Mercurial > repos > yusuf > associate_phenotypes
diff filter_by_gene_ontology_pipe @ 0:6411ca16916e default tip
initial commit
author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:23:29 -0600 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_by_gene_ontology_pipe Wed Mar 25 13:23:29 2015 -0600 @@ -0,0 +1,196 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +my $quiet = 0; +if(@ARGV and $ARGV[0] =~ /^-q/){ + $quiet = 1; + shift @ARGV; +} + +@ARGV == 4 or die "Usage: $0 [-q(uiet)] <GO data dir> <hgvs_annotated.txt> <output.txt> <query>\n", + "Where query has the format \"this or that\", \"this and that\", etc.\n", + "GOA and OBO files must be found in the GO data dir\n"; + +my $go_dir = shift @ARGV; +my $obo_file = "$go_dir/gene_ontology.1_2.obo"; +my $hgvs_file = shift @ARGV; +my $out_file = shift @ARGV; +my $query = shift @ARGV; + +# Terms with meronyms and hyponyms in their free text descriptions, causing overgeneralization problems +my %problematic_terms = ("GO:0033647" => "host intracellular organelle", + "GO:0006996" => "organelle organization", + "GO:0043226" => "organelle", + "GO:0043227" => "membrane-bounded organelle", + "GO:0043229" => "intracellular organelle", + "GO:0043231" => "intracellular membrane-bounded organelle", + "GO:0044384" => "host cell outer membrane", + "GO:0044422" => "organelle part", + "GO:0044446" => "intracellular organelle part", + "GO:0045202" => "synapse", + "GO:0033648" => "host intracellular membrane-bounded organelle"); + +#$query = quotemeta($query); # in case there are meta characters in the query, treat them as literals + +# convert the query to a regex +my $orig_query = $query; +my $and_query = 0; +$query =~ s/\(\s*.+?\s*\)/my $s=$&;$s=~s(\s+or\s+)(|)g; $s/eg; +if($query =~ s/(\S+)\s+and\s+(\S+)/(?:$1.*?$2|$2.*?$1)/gi){ + $and_query = 1; +} +$query =~ s/\s+or\s+/|/gi; +$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 +#print STDERR "Query regex for GO is $query\n" unless $quiet; + +open(OBO, $obo_file) + or die "Cannot open $obo_file for reading: $!\n"; +my %matched_go_ids; +my %go_id2subtypes; +my %go_id2name; +my $record_count; +$/ = "\n[Term]\n"; +<OBO>; # chuck header +while(<OBO>){ + next unless /^id:\s*(GO:\d+)/s; + my $id = $1; + next unless /\nname:\s*(.+?)\s*\n/s; + my $name = $1; + $go_id2name{$id} = $name; + $record_count++; + while(/\nis_a:\s*(GO:\d+)/g){ + my $parent_id = $1; + $go_id2subtypes{$parent_id} = [] unless exists $go_id2subtypes{$parent_id}; + push @{$go_id2subtypes{$parent_id}}, $id; + } + if(exists $problematic_terms{$id}){ + if($name =~ /\b($query)/o){ # strict matching of name only if an entry with problematic free text + my $match = $1; + $match =~ tr/\t\n/ /; + $match =~ s/ {2,}/ /g; + if(not exists $matched_go_ids{$id}){ + $matched_go_ids{$id} = $match; + } + elsif($matched_go_ids{$id} !~ /$match/){ + $matched_go_ids{$id} .= "; $match"; + } + } + } + elsif(/\b($query)/o){ + my $match = $1; + $match =~ tr/\t\n/ /; + $match =~ s/ {2,}/ /g; + if(not exists $matched_go_ids{$id}){ + $matched_go_ids{$id} = $match; + } + elsif($matched_go_ids{$id} !~ /$match/){ + $matched_go_ids{$id} .= "; $match"; + } + #print STDERR "Found match $match for $_\n"; + } +} +close(OBO); +#print STDERR "Found ", scalar(keys %matched_go_ids), "/$record_count go ontology terms matching the query\n"; + +open(OUT, ">$out_file") + or die "Cannot open $out_file for writing: $!