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comparison filter_by_gene_ontology_pipe @ 0:6411ca16916e default tip

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initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:23:29 -0600
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-1:000000000000 0:6411ca16916e
1 #!/usr/bin/env perl
2
3 use strict;
4 use warnings;
5
6 my $quiet = 0;
7 if(@ARGV and $ARGV[0] =~ /^-q/){
8 $quiet = 1;
9 shift @ARGV;
10 }
11
12 @ARGV == 4 or die "Usage: $0 [-q(uiet)] <GO data dir> <hgvs_annotated.txt> <output.txt> <query>\n",
13 "Where query has the format \"this or that\", \"this and that\", etc.\n",
14 "GOA and OBO files must be found in the GO data dir\n";
15
16 my $go_dir = shift @ARGV;
17 my $obo_file = "$go_dir/gene_ontology.1_2.obo";
18 my $hgvs_file = shift @ARGV;
19 my $out_file = shift @ARGV;
20 my $query = shift @ARGV;
21
22 # Terms with meronyms and hyponyms in their free text descriptions, causing overgeneralization problems
23 my %problematic_terms = ("GO:0033647" => "host intracellular organelle",
24 "GO:0006996" => "organelle organization",
25 "GO:0043226" => "organelle",
26 "GO:0043227" => "membrane-bounded organelle",
27 "GO:0043229" => "intracellular organelle",
28 "GO:0043231" => "intracellular membrane-bounded organelle",
29 "GO:0044384" => "host cell outer membrane",
30 "GO:0044422" => "organelle part",
31 "GO:0044446" => "intracellular organelle part",
32 "GO:0045202" => "synapse",
33 "GO:0033648" => "host intracellular membrane-bounded organelle");
34
35 #$query = quotemeta($query); # in case there are meta characters in the query, treat them as literals
36
37 # convert the query to a regex
38 my $orig_query = $query;
39 my $and_query = 0;
40 $query =~ s/\(\s*.+?\s*\)/my $s=$&;$s=~s(\s+or\s+)(|)g; $s/eg;
41 if($query =~ s/(\S+)\s+and\s+(\S+)/(?:$1.*?$2|$2.*?$1)/gi){
42 $and_query = 1;
43 }
44 $query =~ s/\s+or\s+/|/gi;
45 $query =~ s/\b([a-z])([a-z]+\b)/"[".uc($1)."$1]$2"/eg; # allow title case match in regex for letter only lower case words, otherwise make case sensitive as assuming gene name
46 #print STDERR "Query regex for GO is $query\n" unless $quiet;
47
48 open(OBO, $obo_file)
49 or die "Cannot open $obo_file for reading: $!\n";
50 my %matched_go_ids;
51 my %go_id2subtypes;
52 my %go_id2name;
53 my $record_count;
54 $/ = "\n[Term]\n";
55 <OBO>; # chuck header
56 while(<OBO>){
57 next unless /^id:\s*(GO:\d+)/s;
58 my $id = $1;
59 next unless /\nname:\s*(.+?)\s*\n/s;
60 my $name = $1;
61 $go_id2name{$id} = $name;
62 $record_count++;
63 while(/\nis_a:\s*(GO:\d+)/g){
64 my $parent_id = $1;
65 $go_id2subtypes{$parent_id} = [] unless exists $go_id2subtypes{$parent_id};
66 push @{$go_id2subtypes{$parent_id}}, $id;
67 }
68 if(exists $problematic_terms{$id}){
69 if($name =~ /\b($query)/o){ # strict matching of name only if an entry with problematic free text
70 my $match = $1;
71 $match =~ tr/\t\n/ /;
72 $match =~ s/ {2,}/ /g;
73 if(not exists $matched_go_ids{$id}){
74 $matched_go_ids{$id} = $match;
75 }
76 elsif($matched_go_ids{$id} !~ /$match/){
77 $matched_go_ids{$id} .= "; $match";
78 }
79 }
80 }
81 elsif(/\b($query)/o){
82 my $match = $1;
83 $match =~ tr/\t\n/ /;
84 $match =~ s/ {2,}/ /g;
85 if(not exists $matched_go_ids{$id}){
86 $matched_go_ids{$id} = $match;
87 }
88 elsif($matched_go_ids{$id} !~ /$match/){
89 $matched_go_ids{$id} .= "; $match";
90 }
91 #print STDERR "Found match $match for $_\n";
92 }
93 }
94 close(OBO);
95 #print STDERR "Found ", scalar(keys %matched_go_ids), "/$record_count go ontology terms matching the query\n";
