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comparison tools/human_genome_variation/ctd.pl @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5
6 use LWP::UserAgent;
7 require HTTP::Cookies;
8
9 #######################################################
10 # ctd.pl
11 # Submit a batch query to CTD and fetch results into galaxy history
12 # usage: ctd.pl inFile idCol inputType resultType actionType outFile
13 #######################################################
14
15 if (!@ARGV or scalar @ARGV != 6) {
16 print "usage: ctd.pl inFile idCol inputType resultType actionType outFile\n";
17 exit;
18 }
19
20 my $in = shift @ARGV;
21 my $col = shift @ARGV;
22 if ($col < 1) {
23 print "The column number is with a 1 start\n";
24 exit 1;
25 }
26 my $type = shift @ARGV;
27 my $resType = shift @ARGV;
28 my $actType = shift @ARGV;
29 my $out = shift @ARGV;
30
31 my @data;
32 open(FH, $in) or die "Couldn't open $in, $!\n";
33 while (<FH>) {
34 chomp;
35 my @f = split(/\t/);
36 if (scalar @f < $col) {
37 print "ERROR the requested column is not in the file $col\n";
38 exit 1;
39 }
40 push(@data, $f[$col-1]);
41 }
42 close FH or die "Couldn't close $in, $!\n";
43
44 my $url = 'http://ctd.mdibl.org/tools/batchQuery.go';
45 #my $url = 'http://globin.bx.psu.edu/cgi-bin/print-query';
46 my $d = join("\n", @data);
47 #list maintains order, where hash doesn't
48 #order matters at ctd
49 #to use input file (gives error can't find file)
50 #my @form = ('inputType', $type, 'inputTerms', '', 'report', $resType,
51 #'queryFile', [$in, ''], 'queryFileColumn', $col, 'format', 'tsv', 'action', 'Submit');
52 my @form = ('inputType', $type, 'inputTerms', $d, 'report', $resType,
53 'queryFile', '', 'format', 'tsv', 'action', 'Submit');
54 if ($resType eq 'cgixns') { #only add if this type
55 push(@form, 'actionTypes', $actType);
56 }
57 my $ua = LWP::UserAgent->new;
58 $ua->cookie_jar(HTTP::Cookies->new( () ));
59 $ua->agent('Mozilla/5.0');
60 my $page = $ua->post($url, \@form, 'Content_Type'=>'form-data');
61 if ($page->is_success) {
62 open(FH, ">", $out) or die "Couldn't open $out, $!\n";
63 print FH "#";
64 print FH $page->content, "\n";
65 close FH or die "Couldn't close $out, $!\n";
66 }else {
67 print "ERROR failed to get page from CTD, ", $page->status_line, "\n";
68 print $page->content, "\n";
69 my $req = $page->request();
70 print "Requested \n";
71 foreach my $k(keys %$req) {
72 if ($k eq '_headers') {
73 my $t = $req->{$k};
74 foreach my $k2 (keys %$t) { print "$k2 => $t->{$k2}\n"; }
75 }else { print "$k => $req->{$k}\n"; }
76 }
77 exit 1;
78 }
79 exit;
80