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1 # $Id: mega.pm,v 1.8 2002/10/22 07:45:10 lapp Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::mega
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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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 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::AlignIO::mega - Parse and Create MEGA format data files
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::AlignIO;
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20 my $alignio = new Bio::AlignIO(-format => 'mega',
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21 -file => 't/data/hemoglobinA.meg');
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22
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23 while( my $aln = $alignio->next_aln ) {
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24 # process each alignment or convert to another format like NEXUS
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25 }
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26
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27 =head1 DESCRIPTION
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28
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29 This object handles reading and writing data streams in the MEGA
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30 format (Kumar and Nei).
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31
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32
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33 =head1 FEEDBACK
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34
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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
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40 the Bioperl mailing list. 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://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 of the bugs and their resolution. Bug reports can be submitted via
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49 email or the web:
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50
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51 bioperl-bugs@bioperl.org
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHOR - Jason Stajich
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55
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56 Email jason@bioperl.org
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57
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58 Describe contact details here
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59
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60 =head1 CONTRIBUTORS
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61
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62 Additional contributors names and emails here
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63
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64 =head1 APPENDIX
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65
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66 The rest of the documentation details each of the object methods.
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67 Internal methods are usually preceded with a _
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68
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69 =cut
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70
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71
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72 # Let the code begin...
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73
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74
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75 package Bio::AlignIO::mega;
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76 use vars qw(@ISA $MEGANAMELEN %VALID_TYPES $LINELEN $BLOCKLEN);
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77 use strict;
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78
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79 use Bio::AlignIO;
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80 use Bio::SimpleAlign;
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81 use Bio::LocatableSeq;
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82
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83 BEGIN {
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84 $MEGANAMELEN = 10;
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85 $LINELEN = 60;
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86 $BLOCKLEN = 10;
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87 %VALID_TYPES = map {$_, 1} qw( dna rna protein standard);
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88 }
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89 @ISA = qw(Bio::AlignIO );
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90
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91
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92 =head2 next_aln
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93
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94 Title : next_aln
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95 Usage : $aln = $stream->next_aln()
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96 Function: returns the next alignment in the stream.
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97 Supports the following MEGA format features:
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98 - The file has to start with '#mega'
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99 - Reads in the name of the alignment from a comment
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100 (anything after '!TITLE: ') .
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101 - Reads in the format parameters datatype
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102
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103 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
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104 or on error
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105 Args : NONE
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106
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107
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108 =cut
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109
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110 sub next_aln{
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111 my ($self) = @_;
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112 my $entry;
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113 my ($alphabet,%seqs);
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114
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115 my $aln = Bio::SimpleAlign->new(-source => 'mega');
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116
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117 while( defined($entry = $self->_readline()) && ($entry =~ /^\s+$/) ) {}
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118
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119 $self->throw("Not a valid MEGA file! [#mega] not starting the file!")
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120 unless $entry =~ /^#mega/i;
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121
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122 while( defined($entry = $self->_readline() ) ) {
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123 local($_) = $entry;
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124 if(/\!Title:\s*([^\;]+)\s*/i) { $aln->id($1)}
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125 elsif( s/\!Format\s+([^\;]+)\s*/$1/ ) {
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126 my (@fields) = split(/\s+/,$1);
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127 foreach my $f ( @fields ) {
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128 my ($name,$value) = split(/\=/,$f);
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129 if( $name eq 'datatype' ) {
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130 $alphabet = $value;
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131 } elsif( $name eq 'identical' ) {
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132 $aln->match_char($value);
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133 } elsif( $name eq 'indel' ) {
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134 $aln->gap_char($value);
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135 }
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136 }
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137 } elsif( /^\#/ ) {
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138 last;
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139 }
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140 }
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141 my @order;
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142 while( defined($entry) ) {
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143 if( $entry !~ /^\s+$/ ) {
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144 # this is to skip the leading '#'
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145 my $seqname = substr($entry,1,$MEGANAMELEN-1);
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146 $seqname =~ s/(\S+)\s+$/$1/g;
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147 my $line = substr($entry,$MEGANAMELEN);
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148 $line =~ s/\s+//g;
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149 if( ! defined $seqs{$seqname} ) {push @order, $seqname; }
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150 $seqs{$seqname} .= $line;
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151 }
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152 $entry = $self->_readline();
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153 }
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154
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155 foreach my $seqname ( @order ) {
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156 my $s = $seqs{$seqname};
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157 $s =~ s/\-//g;
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158 my $end = length($s);
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159 my $seq = new Bio::LocatableSeq(-alphabet => $alphabet,
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160 -id => $seqname,
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161 -seq => $seqs{$seqname},
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162 -start => 1,
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163 -end => $end);
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164
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165 $aln->add_seq($seq);
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166 }
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167 return $aln;
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168 }
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169
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170 =head2 write_aln
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171
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172 Title : write_aln
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173 Usage : $stream->write_aln(@aln)
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174 Function: writes the $aln object into the stream in MEGA format
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175 Returns : 1 for success and 0 for error
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176 Args : L<Bio::Align::AlignI> object
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177
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178 =cut
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179
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180 sub write_aln{
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181 my ($self,@aln) = @_;
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182 my $count = 0;
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183 my $wrapped = 0;
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184 my $maxname;
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185
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186 foreach my $aln ( @aln ) {
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187 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
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188 $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
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189 return 0;
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190 } elsif( ! $aln->is_flush($self->verbose) ) {
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191 $self->warn("All Sequences in the alignment must be the same length");
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192 return 0;
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193 }
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194 $aln->match();
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195 my $len = $aln->length();
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196 my $format = sprintf('datatype=%s identical=%s indel=%s;',
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197 $aln->get_seq_by_pos(1)->alphabet(),
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198 $aln->match_char, $aln->gap_char);
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199
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200 $self->_print(sprintf("#mega\n!Title: %s;\n!Format %s\n\n\n",
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201 $aln->id, $format));
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202
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203 my ($count, $blockcount,$length) = ( 0,0,$aln->length());
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204 $aln->set_displayname_flat();
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205 while( $count < $length ) {
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206 foreach my $seq ( $aln->each_seq ) {
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207 my $seqchars = $seq->seq();
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208 $blockcount = 0;
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209 my $substring = substr($seqchars, $count, $LINELEN);
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210 my @blocks;
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211 while( $blockcount < length($substring) ) {
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212 push @blocks, substr($substring, $blockcount,$BLOCKLEN);
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213 $blockcount += $BLOCKLEN;
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214 }
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215 $self->_print(sprintf("#%-".($MEGANAMELEN-1)."s%s\n",
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216 substr($aln->displayname($seq->get_nse()),
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217 0,$MEGANAMELEN-2),
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218 join(' ', @blocks)));
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219 }
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220 $self->_print("\n");
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221 $count += $LINELEN;
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222 }
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223 }
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224 $self->flush if $self->_flush_on_write && defined $self->_fh;
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225 return 1;
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226 }
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227
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228
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229 1;
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