96
97 open(OUT, ">$out_file")
98 or die "Cannot open $out_file for writing: $!\n";
99
100 # Implements term subsumption
101 my @matched_go_ids = keys %matched_go_ids;
102 for(my $i = 0; $i <= $#matched_go_ids; $i++){
103 my $go_id = $matched_go_ids[$i];
104 next unless exists $go_id2subtypes{$go_id};
105 for my $sub_type_id (@{$go_id2subtypes{$go_id}}){
106 if(not exists $matched_go_ids{$sub_type_id}){
107 $matched_go_ids{$sub_type_id} = $matched_go_ids{$go_id};
108 push @matched_go_ids, $sub_type_id;
109 }
110 }
111 }
112
113 $/="\n"; # record separator
114 my %gene2go_ids;
115 opendir(GOADIR, $go_dir)
116 or die "Cannot read directory $go_dir: $!\n";
117 while($_ = readdir(GOADIR)){
118 next if /^\./; # hidden
119 next unless /\.goa$/; # not a goa formatted file
120 my $goa_file = $_;
121 open(GOA, "$go_dir/$goa_file")
122 or die "Cannot open $go_dir/$goa_file for reading: $!\n";
123 #print STDERR "Processing file $goa_file\n";
124 # example line:
125 # UniProtKB A0ASJ9 GO:0001664 GO_REF:0000033 ISS PANTHER:PTN000026392 F G protein alpha subunit AgGq6 A0ASJ9_ANOGA protein taxon:7165 20110125 RefGenome
126 while(<GOA>){
127 next if /^!/; # comment
128 chomp;
129 my @F = split /\t/, $_;
130 next unless $F[2] and $#F > 3; # does it have the gene name and go id fields?
131 my $genename = uc($F[2]); # standardize gene names to upper case
132 $genename =~ s/-//g;
133 my $go_id = $F[4];
134 $gene2go_ids{$genename} = [] unless exists $gene2go_ids{$genename};
135 push @{$gene2go_ids{$genename}}, $go_id;
136 }
137 close(GOA);
138 }
139 close(GOADIR);
140 #print STDERR "Found ", scalar(keys %gene2go_ids), " total genes\n";
141
142 # remove genes if they don't have a matching go term
143 for my $genename (keys %gene2go_ids){
144 my $keep = 0;
145 for my $go_id (@{$gene2go_ids{$genename}}){
146 if(exists $matched_go_ids{$go_id}){
147 $keep = 1;
148 last;
149 }
150 }
151 delete $gene2go_ids{$genename} unless $keep;
152 }
153 #print STDERR "Found ", scalar(keys %gene2go_ids), " genes with gene ontology terms matching the query\n" unless $quiet;
154
155 $/ = "\n"; # one line at, a time from the HGVS file please!
156 open(HGVS, $hgvs_file)
157 or die "Cannot open $hgvs_file for reading: $!\n";
158 my $header = <HGVS>;
159 chomp $header;
160 my @header_columns = split /\t/, $header;
161 my $gene_name_column;
162 for(my $i = 0; $i <= $#header_columns; $i++){
163 if($header_columns[$i] eq "Gene Name"){
164 $gene_name_column = $i;
165 }
166 }
167 if(not defined $gene_name_column){
168 die "Could not find 'Gene Name' column in the input header, aborting\n";
169 }
170
171 print OUT "$header\tQuickGO Gene Ontology Terms (matching $orig_query)\tQuickGO Gene Ontology Terms (other)\n";
172 # Check if any of the variants in the annotated HGVS table are in knockout genes matching the target go term list
173 while(<HGVS>){
174 chomp;
175 my @F = split /\t/, $_, -1;
176 my (@target_gos, @other_gos);
177 for my $gene_name (split /\s*;\s*/, $F[$gene_name_column]){
178 next unless exists $gene2go_ids{$gene_name};
179 for my $id (@{$gene2go_ids{$gene_name}}){
180 if(exists $matched_go_ids{$id}){
181 push @target_gos, $go_id2name{$id}."($matched_go_ids{$id})";
182 }
183 else{
184 push @other_gos, $go_id2name{$id};
185 }
186 }
187 }
188 if(@target_gos){
189 my (%t,%o);
190 # print unique terms
191 print OUT join("\t", @F, join("; ", sort grep {not $t{$_}++} @target_gos), join("; ", sort grep {not $o{$_}++} @other_gos)), "\n";
192 }
193 else{
194 print OUT join("\t", @F, "", ""), "\n";
195 }
196 }