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1 # $Id: Tmhmm.pm,v 1.6 2002/10/22 07:45:22 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Tmhmm
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4 #
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5 # Copyright Balamurugan Kumarasamy
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8 #
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9 # POD documentation - main docs before the code
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10 #
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11 # Copyright
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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
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15 =head1 NAME
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16
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17 Bio::Tools::Tmhmm - parse TmHMM output (transmembrane HMM)
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18
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19 =head1 SYNOPSIS
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20
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21 use Bio::Tools::Tmhmm;
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22 my $parser = new Bio::Tools::Tmhmm(-fh =>$filehandle );
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23 while( my $tmhmm_feat = $parser->next_result ) {
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24 #do something
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25 #eg
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26 push @tmhmm_feat, $tmhmm_feat;
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27 }
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28
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29 =head1 DESCRIPTION
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30
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31 Parser for Tmhmm output
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32
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33 =head1 FEEDBACK
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34
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35 =head2 Mailing Lists
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36
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37 user feedback is an integral part of the evolution of this and other
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38 Bioperl modules. Send your comments and suggestions preferably to
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39 the Bioperl mailing list. Your participation is much appreciated.
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40
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41 bioperl-l@bioperl.org - General discussion
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42 http://bioperl.org/MailList.shtml - About the mailing lists
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43
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44 =head2 Reporting Bugs
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45
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46 Report bugs to the Bioperl bug tracking system to help us keep track
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47 of the bugs and their resolution. Bug reports can be submitted via
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48 email or the web:
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49
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50 bioperl-bugs@bioperl.org
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51 http://bugzilla.bioperl.org/
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52
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53 =head1 AUTHOR - Bala
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54
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55 Email savikalpa@fugu-sg.org
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56
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57
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58 =head1 APPENDIX
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59
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60 The rest of the documentation details each of the object methods.
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61 Internal methods are usually preceded with a _
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62
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63 =cut
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64
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65 package Bio::Tools::Tmhmm;
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66 use vars qw(@ISA);
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67 use strict;
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68
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69 use Bio::Tools::AnalysisResult;
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70 use Bio::Root::Root;
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71 use Bio::SeqFeature::FeaturePair;
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72 use Bio::Root::IO;
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73 use Bio::SeqFeature::Generic;
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74 @ISA = qw(Bio::Root::Root Bio::Root::IO Bio::Tools::AnalysisResult);
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75
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76
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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 : my $obj = new Bio::Tools::Tmhmm();
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82 Function: Builds a new Bio::Tools::Tmhmm object
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83 Returns : Bio::Tools::Tmhmm
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84 Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
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85
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86
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87 =cut
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88
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89 sub new {
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90 my($class,@args) = @_;
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91
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92 my $self = $class->SUPER::new(@args);
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93 $self->_initialize_io(@args);
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94
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95 return $self;
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96 }
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97
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98
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99 =head2 next_result
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100
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101 Title : next_result
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102 Usage : my $feat = $Tmhmm->next_result
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103 Function: Get the next result set from parser data
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104 Returns : Bio::SeqFeature::Generic
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105 Args : none
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106
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107
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108 =cut
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109
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110 sub next_result {
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111 my ($self) = @_;
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112
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113 my $line;
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114
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115 # parse
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116 my $id;
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117 while ($_=$self->_readline()) {
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118 $line = $_;
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119 chomp $line;
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120
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121
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122 next if /^$/;
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123 if ($line=~/^#\s+(\S+)/) {
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124 #if the line starts with a '#' for example in # 13 Length: 522
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125 #assign 13 as the id.
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126
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127 $id = $1;
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128 my ($junk, $values) = split /:/;
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129 $self->_seqname($id);
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130 next;
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131 }
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132
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133 elsif ($line=~/^(\S+)\s+(\S+)\s+(\w+)\s+(\d+)\s+(\d+)/) {
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134
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135 # Example :- 13 TMHMM2.0 inside 1 120
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136 # assign $orien(inside) $start(1) and $end(120)
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137
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138
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139 my $orien = $3;
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140 my $start = $4;
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141 my $end = $5;
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142 $orien = uc ($orien);
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143
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144 if ($orien eq "TMHELIX") {
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145 my (%feature);
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146 $feature{name} = $self->_seqname;
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147 $feature{start} = $start;
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148 $feature{end} = $end;
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149 $feature{source} ='tmhmm';
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150 $feature{primary}= 'transmembrane';
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151 $feature{program} ='tmhmm';
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152 $feature{logic_name} = 'TMHelix';
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153 my $new_feat= $self->create_feature(\%feature);
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154 return $new_feat;
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155 }
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156 next;
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157 }
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158 next;
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159 }
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160 }
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161
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162 =head2 create_feature
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163
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164 Title : create_feature
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165 Usage : obj->create_feature(\%feature)
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166 Function: Internal(not to be used directly)
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167 Returns : A Bio::SeqFeature::Generic object
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168 Args :
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169
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170 =cut
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171
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172 sub create_feature {
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173 my ($self, $feat) = @_;
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174
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175
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176 # create feature object
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177 my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name},
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178 -start => $feat->{start},
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179 -end => $feat->{end},
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180 -score => $feat->{score},
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181 -source => $feat->{source},
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182 -primary => $feat->{primary},
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183 -logic_name => $feat->{logic_name},
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184 );
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185 return $feature;
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186 }
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187
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188 =head2 _seqname
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189
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190 Title : _seqname
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191 Usage : obj->_seqname($seqname)
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192 Function: Internal(not to be used directly)
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193 Returns :
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194 Args : seqname
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195
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196 =cut
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197
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198 sub _seqname{
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199 my ($self,$seqname)=@_;
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200
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201 if (defined $seqname){
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202
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203 $self->{'seqname'}=$seqname;
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204 }
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205
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206 return $self->{'seqname'};
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207
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208 }
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209
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210
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211 1;
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212
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213
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