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1 # $Id: clustalw.pm,v 1.21 2002/10/22 07:38:25 lapp Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::clustalw
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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::clustalw - clustalw 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 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::Align::AlignI objects to and from clustalw 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 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to one
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37 of the Bioperl mailing lists. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bio.perl.org/MailList.html - About the mailing lists
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41
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42
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43 =head2 Reporting Bugs
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44
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45 Report bugs to the Bioperl bug tracking system to help us keep track
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46 the bugs and their resolution. Bug reports can be submitted via email
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47 or the web:
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48
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49 bioperl-bugs@bio.perl.org
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50 http://bugzilla.bioperl.org/
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51
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52 =head1 AUTHORS - Peter Schattner
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53
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54 Email: schattner@alum.mit.edu
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55
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56
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57 =head1 APPENDIX
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58
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59 The rest of the documentation details each of the object
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60 methods. Internal methods are usually preceded with a _
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61
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62 =cut
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63
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64 # Let the code begin...
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65
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66 package Bio::AlignIO::clustalw;
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67 use vars qw(@ISA $LINELENGTH);
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68 use strict;
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69
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70 use Bio::AlignIO;
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71 use Bio::LocatableSeq;
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72 use Bio::SimpleAlign; # to be Bio::Align::Simple
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73
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74 $LINELENGTH = 60;
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75
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76 @ISA = qw(Bio::AlignIO);
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77
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78 =head2 new
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79
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80 Title : new
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81 Usage : $alignio = new Bio::AlignIO(-format => 'clustalw',
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82 -file => 'filename');
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83 Function: returns a new Bio::AlignIO object to handle clustalw files
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84 Returns : Bio::AlignIO::clustalw object
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85 Args : -verbose => verbosity setting (-1,0,1,2)
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86 -file => name of file to read in or with ">" - writeout
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87 -fh => alternative to -file param - provide a filehandle
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88 to read from/write to
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89 -format => type of Alignment Format to process or produce
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90 -percentages => (clustalw only) display a percentage of identity
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91 in each line of the alignment.
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92
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93 -linelength=> Set the alignment output line length (default 60)
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94
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95 =cut
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96
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97 sub _initialize {
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98 my ($self, @args) = @_;
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99 $self->SUPER::_initialize(@args);
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100 my ($percentages,
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101 $ll) = $self->_rearrange([qw(PERCENTAGES LINELENGTH)], @args);
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102 defined $percentages && $self->percentages($percentages);
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103 $self->line_length($ll || $LINELENGTH);
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104 }
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105
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106 =head2 next_aln
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107
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108 Title : next_aln
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109 Usage : $aln = $stream->next_aln()
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110 Function: returns the next alignment in the stream
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111 Returns : Bio::Align::AlignI object
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112 Args : NONE
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113
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114 See L<Bio::Align::AlignI> for details
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115
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116 =cut
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117
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118 sub next_aln {
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119 my ($self) = @_;
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120
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121 my $first_line;
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122 if( defined ($first_line = $self->_readline )
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123 && $first_line !~ /CLUSTAL/ ) {
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124 $self->warn("trying to parse a file which does not start with a CLUSTAL header");
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125 }
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126 my %alignments;
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127 my $aln = Bio::SimpleAlign->new(-source => 'clustalw');
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128 my $order = 0;
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129 my %order;
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130 $self->{_lastline} = '';
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131 while( defined ($_ = $self->_readline) ) {
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132 next if ( /^\s+$/ );
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133
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134 my ($seqname, $aln_line) = ('', '');
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135 if( /^\s*(\S+)\s*\/\s*(\d+)-(\d+)\s+(\S+)\s*$/ ) {
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136 # clustal 1.4 format
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137 ($seqname,$aln_line) = ("$1:$2-$3",$4);
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138 } elsif( /^(\S+)\s+([A-Z\-]+)\s*$/ ) {
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139 ($seqname,$aln_line) = ($1,$2);
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140 } else { $self->{_lastline} = $_; next }
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141
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142 if( !exists $order{$seqname} ) {
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143 $order{$seqname} = $order++;
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144 }
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145
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146 $alignments{$seqname} .= $aln_line;
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147 }
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148 my ($sname,$start,$end);
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149 foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments ) {
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150 if( $name =~ /(\S+):(\d+)-(\d+)/ ) {
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151 ($sname,$start,$end) = ($1,$2,$3);
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152 } else {
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153 ($sname, $start) = ($name,1);
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154 my $str = $alignments{$name};
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155 $str =~ s/[^A-Za-z]//g;
