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1 # $Id: Seg.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::Seg
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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 # POD documentation - main docs before the code
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15
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16 =head1 NAME
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17
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18 Bio::Tools::Seg - parse Seg output (filter low complexity protein sequence)
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19
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20 =head1 SYNOPSIS
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21
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22 use Bio::Tools::Seg;
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23 my $parser = new Bio::Tools::Seg(-fh =>$filehandle );
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24 while( my $seg_feat = $parser->next_result ) {
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25 #do something
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26 #eg
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27 push @seg_feat, $seg_feat;
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28 }
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29
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30 =head1 DESCRIPTION
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31
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32 Parser for Seg output
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33
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34 =head1 FEEDBACK
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35
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36 =head2 Mailing Lists
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37
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38 User feedback is an integral part of the evolution of this and other
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39 Bioperl modules. Send your comments and suggestions preferably to
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40 the Bioperl mailing list. Your participation is much appreciated.
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41
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42 bioperl-l@bioperl.org - General discussion
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43 http://bioperl.org/MailList.shtml - About the mailing lists
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44
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45 =head2 Reporting Bugs
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46
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47 Report bugs to the Bioperl bug tracking system to help us keep track
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48 of the bugs and their resolution. Bug reports can be submitted via
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49 email or the web:
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50
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51 bioperl-bugs@bioperl.org
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52 http://bugzilla.bioperl.org/
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53
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54 =head1 AUTHOR - Bala
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55
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56 Email savikalpa@fugu-sg.org
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57
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58
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59 =head1 CONTRIBUTORS
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60
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61 Additional contributors names and emails here
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62
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63 =head1 APPENDIX
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64
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65 The rest of the documentation details each of the object methods.
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66 Internal methods are usually preceded with a _
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67
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68 =cut
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69
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70 package Bio::Tools::Seg;
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71 use vars qw(@ISA);
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72 use strict;
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73
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74 use Bio::Root::Root;
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75 use Bio::SeqFeature::FeaturePair;
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76 use Bio::Root::IO;
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77 use Bio::SeqFeature::Generic;
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78 @ISA = qw(Bio::Root::Root Bio::Root::IO);
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79
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80
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81
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82
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83
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84 =head2 new
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85
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86 Title : new
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87 Usage : my $obj = new Bio::Tools::Seg();
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88 Function: Builds a new Bio::Tools::Seg object
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89 Returns : Bio::Tools::Seg
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90 Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
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91
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92
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93 =cut
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94
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95
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96 sub new {
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97 my($class,@args) = @_;
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98
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99 my $self = $class->SUPER::new(@args);
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100 $self->_initialize_io(@args);
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101
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102 return $self;
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103 }
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104
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105 =head2 next_result
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106
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107 Title : next_result
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108 Usage : my $feat = $seg->next_result
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109 Function: Get the next result set from parser data
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110 Returns : Bio::SeqFeature::Generic
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111 Args : none
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112
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113
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114 =cut
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115
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116 sub next_result {
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117 my ($self) = @_;
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118
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119 my $line;
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120 # parse
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121 my $id;
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122 while ($_=$self->_readline()) {
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123 $line = $_;
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124 chomp $line;
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125
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126 next if /^$/;
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127 if ($line=~/^\>/) { #if it is a line starting with a ">"
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128 $line=~/^\>\s*(\S+)\s*\((\d+)\-(\d+)\)\s*complexity=(\S+)/;
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129 my $id = $1;
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130 my $start = $2;
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131 my $end = $3;
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132 my $score = $4;
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133
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134 #for example in this line test_prot(214-226) complexity=2.26 (12/2.20/2.50)
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135 #$1 is test_prot $2 is 214 $3 is 226 and $4 is 2.26
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136
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137 my (%feature);
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138 $feature{name} = $id;
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139 $feature{score} = $score;
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140 $feature{start} = $start;
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141 $feature{end} = $end;
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142 $feature{source} = "Seg";
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143 $feature{primary} = 'low_complexity';
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144 $feature{program} = "Seg";
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145 $feature{logic_name} = 'low_complexity';
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146 my $new_feat = $self->create_feature (\%feature);
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147 return $new_feat;
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148 }
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149 next;
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150 }
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151
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152 }
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153
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154
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155 =head2 create_feature
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156
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157 Title : create_feature
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158 Usage : obj->create_feature(\%feature)
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159 Function: Internal(not to be used directly)
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160 Returns :
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161 Args :
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162
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163
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164 =cut
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165
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166 sub create_feature {
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167 my ($self, $feat) = @_;
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168
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169
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170 # create feature object
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171 my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name},
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172 -start => $feat->{start},
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173 -end => $feat->{end},
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174 -score => $feat->{score},
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175 -source => $feat->{source},
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176 -primary => $feat->{primary},
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177 -logic_name => $feat->{logic_name},
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178 );
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179
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180 return $feature;
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181
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182 }
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183
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184 1;
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185
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186
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