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1 # $Id: ace.pm,v 1.15 2002/10/25 16:23:16 jason Exp $
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2 #
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3 # BioPerl module for Bio::SeqIO::ace
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4 #
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5 # Cared for by James Gilbert <jgrg@sanger.ac.uk>
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::SeqIO::ace - ace sequence input/output stream
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14
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15 =head1 SYNOPSIS
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16
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17 Do not use this module directly. Use it via the Bio::SeqIO class.
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18
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19 =head1 DESCRIPTION
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20
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21 This object can transform Bio::Seq objects to and
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22 from ace file format. It only parses a DNA or
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23 Peptide objects contained in the ace file,
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24 producing PrimarySeq objects from them. All
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25 other objects in the files will be ignored. It
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26 doesn't attempt to parse any annotation attatched
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27 to the containing Sequence or Protein objects,
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28 which would probably be impossible, since
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29 everyone's ACeDB schema can be different.
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30
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31 It won't parse ace files containing Timestamps
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32 correctly either. This can easily be added if
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33 considered necessary.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this
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40 and other Bioperl modules. Send your comments and suggestions preferably
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41 to one of the Bioperl mailing lists.
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42 Your participation is much appreciated.
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43
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44 bioperl-l@bioperl.org - General discussion
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45 http://www.bioperl.org/MailList.shtml - About the mailing lists
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46
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47 =head2 Reporting Bugs
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48
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49 Report bugs to the Bioperl bug tracking system to help us keep track
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50 the bugs and their resolution.
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51 Bug reports can be submitted via email or the web:
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52
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53 bioperl-bugs@bio.perl.org
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54 http://bugzilla.bioperl.org/
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55
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56 =head1 AUTHORS - James Gilbert
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57
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58 Email: jgrg@sanger.ac.uk
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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 #'
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68 # Let the code begin...
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69
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70 package Bio::SeqIO::ace;
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71 use strict;
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72 use vars qw(@ISA);
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73
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74 use Bio::SeqIO;
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75 use Bio::Seq;
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76 use Bio::Seq::SeqFactory;
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77
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78 @ISA = qw(Bio::SeqIO);
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79
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80 sub _initialize {
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81 my($self,@args) = @_;
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82 $self->SUPER::_initialize(@args);
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83 if( ! defined $self->sequence_factory ) {
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84 $self->sequence_factory(new Bio::Seq::SeqFactory(-verbose => $self->verbose(), -type => 'Bio::PrimarySeq'));
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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 {
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99 my %bio_mol_type = (
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100 'dna' => 'dna',
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101 'peptide' => 'protein',
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102 );
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103
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104 sub next_seq {
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105 my( $self ) = @_;
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106 local $/ = ""; # Split input on blank lines
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107
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108 my $fh = $self->_filehandle;
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109 my( $type, $id );
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110 while (<$fh>) {
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111 if (($type, $id) = /^(DNA|Peptide)[\s:]+(.+?)\s*\n/si) {
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112 s/^.+$//m; # Remove first line
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113 s/\s+//g; # Remove whitespace
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114 last;
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115 }
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116 }
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117 # Return if there weren't any DNA or peptide objects
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118 return unless $type;
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119
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120 # Choose the molecule type
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121 my $mol_type = $bio_mol_type{lc $type}
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122 or $self->throw("Can't get Bio::Seq molecule type for '$type'");
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123
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124 # Remove quotes from $id
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125 $id =~ s/^"|"$//g;
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126
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127 # Un-escape forward slashes, double quotes, percent signs,
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128 # semi-colons, tabs, and backslashes (if you're mad enough
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129 # to have any of these as part of object names in your acedb
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130 # database).
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131 $id =~ s/\\([\/"%;\t\\])/$1/g;
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132 #"
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133 # Called as next_seq(), so give back a Bio::Seq
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134 return $self->sequence_factory->create(
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135 -seq => $_,
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136 -primary_id => $id,
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137 -display_id => $id,
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138 -alphabet => $mol_type,
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139 );
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140 }
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141 }
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142
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143 =head2 write_seq
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144
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145 Title : write_seq
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146 Usage : $stream->write_seq(@seq)
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147 Function: writes the $seq object into the stream
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148 Returns : 1 for success and 0 for error
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149 Args : Bio::Seq object(s)
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150
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151
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152 =cut
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153
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154 sub write_seq {
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155 my ($self, @seq) = @_;
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156
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157 foreach my $seq (@seq) {
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158 $self->throw("Did not provide a valid Bio::PrimarySeqI object")
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159 unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
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160 my $mol_type = $seq->alphabet;
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161 my $id = $seq->display_id;
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162
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163 # Escape special charachers in id
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164 $id =~ s/([\/"%;\t\\])/\\$1/g;
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165 #"
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166 # Print header for DNA or Protein object
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167 if ($mol_type eq 'dna') {
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168 $self->_print(
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169 qq{\nSequence : "$id"\nDNA "$id"\n},
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170 qq{\nDNA : "$id"\n},
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171 );
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172 }
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173 elsif ($mol_type eq 'protein') {
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174 $self->_print(
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175 qq{\nProtein : "$id"\nPeptide "$id"\n},
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176 qq{\nPeptide : "$id"\n},
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177 );
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178 }
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179 else {
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180 $self->throw("Don't know how to produce ACeDB output for '$mol_type'");
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181 }
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182
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183 # Print the sequence
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184 my $str = $seq->seq;
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185 my( $formatted_seq );
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186 while ($str =~ /(.{1,60})/g) {
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187 $formatted_seq .= "$1\n";
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188 }
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189 $self->_print($formatted_seq, "\n");
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190 }
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191
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192 $self->flush if $self->_flush_on_write && defined $self->_fh;
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193 return 1;
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194 }
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195
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196 1;
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