\n"; + +# Implements term subsumption +my @matched_go_ids = keys %matched_go_ids; +for(my $i = 0; $i <= $#matched_go_ids; $i++){ + my $go_id = $matched_go_ids[$i]; + next unless exists $go_id2subtypes{$go_id}; + for my $sub_type_id (@{$go_id2subtypes{$go_id}}){ + if(not exists $matched_go_ids{$sub_type_id}){ + $matched_go_ids{$sub_type_id} = $matched_go_ids{$go_id}; + push @matched_go_ids, $sub_type_id; + } + } +} + +$/="\n"; # record separator +my %gene2go_ids; +opendir(GOADIR, $go_dir) + or die "Cannot read directory $go_dir: $!\n"; +while($_ = readdir(GOADIR)){ + next if /^\./; # hidden + next unless /\.goa$/; # not a goa formatted file + my $goa_file = $_; + open(GOA, "$go_dir/$goa_file") + or die "Cannot open $go_dir/$goa_file for reading: $!\n"; + #print STDERR "Processing file $goa_file\n"; + # example line: + # UniProtKB A0ASJ9 GO:0001664 GO_REF:0000033 ISS PANTHER:PTN000026392 F G protein alpha subunit AgGq6 A0ASJ9_ANOGA protein taxon:7165 20110125 RefGenome + while(<GOA>){ + next if /^!/; # comment + chomp; + my @F = split /\t/, $_; + next unless $F[2] and $#F > 3; # does it have the gene name and go id fields? + my $genename = uc($F[2]); # standardize gene names to upper case + $genename =~ s/-//g; + my $go_id = $F[4]; + $gene2go_ids{$genename} = [] unless exists $gene2go_ids{$genename}; + push @{$gene2go_ids{$genename}}, $go_id; + } + close(GOA); +} +close(GOADIR); +#print STDERR "Found ", scalar(keys %gene2go_ids), " total genes\n"; + +# remove genes if they don't have a matching go term +for my $genename (keys %gene2go_ids){ + my $keep = 0; + for my $go_id (@{$gene2go_ids{$genename}}){ + if(exists $matched_go_ids{$go_id}){ + $keep = 1; + last; + } + } + delete $gene2go_ids{$genename} unless $keep; +} +#print STDERR "Found ", scalar(keys %gene2go_ids), " genes with gene ontology terms matching the query\n" unless $quiet; + +$/ = "\n"; # one line at, a time from the HGVS file please! +open(HGVS, $hgvs_file) + or die "Cannot open $hgvs_file for reading: $!\n"; +my $header = <HGVS>; +chomp $header; +my @header_columns = split /\t/, $header; +my $gene_name_column; +for(my $i = 0; $i <= $#header_columns; $i++){ + if($header_columns[$i] eq "Gene Name"){ + $gene_name_column = $i; + } +} +if(not defined $gene_name_column){ + die "Could not find 'Gene Name' column in the input header, aborting\n"; +} + +print OUT "$header\tQuickGO Gene Ontology Terms (matching $orig_query)\tQuickGO Gene Ontology Terms (other)\n"; +# Check if any of the variants in the annotated HGVS table are in knockout genes matching the target go term list +while(<HGVS>){ + chomp; + my @F = split /\t/, $_, -1; + my (@target_gos, @other_gos); + for my $gene_name (split /\s*;\s*/, $F[$gene_name_column]){ + next unless exists $gene2go_ids{$gene_name}; + for my $id (@{$gene2go_ids{$gene_name}}){ + if(exists $matched_go_ids{$id}){ + push @target_gos, $go_id2name{$id}."($matched_go_ids{$id})"; + } + else{ + push @other_gos, $go_id2name{$id}; + } + } + } + if(@target_gos){ + my (%t,%o); + # print unique terms + print OUT join("\t", @F, join("; ", sort grep {not $t{$_}++} @target_gos), join("; ", sort grep {not $o{$_}++} @other_gos)), "\n"; + } + else{ + print OUT join("\t", @F, "", ""), "\n"; + } +}