/usr/share/perl5/Bio/Tools/Profile.pm is in libbio-perl-perl 1.6.923-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 | # BioPerl module for Bio::Tools::Profile
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Profile - parse Profile output
=head1 SYNOPSIS
use Bio::Tools::Profile;
my $profile_parser = Bio::Tools::Profile->new(-fh =>$filehandle );
while( my $profile_feat = $profile_parser->next_result ) {
push @profile_feat, $profile_feat;
}
=head1 DESCRIPTION
Parser for Profile output
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Balamurugan Kumarasamy
Email: fugui@worf.fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Tools::Profile;
use strict;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Profile->new();
Function: Builds a new Bio::Tools::Profile object
Returns : Bio::Tools::Profile
Args : -filename
-fh ($filehandle)
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : my $feat = $profile_parser->next_result
Function: Get the next result set from parser data
Returns : L<Bio::SeqFeature::FeaturePair>
Args : none
=cut
sub next_result {
my ($self) = @_;
my %printsac;
my $line;
my @features;
while ($_=$self->_readline()) {
$line = $_;
chomp $line;
my ($nscore,$rawscore,$from,$to,$hfrom,$hto,$ac) = $line =~ /(\S+)\s+(\d+)\s*pos.\s+(\d*)\s*-\s+(\d*)\s*\[\s+(\d*),\s+(\S*)\]\s*(\w+)/;
#for example in this output line
#38.435 2559 pos. 19958 - 20212 [ 1, -1] PS50011|PROTEIN_KINASE_DOM Protein kinase domain profile.
#$nscore = 38.435
#$rawscore = 2559
#$from = 19958
#$end = 20212
#$hfrom = 1
#$hto =-1
#$ac = PS50011
my $feat = "$ac,$from,$to,$hfrom,$hto,$nscore";
my $new_feat= $self->create_feature($feat);
return $new_feat
}
}
=head2 create_feature
Title : create_feature
Usage : my $feat= $profile_parser->create_feature($feature)
Function: creates a Bio::SeqFeature::FeaturePair object
Returns : L<Bio::SeqFeature::FeaturePair>
Args :
=cut
sub create_feature {
my ($self, $feat) = @_;
my @f = split (/,/,$feat);
my $hto = $f[4];
if ($f[4] =~ /-1/) {
$hto = $f[2] - $f[1] + 1;
}
my $feat1 = Bio::SeqFeature::Generic->new( -start => $f[1],
-end => $f[2],
-score => $f[5],
-source=>'pfscan',
-primary=>$f[0]);
my $feat2 = Bio::SeqFeature::Generic->new(-start => $f[3],
-end => $hto,
);
my $feature = Bio::SeqFeature::FeaturePair->new(-feature1 => $feat1,
-feature2 => $feat2);
return $feature;
}
1;
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