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1 #BioPerl module for Bio::Tools::Hmmpfam
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2 #
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3 # Cared for by Balamurugan Kumarasamy
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4 #
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5 # You may distribute this module under the same terms as perl itself
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6 # POD documentation - main docs before the code
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7 #
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8
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9 =head1 NAME
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10
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11 Bio::Tools::Hmmpfam
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12
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13 =head1 SYNOPSIS
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14
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15 use Bio::Tools::Hmmpfam;
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16 my $hmmpfam_parser = new Bio::Tools::Hmmpfam(-fh =>$filehandle );
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17 while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
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18 push @hmmpfam_feat, $hmmpfam_feat;
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19 }
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20
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21 =head1 DESCRIPTION
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22
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23 Parser for Hmmpfam program
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Balamurugan Kumarasamy
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46
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47 Email: fugui@worf.fugu-sg.org
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48
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49 =head1 APPENDIX
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50
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51 The rest of the documentation details each of the object methods.
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52 Internal methods are usually preceded with a _
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53
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54
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55 =cut
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56
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57 package Bio::Tools::Hmmpfam;
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58 use vars qw(@ISA);
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59 use strict;
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60
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61 use Bio::Root::Root;
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62 use Bio::SeqFeature::FeaturePair;
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63 use Bio::Root::IO;
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64 use Bio::SeqFeature::Generic;
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65 @ISA = qw(Bio::Root::Root Bio::Root::IO );
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66
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67
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68
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69 =head2 new
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70
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71 Title : new
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72 Usage : my $obj = new Bio::Tools::Hmmpfam(-fh=>$filehandle);
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73 Function: Builds a new Bio::Tools::Hmmpfam object
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74 Returns : Bio::Tools::Hmmpfam
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75 Args : -filename
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76 -fh (filehandle)
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77
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78 =cut
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79
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80 sub new {
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81 my($class,@args) = @_;
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82
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83 my $self = $class->SUPER::new(@args);
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84 $self->_initialize_io(@args);
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85
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86 return $self;
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87 }
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88
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89
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90 =head2 next_result
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91
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92 Title : next_result
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93 Usage : my $feat = $hmmpfam_parser->next_result
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94 Function: Get the next result set from parser data
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95 Returns : L<Bio::SeqFeature::Generic>
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96 Args : none
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97
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98 =cut
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99
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100 sub next_result {
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101 my ($self) = @_;
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102 my $filehandle;
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103
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104 my $line;
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105
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106 my $id;
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107 while ($_=$self->_readline()) {
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108 $line = $_;
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109 chomp $line;
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110
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111
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112 last if $line=~m/^Alignments of top-scoring domains/;
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113 next if ($line=~m/^Model/ || /^\-/ || /^$/);
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114
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115 if ($line=~m/^Query sequence:\s+(\S+)/) {
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116 $id = $1;
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117 $self->seqname($id);
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118 }
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119
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120 if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = $line=~m/^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) {
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121 my %feature;
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122
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123 ($feature{name}) = $self->seqname;
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124 $feature{score} = $score;
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125 $feature{p_value} = sprintf ("%.3e", $evalue);
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126 $feature{start} = $start;
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127 $feature{end} = $end;
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128 $feature{hname} = $hid;
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129 $feature{hstart} = $hstart;
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130 $feature{hend} = $hend;
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131 ($feature{source}) = 'pfam';
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132 $feature{primary} = $hid;
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133 ($feature{program}) = 'pfam';
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134 ($feature{db}) = 'db1';
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135 ($feature{logic_name}) = 'hmmpfam';
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136 my $new_feat = $self->create_feature (\%feature);
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137 return $new_feat
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138
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139 }
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140 next;
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141
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142 }
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143 return;
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144 }
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145
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146 =head2 create_feature
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147
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148 Title : create_feature
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149 Usage : my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
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150 Function: creates a SeqFeature Generic object
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151 Returns : L<Bio::SeqFeature::Generic>
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152 Args :
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153
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154
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155 =cut
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156
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157 sub create_feature {
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158 my ($self, $feat) = @_;
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159
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160
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161
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162 my $feature1= Bio::SeqFeature::Generic->new( -seqname =>$feat->{name},
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163 -start =>$feat->{start},
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164 -end =>$feat->{end},
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165 -score =>$feat->{score},
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166 -source =>$feat->{source},
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167 -primary =>$feat->{primary},
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168 );
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169
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170
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171
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172 my $feature2= Bio::SeqFeature::Generic->new(
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173 -start =>$feat->{hstart},
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174 -end =>$feat->{hend},
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175 );
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176
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177
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178
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179
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180 my $featurepair = Bio::SeqFeature::FeaturePair->new;
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181 $featurepair->feature1 ($feature1);
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182 $featurepair->feature2 ($feature2);
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183
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184 $featurepair->add_tag_value('evalue',$feat->{p_value});
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185 $featurepair->add_tag_value('percent_id','NULL');
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186 $featurepair->add_tag_value("hid",$feat->{primary});
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187 return $featurepair;
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188
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189 }
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190
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191 =head2 seqname
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192
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193 Title : seqname
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194 Usage : obj->seqname($seqname)
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195 Function: Internal(not to be used directly)
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196 Returns :
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197 Args : seqname
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198
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199 =cut
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200
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201 sub seqname{
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202 my($self,$seqname)=@_;
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203
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204 if(defined($seqname))
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205 {
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206 $self->{'seqname'}=$seqname;
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207 }
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208
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209 return $self->{'seqname'};
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210
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211 }
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212
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213 1;
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214
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215
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