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1 # $Id: bl2seq.pm,v 1.13.2.1 2003/06/18 12:19:52 jason Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::bl2seq
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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 # the Bio::Tools::BPlite modules by
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10 # Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf),
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11 # Lorenz Pollak (lorenz@ist.org, bioperl port)
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12 #
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13 # and the SimpleAlign.pm module of Ewan Birney
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14 #
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15 # Copyright Peter Schattner
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16 #
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17 # You may distribute this module under the same terms as perl itself
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18 # _history
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19 # September 5, 2000
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20 # POD documentation - main docs before the code
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21
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22 =head1 NAME
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23
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24 Bio::AlignIO::bl2seq - bl2seq sequence input/output stream
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25
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26 =head1 SYNOPSIS
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27
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28 Do not use this module directly. Use it via the L<Bio::AlignIO> class, as in:
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29
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30 use Bio::AlignIO;
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31
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32 $in = Bio::AlignIO->new(-file => "inputfilename" , '-format' => 'bl2seq');
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33 $aln = $in->next_aln();
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34
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35
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36 =head1 DESCRIPTION
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37
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38 This object can create L<Bio::SimpleAlign> sequence alignment objects (of
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39 2 sequences) from bl2seq BLAST reports.
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40
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41 A nice feature of this module is that- in combination with
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42 StandAloneBlast.pm or remote blasting - it can be used to align 2
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43 sequences and make a SimpleAlign object from them which can then be
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44 manipulated using any SimpleAlign.pm methods, eg:
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45
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46 #Get 2 sequences
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47 $str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
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48 my $seq3 = $str->next_seq();
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49 my $seq4 = $str->next_seq();
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50
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51 # Run bl2seq on them
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52 $factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp',
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53 'outfile' => 'bl2seq.out');
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54 my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
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55
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56 # Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
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57 $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
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58 $aln = $str->next_aln();
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59
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60 Pass in -report_type flag when initializing the object to have this
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61 pass through to the Bio::Tools::BPbl2seq object. See that object.
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62
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63 =head1 FEEDBACK
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64
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65 =head2 Mailing Lists
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66
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67 User feedback is an integral part of the evolution of this and other
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68 Bioperl modules. Send your comments and suggestions preferably to one
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69 of the Bioperl mailing lists. Your participation is much appreciated.
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70
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71 bioperl-l@bioperl.org - General discussion
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72 http://bio.perl.org/MailList.html - About the mailing lists
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73
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74 =head2 Reporting Bugs
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75
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76 Report bugs to the Bioperl bug tracking system to help us keep track
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77 the bugs and their resolution.
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78 Bug reports can be submitted via email or the web:
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79
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80 bioperl-bugs@bio.perl.org
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81 http://bugzilla.bioperl.org/
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82
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83 =head1 AUTHOR - Peter Schattner
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84
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85 Email: schattner@alum.mit.edu
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86
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87
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88 =head1 APPENDIX
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89
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90 The rest of the documentation details each of the object
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91 methods. Internal methods are usually preceded with a _
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92
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93 =cut
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94
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95 # Let the code begin...
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96
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97 package Bio::AlignIO::bl2seq;
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98 use vars qw(@ISA);
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99 use strict;
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100 # Object preamble - inherits from Bio::Root::Object
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101
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102 use Bio::AlignIO;
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103 use Bio::Tools::BPbl2seq;
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104
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105 @ISA = qw(Bio::AlignIO);
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106
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107
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108
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109 sub _initialize {
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110 my ($self,@args) = @_;
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111 $self->SUPER::_initialize(@args);
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112 ($self->{'report_type'}) = $self->_rearrange([qw(REPORT_TYPE)],
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113 @args);
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114 return 1;
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115 }
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116
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117 =head2 next_aln
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118
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119 Title : next_aln
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120 Usage : $aln = $stream->next_aln()
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121 Function: returns the next alignment in the stream.
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122 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
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123 or on error
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124 Args : NONE
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125
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126 =cut
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127
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128 sub next_aln {
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129 my $self = shift;
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130 my ($start,$end,$name,$seqname,$seq,$seqchar);
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131 my $aln = Bio::SimpleAlign->new(-source => 'bl2seq');
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132 $self->{'bl2seqobj'} =
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133 $self->{'bl2seqobj'} || Bio::Tools::BPbl2seq->new(-fh => $self->_fh,
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134 -report_type => $self->{'report_type'});
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135 my $bl2seqobj = $self->{'bl2seqobj'};
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136 my $hsp = $bl2seqobj->next_feature;
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137 $seqchar = $hsp->querySeq;
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138 $start = $hsp->query->start;
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139 $end = $hsp->query->end;
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140 $seqname = 'Query-sequence'; # Query name not present in bl2seq report
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141
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142 # unless ($seqchar && $start && $end && $seqname) {return 0} ;
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143 unless ($seqchar && $start && $end ) {return 0} ;
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144
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145 $seq = new Bio::LocatableSeq('-seq'=>$seqchar,
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146 '-id'=>$seqname,
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147 '-start'=>$start,
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148 '-end'=>$end,
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149 );
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150
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151 $aln->add_seq($seq);
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152
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153 $seqchar = $hsp->sbjctSeq;
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154 $start = $hsp->hit->start;
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155 $end = $hsp->hit->end;
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156 $seqname = $bl2seqobj->sbjctName;
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157
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158 unless ($seqchar && $start && $end && $seqname) {return 0} ;
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159
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160 $seq = new Bio::LocatableSeq('-seq'=>$seqchar,
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161 '-id'=>$seqname,
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162 '-start'=>$start,
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163 '-end'=>$end,
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164 );
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165
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166 $aln->add_seq($seq);
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167
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168 return $aln;
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169
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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 $aln object into the stream in bl2seq format
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178 Returns : 1 for success and 0 for error
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179 Args : L<Bio::Align::AlignI> object
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180
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181
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182 =cut
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183
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184 sub write_aln {
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185 my ($self,@aln) = @_;
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186
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187 $self->throw("Sorry: writing bl2seq output is not available! /n");
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188 }
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189
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190 1;
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