));
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99 }
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100 }
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101
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102 =head2 next_seq
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103
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104 Title : next_seq
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105 Usage : $seq = $stream->next_seq()
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106 Function: returns the next sequence in the stream
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107 Returns : Bio::Seq object
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108 Args :
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109
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110
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111 =cut
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112
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113 sub next_seq{
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114 my ($self,@args) = @_;
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115 ## When its 1 sequence per line with no formatting at all,
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116 ## grabbing it should be easy :)
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117
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118 my $nextline = $self->_readline();
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119 if( !defined $nextline ){ return undef; }
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120
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121 my $sequence = uc($nextline);
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122 $sequence =~ s/\W//g;
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123
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124 return $self->sequence_factory->create(-seq => $sequence);
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125 }
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126
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127 =head2 write_seq
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128
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129 Title : write_seq
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130 Usage : $stream->write_seq($seq)
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131 Function: writes the $seq object into the stream
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132 Returns : 1 for success and 0 for error
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133 Args : Array of Bio::PrimarySeqI objects
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134
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135
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136 =cut
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137
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138 sub write_seq {
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139 my ($self,@seq) = @_;
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140 foreach my $seq (@seq) {
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141 $self->throw("Must provide a valid Bio::PrimarySeqI object")
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142 unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
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143 $self->_print($seq->seq, "\n") or return;
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144 }
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145 $self->flush if $self->_flush_on_write && defined $self->_fh;
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146 return 1;
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147 }
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148
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149 =head2 write_qual
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150
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151 Title : write_qual
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152 Usage : $stream->write_qual($seq)
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153 Function: writes the $seq object into the stream
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154 Returns : 1 for success and 0 for error
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155 Args : Bio::Seq object
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156
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157
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158 =cut
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159
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160 sub write_qual {
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161 my ($self,@seq) = @_;
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162 my @qual = ();
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163 foreach (@seq) {
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164 unless ($_->isa("Bio::Seq::SeqWithQuality")){
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165 warn("You cannot write raw qualities without supplying a Bio::Seq::SeqWithQuality object! You passed a ", ref($_), "\n");
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166 next;
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167 }
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168 @qual = @{$_->qual};
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169 if(scalar(@qual) == 0) {
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170 $qual[0] = "\n";
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171 }
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172
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173 $self->_print (join " ", @qual,"\n") or return;
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174
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175 }
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176 return 1;
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177 }
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178 1;
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