gene_search

   1 #! /usr/bin/perl
   2 # , and is released
   3 # under the terms of the GPL version 2, or any later version, at your
   4 # option. See the file README and COPYING for more information.
   5 # Copyright 2011 by Don Armstrong <don@donarmstrong.com>.
   6 # $Id: perl_script 1825 2011-01-02 01:53:43Z don $
   7
   8
   9 use warnings;
  10 use strict;
  11
  12 use Getopt::Long;
  13 use Pod::Usage;
  14
  15 use Bio::DB::EUtilities;
  16
  17 use Encode qw(encode_utf8);
  18 use Term::ANSIColor qw(:constants);
  19 use Text::Wrap;
  20
  21
  22 =head1 NAME
  23
  24 pubmed_search -
  25
  26 =head1 SYNOPSIS
  27
  28  pubmed_search [options] [searchterms]
  29
  30  Options:
  31   --debug, -d debugging level (Default 0)
  32   --help, -h display this help
  33   --man, -m display manual
  34
  35 =head1 OPTIONS
  36
  37 =over
  38
  39 =item B<--debug, -d>
  40
  41 Debug verbosity. (Default 0)
  42
  43 =item B<--help, -h>
  44
  45 Display brief usage information.
  46
  47 =item B<--man, -m>
  48
  49 Display this manual.
  50
  51 =back
  52
  53 =head1 EXAMPLES
  54
  55
  56 =cut
  57
  58
  59 use vars qw($DEBUG);
  60
  61 my %options = (debug           => 0,
  62                help            => 0,
  63                man             => 0,
  64                color           => 1,
  65                org_mode        => 0,
  66                symbol          => 0,
  67                organism        => 'Homo sapiens',
  68                );
  69
  70 GetOptions(\%options,
  71            'color|c!',
  72            'org_mode|org-mode!',
  73            'symbol|s!',
  74            'organism|o=s',
  75            'debug|d+','help|h|?','man|m');
  76
  77 pod2usage() if $options{help};
  78 pod2usage({verbose=>2}) if $options{man};
  79
  80 $DEBUG = $options{debug};
  81
  82 my @USAGE_ERRORS;
  83 if (not @ARGV) {
  84     push @USAGE_ERRORS,"You must pass something";
  85 }
  86
  87 pod2usage(join("\n",@USAGE_ERRORS)) if @USAGE_ERRORS;
  88
  89 my $term = join(' ',@ARGV);
  90 if ($options{symbol}) {
  91     $term = join(' OR ',map {'('.$_.'[Preferred Symbol] AND '.$options{organism}.'[Orgn])'} @ARGV);
  92 }
  93
  94 my $search = Bio::DB::EUtilities->new(-eutil => 'esearch',
  95                                        -email => 'don@donarmstrong.com',
  96                                        -db    => 'gene',
  97                                        -term => $term,
  98                                        -retmax => 1000,
  99                                       );
 100 my @ids = $search->get_ids();
 101 # print scalar(@ids)." results:\n";
 102 exit 0 unless @ids;
 103 my $esummary = Bio::DB::EUtilities->new(-eutil => 'efetch',
 104                                         -email => 'don@donarmstrong.com',
 105                                         -db    => 'gene',
 106                                         -id  => \@ids,
 107                                         -retmode => 'xml',
 108                                        );
 109 #print $esummary->get_Response()->content() if $DEBUG;
 110 use XML::LibXML;
 111 my $xml = XML::LibXML->load_xml(string => $esummary->get_Response()->content());
 112 for my $gene ($xml->findnodes('Entrezgene-Set/Entrezgene')) {
 113     print $gene->toString if $DEBUG;
 114     my ($locus) = $gene->findnodes('.//Gene-ref_locus');
 115     my ($desc) = $gene->findnodes('.//Gene-ref_desc');
 116     my ($summary) = $gene->findnodes('.//Entrezgene_summary');
 117     my ($idiogram) = $gene->findnodes('.//Gene-ref_maploc');
 118     next unless defined $idiogram;
 119     my ($start) = $gene->findnodes('.//Gene-commentary_seqs/Seq-loc/Seq-loc_int/Seq-interval/Seq-interval_from');
 120     my ($stop) = $gene->findnodes('.//Gene-commentary_seqs/Seq-loc/Seq-loc_int/Seq-interval/Seq-interval_to');
 121     if ($options{org_mode}) {
 122         print "* ";
 123     }
 124     print BOLD GREEN if $options{color};
 125     print $locus->textContent();
 126     print ": ";
 127     print RESET if $options{color};
 128     print "(".$idiogram->textContent();
 129     print " ".$start->textContent().":";
 130     print $stop->textContent().") ";
 131     print BOLD CYAN if $options{color};
 132     print encode_utf8($desc->textContent())."\n";
 133     print RESET if $options{color};
 134     print BOLD MAGENTA if $options{color};
 135     if (defined $summary) {
 136         if ($options{org_mode}) {
 137             print "** Summary\n";
 138         }
 139         $summary = $summary->textContent();
 140         $summary =~ s/^\s*//mg;
 141         $summary = encode_utf8($summary);
 142         print wrap('','',$summary);
 143         print "\n\n";
 144         print RESET if $options{color};
 145     }
 146 }
 147
 148 __END__