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1 # $Id: pfam.pm,v 1.10 2002/10/22 07:38:26 lapp Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::pfam
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4
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5 # based on the Bio::SeqIO:: modules
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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::pfam - pfam 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 Bio::SimpleAlign objects to and from pfam flat
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29 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.
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37 Bug reports can be submitted via email 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
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47 =head1 APPENDIX
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48
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49 The rest of the documentation details each of the object
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50 methods. Internal methods are usually preceded with a _
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51
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52 =cut
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53
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54 # Let the code begin...
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55
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56 package Bio::AlignIO::pfam;
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57 use vars qw(@ISA);
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58 use strict;
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59
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60 use Bio::AlignIO;
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61 use Bio::SimpleAlign;
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62 @ISA = qw(Bio::AlignIO);
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63
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64 =head2 next_aln
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65
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66 Title : next_aln
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67 Usage : $aln = $stream->next_aln()
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68 Function: returns the next alignment in the stream
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69 Returns : L<Bio::Align::AlignI> object
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70 Args : NONE
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71
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72 =cut
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73
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74 sub next_aln {
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75 my $self = shift;
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76 my $entry;
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77 my $name;
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78 my $start;
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79 my $end;
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80 my $seq;
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81 my $add;
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82 my $acc;
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83 my %names;
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84
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85 my $aln = Bio::SimpleAlign->new(-source => 'pfam');
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86
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87 while( $entry = $self->_readline) {
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88 chomp $entry;
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89 $entry =~ /^\/\// && last;
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90 if($entry !~ /^(\S+)\/(\d+)-(\d+)\s+(\S+)\s*/ ) {
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91 $self->throw("Found a bad line [$_] in the pfam format alignment");
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92 next;
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93 }
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94
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95 $name = $1;
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96 $start = $2;
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97 $end = $3;
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98 $seq = $4;
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99
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100
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101 $add = new Bio::LocatableSeq('-seq'=>$seq,
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102 '-id'=>$name,
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103 '-start'=>$start,
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104 '-end'=>$end,
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105 );
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106
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107 $aln->add_seq($add);
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108
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109 }
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110
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111 # If $end <= 0, we have either reached the end of
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112 # file in <> or we have encountered some other error
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113 #
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114 if ($end <= 0) { undef $aln;}
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115
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116 return $aln;
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117 }
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118
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119
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120
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121 =head2 write_aln
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122
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123 Title : write_aln
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124 Usage : $stream->write_aln(@aln)
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125 Function: writes the $aln object into the stream
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126 Returns : 1 for success and 0 for error
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127 Args : L<Bio::Align::AlignI> object
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128
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129
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130 =cut
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131
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132 sub write_aln {
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133 my ($self,@aln) = @_;
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134 if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); }
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135 my $aln = shift @aln;
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136 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
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137 $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
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138 next;
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139 }
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140 my ($namestr,$seq,$add);
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141 my ($maxn);
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142 $maxn = $aln->maxdisplayname_length();
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143
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144 foreach $seq ( $aln->each_seq() ) {
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145 $namestr = $aln->displayname($seq->get_nse());
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146 $add = $maxn - length($namestr) + 2;
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147 $namestr .= " " x $add;
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148 $self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
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149 }
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150 $self->flush() if $self->_flush_on_write && defined $self->_fh;
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151 return 1;
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152 }
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153
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154 1;
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