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1 # $Id: Prints.pm,v 1.7 2002/10/22 07:45:22 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Prints
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4 #
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5 # Cared for by 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 # POD documentation - main docs before the code
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9 #
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10
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11 =head1 NAME
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12
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13 Bio::Tools::Prints - Parser for FingerPRINTScanII program
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14
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15 =head1 SYNOPSIS
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16
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17 use Bio::Tools::Prints;
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18 my $prints_parser = new Bio::Tools::Prints(-fh =>$filehandle );
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19 while( my $prints_feat = $prints_parser->next_result ) {
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20 push @prints_feat, $prints_feat;
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21 }
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22
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23 =head1 DESCRIPTION
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24
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25 PRINTScan II is a PRINTS fingerprint identification algorithm.
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26 Copyright (C) 1998,1999 Phil Scordis
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27
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28 =head1 FEEDBACK
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29
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30 =head2 Mailing Lists
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31
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32 User feedback is an integral part of the evolution of this and other
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33 Bioperl modules. Send your comments and suggestions preferably to
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34 the Bioperl mailing list. Your participation is much appreciated.
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35
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36 bioperl-l@bioperl.org - General discussion
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37 http://bioperl.org/MailList.shtml - About the mailing lists
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38
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39 =head2 Reporting Bugs
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40
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41 Report bugs to the Bioperl bug tracking system to help us keep track
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42 of the bugs and their resolution. Bug reports can be submitted via
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43 email or the web:
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44
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45 bioperl-bugs@bioperl.org
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46 http://bugzilla.bioperl.org/
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47
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48 =head1 AUTHOR - Balamurugan Kumarasamy
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49
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50 Email: fugui@worf.fugu-sg.org
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51
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52 =head1 APPENDIX
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53
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54 The rest of the documentation details each of the object methods.
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55 Internal methods are usually preceded with a _
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56
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57
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58 =cut
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59
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60 package Bio::Tools::Prints;
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61 use vars qw(@ISA);
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62 use strict;
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63
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64 use Bio::Root::Root;
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65 use Bio::SeqFeature::FeaturePair;
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66 use Bio::Root::IO;
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67 use Bio::SeqFeature::Generic;
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68 @ISA = qw(Bio::Root::Root Bio::Root::IO );
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69
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70
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71
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72 =head2 new
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73
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74 Title : new
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75 Usage : my $obj = new Bio::Tools::Prints(-fh=>$filehandle);
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76 Function: Builds a new Bio::Tools::Prints object
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77 Returns : Bio::Tools::Prints
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78 Args : -filename
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79 -fh (filehandle)
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80
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81 =cut
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82
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83 sub new {
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84 my($class,@args) = @_;
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85
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86 my $self = $class->SUPER::new(@args);
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87 $self->_initialize_io(@args);
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88
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89 return $self;
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90 }
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91
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92
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93 =head2 next_result
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94
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95 Title : next_result
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96 Usage : my $feat = $prints_parser->next_result
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97 Function: Get the next result set from parser data
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98 Returns : L<Bio::SeqFeature::Generic>
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99 Args : none
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100
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101 =cut
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102
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103 sub next_result {
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104 my ($self) = @_;
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105 my %printsac;
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106 my @features;
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107 my $line;
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108 my $sequenceId;
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109
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110 while ($_=$self->_readline()) {
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111
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112
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113 $line = $_;
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114 chomp $line;
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115
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116 if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:
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117
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118 ($sequenceId) = $line =~ /^\s*(\w+)/;
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119 $self->seqname($sequenceId);
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120 next;
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121 }
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122
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123
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124 if ($line =~ s/^1TBH//) {
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125 my ($id) = $line =~ /^\s*(\w+)/;
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126 my ($ac) = $line =~ /(PR\w+)\s*$/;
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127 $printsac{$id} = $ac;
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128 $self->print_sac(\%printsac);
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129 next;
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130 }
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131
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132
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133 if ($line =~ s/^3TB//) {
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134
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135
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136
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137
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138 if ($line =~ s/^[HN]//) {
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139 my($num)="";
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140 $line =~ s/^\s+//;
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141
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142 my @elements = split /\s+/, $line;
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143
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144 my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements;
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145
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146 my $start = $matchPosition;
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147 my $end = $matchPosition + $motifLength - 1;
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148 my $print_sac = $self->print_sac;
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149
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150 my %printsac = %{$print_sac};
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151 my $print = $printsac{$fingerprintName};
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152 my $seqname=$self->seqname;
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153 my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue";
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154 my $new_feat = $self->create_feature($feat,$seqname);
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155 return $new_feat;
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156 }
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157 if ($line =~ s/^F//) {
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158 return;
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159 }
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160 next; }
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161 next;
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162
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163 }
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164
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165
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166
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167 }
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168
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169 =head2 create_feature
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170
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171 Title : create_feature
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172 Usage : my $feat=$prints_parser->create_feature($feature,$seqname)
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173 Function: creates a SeqFeature Generic object
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174 Returns : L<Bio::SeqFeature::Generic>
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175 Args :
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176
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177
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178 =cut
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179
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180 sub create_feature {
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181 my ($self, $feat,$sequenceId) = @_;
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182
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183 my @f = split (/,/,$feat);
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184 # create feature object
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185 my $feature= Bio::SeqFeature::Generic->new(-seq_id =>$sequenceId,
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186 -start=>$f[1],
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187 -end => $f[2],
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188 -score => $f[4],
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189 -source => "PRINTS",
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190 -primary =>$f[0],
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191 -logic_name => "PRINTS",
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192 );
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193 $feature->add_tag_value('evalue',$f[5]);
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194 $feature->add_tag_value('percent_id',$f[3]);
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195
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196
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197
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198 return $feature;
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199
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200 }
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201
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202 =head2 print_sac
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203
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204 Title : print_sac
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205 Usage : $prints_parser->print_sac($print_sac)
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206 Function: get/set for print_sac
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207 Returns :
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208 Args :
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209
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210
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211 =cut
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212
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213 sub print_sac{
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214 my($self,$printsac)=@_;
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215
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216 if(defined($printsac))
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217 {
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218 $self->{'print_sac'}=$printsac;
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219 }
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220 return $self->{'print_sac'};
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221
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222 }
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223
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224 =head2 seqname
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225
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226 Title : seqname
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227 Usage : $prints_parser->seqname($seqname)
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228 Function: get/set for seqname
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229 Returns :
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230 Args :
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231
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232
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233 =cut
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234
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235 sub seqname{
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236 my($self,$seqname)=@_;
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237
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238 if(defined($seqname))
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239 {
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240 $self->{'seqname'}=$seqname;
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241 }
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242
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243 return $self->{'seqname'};
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244
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245 }
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246
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247 1;
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