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156 $end = length($str);
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157 }
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158 my $seq = new Bio::LocatableSeq('-seq' => $alignments{$name},
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159 '-id' => $sname,
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160 '-start' => $start,
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161 '-end' => $end);
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162 $aln->add_seq($seq);
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163 }
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164 undef $aln if( !defined $end || $end <= 0);
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165 return $aln;
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166 }
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167
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168 =head2 write_aln
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169
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170 Title : write_aln
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171 Usage : $stream->write_aln(@aln)
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172 Function: writes the clustalw-format object (.aln) into the stream
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173 Returns : 1 for success and 0 for error
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174 Args : L<Bio::Align::AlignI> object
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175
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176
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177 =cut
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178
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179 sub write_aln {
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180 my ($self,@aln) = @_;
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181 my ($count,$length,$seq,@seq,$tempcount,$line_len);
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182 $line_len = $self->line_length || $LINELENGTH;
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183 foreach my $aln (@aln) {
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184 if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
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185 $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
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186 next;
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187 }
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188 my $matchline = $aln->match_line;
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189
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190 $self->_print (sprintf("CLUSTAL W(1.81) multiple sequence alignment\n\n\n")) or return;
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191
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192 $length = $aln->length();
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193 $count = $tempcount = 0;
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194 @seq = $aln->each_seq();
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195 my $max = 22;
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196 foreach $seq ( @seq ) {
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197 $max = length ($aln->displayname($seq->get_nse()))
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198 if( length ($aln->displayname($seq->get_nse())) > $max );
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199 }
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200 while( $count < $length ) {
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201 foreach $seq ( @seq ) {
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202 #
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203 # Following lines are to suppress warnings
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204 # if some sequences in the alignment are much longer than others.
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205
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206 my ($substring);
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207 my $seqchars = $seq->seq();
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208 SWITCH: {
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209 if (length($seqchars) >= ($count + $line_len)) {
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210 $substring = substr($seqchars,$count,$line_len);
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211 last SWITCH;
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212 } elsif (length($seqchars) >= $count) {
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213 $substring = substr($seqchars,$count);
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214 last SWITCH;
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215 }
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216 $substring = "";
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217 }
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218
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219 $self->_print (sprintf("%-".$max."s %s\n",
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220 $aln->displayname($seq->get_nse()),
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221 $substring)) or return;
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222 }
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223
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224 my $linesubstr = substr($matchline, $count,$line_len);
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225 my $percentages = '';
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226 if( $self->percentages ) {
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227 my ($strcpy) = ($linesubstr);
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228 my $count = ($strcpy =~ tr/\*//);
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229 $percentages = sprintf("\t%d%%", 100 * ($count / length($linesubstr)));
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230 }
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231 $self->_print (sprintf("%-".$max."s %s%s\n", '', $linesubstr,
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232 $percentages));
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233 $self->_print (sprintf("\n\n")) or return;
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234 $count += $line_len;
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235 }
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236 }
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237 $self->flush if $self->_flush_on_write && defined $self->_fh;
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238 return 1;
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239 }
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240
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241 =head2 percentages
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242
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243 Title : percentages
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244 Usage : $obj->percentages($newval)
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245 Function: Set the percentages flag - whether or not to show percentages in
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246 each output line
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247 Returns : value of percentages
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248 Args : newvalue (optional)
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249
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250
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251 =cut
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252
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253 sub percentages {
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254 my ($self,$value) = @_;
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255 if( defined $value) {
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256 $self->{'_percentages'} = $value;
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257 }
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258 return $self->{'_percentages'};
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259 }
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260
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261 =head2 line_length
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262
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263 Title : line_length
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264 Usage : $obj->line_length($newval)
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265 Function: Set the alignment output line length
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266 Returns : value of line_length
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267 Args : newvalue (optional)
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268
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269
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270 =cut
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271
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272 sub line_length {
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273 my ($self,$value) = @_;
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274 if( defined $value) {
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275 $self->{'_line_length'} = $value;
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276 }
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277 return $self->{'_line_length'};
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278 }
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279
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280 1;
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