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1 # $Id: stockholm.pm,v 1.10.2.1 2003/03/14 09:14:59 heikki Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::stockholm
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4
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5 # based on the Bio::SeqIO::stockholm module
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6 # by Ewan Birney <birney@sanger.ac.uk>
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7 # and Lincoln Stein <lstein@cshl.org>
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8 #
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9 # and the SimpleAlign.pm module of Ewan Birney
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10 #
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11 # Copyright Peter Schattner
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12 #
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13 # You may distribute this module under the same terms as perl itself
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14 # _history
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15 # September 5, 2000
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16 # POD documentation - main docs before the code
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17
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18 =head1 NAME
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19
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20 Bio::AlignIO::stockholm - stockholm sequence input/output stream
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21
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22 =head1 SYNOPSIS
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23
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24 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
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25
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26 =head1 DESCRIPTION
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27
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28 This object can transform L<Bio::Align::AlignI> objects to and from
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29 stockholm flat file databases.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Reporting Bugs
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34
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35 Report bugs to the Bioperl bug tracking system to help us keep track
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36 the bugs and their resolution. Bug reports can be submitted via email
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37 or the web:
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38
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39 bioperl-bugs@bio.perl.org
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40 http://bugzilla.bioperl.org/
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41
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42 =head1 AUTHORS - Peter Schattner
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43
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44 Email: schattner@alum.mit.edu
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45
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46 =head1 CONTRIBUTORS
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47
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48 Andreas Kahari, ak@ebi.ac.uk
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49
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50 =head1 APPENDIX
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51
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52 The rest of the documentation details each of the object
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53 methods. Internal methods are usually preceded with a _
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54
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55 =cut
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56
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57 # Let the code begin...
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58
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59 package Bio::AlignIO::stockholm;
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60 use vars qw(@ISA);
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61 use strict;
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62
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63 use Bio::AlignIO;
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64
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65 @ISA = qw(Bio::AlignIO);
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66
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67 =head2 next_aln
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68
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69 Title : next_aln
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70 Usage : $aln = $stream->next_aln()
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71 Function: returns the next alignment in the stream.
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72 Returns : L<Bio::Align::AlignI> object
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73 Args : NONE
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74
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75 =cut
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76
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77 sub next_aln {
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78 my $self = shift;
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79 my $entry;
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80
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81 my ($start,$end,%align,$name,$seqname,$seq,$count,
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82 %hash,%c2name, %accession, $no);
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83
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84 # in stockholm format, every non-blank line that does not start
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85 # with '#=' is an alignment segment; the '#=' lines are mark up lines.
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86 # Of particular interest are the '#=GF <name/st-ed> AC <accession>'
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87 # lines, which give accession numbers for each segment
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88
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89 my $aln = Bio::SimpleAlign->new(-source => 'stockholm');
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90
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91 while( defined($entry = $self->_readline) ) {
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92 $entry !~ /\w+/ && next;
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93
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94 if ($entry =~ /^#\s*STOCKHOLM\s+/) {
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95 last;
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96 }
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97 else {
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98 $self->throw("Not Stockholm format: Expecting \"# STOCKHOLM 1.0\"; Found \"$_\"");
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99 }
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100 }
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101 #
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102 # Next section is same as for selex format
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103 #
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104 while( defined($entry = $self->_readline) ) {
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105 # Double slash (//) signals end of file. The flat Pfam-A data from
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106 # ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Pfam-A.full.gz consists
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107 # of several concatenated Stockholm-formatted files. The following
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108 # line makes it possible to parse it without this module trying to
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109 # read the whole file into memory. Andreas Kähäri 10/3/2003.
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110 last if $entry =~ /^\/\//;
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111
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112 # Extra bonus: Get the name of the alignment.
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113 # Andreas Kähäri 10/3/2003.
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114 if ($entry =~ /^#=GF\s+AC\s+(\S+)/) {
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115 $aln->id($1);
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116 next;
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117 }
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118
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119 $entry =~ /^#=GS\s+(\S+)\s+AC\s+(\S+)/ && do {
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120 $accession{ $1 } = $2;
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121 next;
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122 };
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123 $entry =~ /^([A-Za-z.-]+)$/ && ( $align{$name} .= $1 ) && next;
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124 $entry !~ /^([^#]\S+)\s+([A-Za-z.-]+)\s*/ && next;
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125
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126
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127 $name = $1;
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128 $seq = $2;
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129
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130 if( ! defined $align{$name} ) {
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131 $count++;
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132 $c2name{$count} = $name;
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133 }
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134 $align{$name} .= $seq;
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135 }
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136
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137 # ok... now we can make the sequences
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138
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139 foreach $no ( sort { $a <=> $b } keys %c2name ) {
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140 $name = $c2name{$no};
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141
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142 if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
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143 $seqname = $1;
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144 $start = $2;
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145 $end = $3;
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146 } else {
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147 $seqname=$name;
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148 $start = 1;
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149 $end = length($align{$name});
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150 }
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151 $seq = new Bio::LocatableSeq('-seq'=>$align{$name},
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152 '-id'=>$seqname,
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153 '-start'=>$start,
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154 '-end'=>$end,
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155 '-type'=>'aligned',
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156 '-accession_number' => $accession{$name},
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157
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158 );
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159
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160 $aln->add_seq($seq);
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161
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162 }
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163
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164 # If $end <= 0, we have either reached the end of
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165 # file in <fh> or we have encountered some other error
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166 #
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167 if ($end <= 0) { undef $aln;}
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168
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169 return $aln;
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170 }
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171
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172
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173 =head2 write_aln
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174
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175 Title : write_aln
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176 Usage : $stream->write_aln(@aln)
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177 Function: writes the $aln object into the stream in stockholm format ###Not yet implemented!###
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178 Returns : 1 for success and 0 for error
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179 Args : L<Bio::Align::AlignI> object
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180
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181
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182 =cut
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183
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184 sub write_aln {
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185 my ($self,@aln) = @_;
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186
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187 $self->throw("Sorry: stockholm-format output, not yet implemented! /n");
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188 }
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189
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190 1;
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