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1 # $Id: pir.pm,v 1.18 2002/10/25 16:23:16 jason Exp $
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2 #
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3 # BioPerl module for Bio::SeqIO::PIR
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4 #
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5 # Cared for by Aaron Mackey <amackey@virginia.edu>
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6 #
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7 # Copyright Aaron Mackey
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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 # _history
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12 # October 18, 1999 Largely rewritten by Lincoln Stein
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13
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14 # POD documentation - main docs before the code
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15
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16 =head1 NAME
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17
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18 Bio::SeqIO::pir - PIR sequence input/output stream
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19
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20 =head1 SYNOPSIS
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21
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22 Do not use this module directly. Use it via the Bio::SeqIO class.
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23
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24 =head1 DESCRIPTION
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25
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26 This object can transform Bio::Seq objects to and from pir flat
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27 file databases.
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28
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29 Note: This does not completely preserve the PIR format - quality
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30 information about sequence is currently discarded since bioperl
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31 does not have a mechanism for handling these encodings in sequence
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32 data.
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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 and other
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39 Bioperl modules. Send your comments and suggestions preferably to one
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40 of the Bioperl mailing lists. Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://www.bioperl.org/MailList.shtml - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 the bugs and their resolution.
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49 Bug reports can be submitted via email or the web:
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50
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51 bioperl-bugs@bio.perl.org
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHORS
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55
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56 Aaron Mackey E<lt>amackey@virginia.eduE<gt>
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57 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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58 Jason Stajich E<lt>jason@bioperl.orgE<gt>
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59
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60 =head1 APPENDIX
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61
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62 The rest of the documentation details each of the object
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63 methods. Internal methods are usually preceded with a _
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64
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65 =cut
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66
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67 # Let the code begin...
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68
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69 package Bio::SeqIO::pir;
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70 use vars qw(@ISA);
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71 use strict;
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72
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73 use Bio::SeqIO;
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74 use Bio::Seq::SeqFactory;
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75
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76 @ISA = qw(Bio::SeqIO);
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77
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78 sub _initialize {
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79 my($self,@args) = @_;
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80 $self->SUPER::_initialize(@args);
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81 if( ! defined $self->sequence_factory ) {
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82 $self->sequence_factory(new Bio::Seq::SeqFactory
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83 (-verbose => $self->verbose(),
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84 -type => 'Bio::Seq'));
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85 }
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86 }
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87
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88 =head2 next_seq
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89
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90 Title : next_seq
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91 Usage : $seq = $stream->next_seq()
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92 Function: returns the next sequence in the stream
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93 Returns : Bio::Seq object
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94 Args : NONE
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95
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96 =cut
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97
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98 sub next_seq {
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99 my ($self) = @_;
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100 local $/ = "\n>";
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101 return unless my $line = $self->_readline;
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102 if( $line eq '>' ) { # handle the very first one having no comment
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103 return unless $line = $self->_readline;
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104 }
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105 my ($top, $desc,$seq) = ( $line =~ /^(.+?)\n(.+?)\n([^>]*)/s ) or
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106 $self->throw("Cannot parse entry PIR entry [$line]");
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107
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108
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109 my ( $type,$id ) = ( $top =~ /^>?([PF])1;(\S+)\s*$/ ) or
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110 $self->throw("PIR stream read attempted without leading '>P1;' [ $line ]");
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111
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112 # P - indicates complete protein
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113 # F - indicates protein fragment
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114 # not sure how to stuff these into a Bio object
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115 # suitable for writing out.
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116 $seq =~ s/\*//g;
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117 $seq =~ s/[\(\)\.\/\=\,]//g;
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118 $seq =~ s/\s+//g; # get rid of whitespace
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119
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120 my ($alphabet) = ('protein');
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121 # TODO - not processing SFS data
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122 return $self->sequence_factory->create
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123 (-seq => $seq,
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124 -primary_id => $id,
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125 -id => $type. '1;' . $id,
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126 -desc => $desc,
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127 -alphabet => $alphabet
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128 );
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129 }
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130
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131 =head2 write_seq
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132
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133 Title : write_seq
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134 Usage : $stream->write_seq(@seq)
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135 Function: writes the $seq object into the stream
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136 Returns : 1 for success and 0 for error
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137 Args : Array of Bio::PrimarySeqI objects
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138
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139
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140 =cut
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141
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142 sub write_seq {
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143 my ($self, @seq) = @_;
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144 for my $seq (@seq) {
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145 $self->throw("Did not provide a valid Bio::PrimarySeqI object")
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146 unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
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147 my $str = $seq->seq();
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148 return unless $self->_print(">".$seq->id(),
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149 "\n", $seq->desc(), "\n",
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150 $str, "*\n");
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151 }
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152
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153 $self->flush if $self->_flush_on_write && defined $self->_fh;
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154 return 1;
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155 }
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156
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157 1;
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