Mercurial > repos > yusuf > associate_phenotypes
view filter_by_mouse_knockout_pipe @ 0:6411ca16916e default tip
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author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:23:29 -0600 |
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#!/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)] <MGI knockout pheno data dir> <hgvs_annotated.txt> <output.txt> <query>\n", "Where query has the format \"this or that\", \"this and that\", etc.\n", "Knockout files are available from ftp://ftp.informatics.jax.org/pub/reports/MPheno_OBO.ontology and ftp://ftp.informatics.jax.org/pub/reports/HMD_HumanPhenotype.rpt\n"; my $mgi_dir = shift @ARGV; my $obo_file = "$mgi_dir/MPheno_OBO.ontology"; my $human_mouse_file = "$mgi_dir/HMD_HumanPhenotype.rpt"; my $geno_pheno_file = "$mgi_dir/MGI_PhenoGenoMP.rpt"; my $hgvs_file = shift @ARGV; my $out_file = shift @ARGV; my $query = shift @ARGV; #$query = quotemeta($query); # in case there are meta characters in the query, treat them as literals my %problematic_terms = (); # 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 is $query\n" unless $quiet; open(OBO, $obo_file) or die "Cannot open $obo_file for reading: $!\n"; my %matched_pheno_ids; my %pheno_id2subtypes; my %pheno_id2name; my $record_count; $/ = "\n[Term]\n"; <OBO>; # chuck header while(<OBO>){ next unless /^id:\s*(MP:\d+)/s; my $id = $1; next unless /\nname:\s*(.+?)\s*\n/s; my $name = $1; $pheno_id2name{$id} = $name; $record_count++; while(/\nis_a:\s*(MP:\d+)/g){ my $parent_id = $1; $pheno_id2subtypes{$parent_id} = [] unless exists $pheno_id2subtypes{$parent_id}; push @{$pheno_id2subtypes{$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 $matched_pheno_ids{$id}){ $matched_pheno_ids{$id} = $match; } elsif($matched_pheno_ids{$id} !~ /$match/){ $matched_pheno_ids{$id} .= "; $match"; } } } elsif(/\b($query)/o){ my $match = $1; $match =~ tr/\t\n/ /; $match =~ s/ {2,}/ /g; if(not exists $matched_pheno_ids{$id}){ $matched_pheno_ids{$id} = $match; } elsif($matched_pheno_ids{$id} !~ /$match/){ $matched_pheno_ids{$id} .= "; $match"; } } } close(OBO); #print STDERR "Found ", scalar(keys %matched_pheno_ids), "/$record_count phenotype ontology terms matching the query\n"; open(OUT, ">$out_file") or die "Cannot open $out_file for writing: $!\n"; # Implements term subsumption my @matched_pheno_ids = keys %matched_pheno_ids; for(my $i = 0; $i <= $#matched_pheno_ids; $i++){ my $pheno_id = $matched_pheno_ids[$i]; next unless exists $pheno_id2subtypes{$pheno_id}; for my $sub_type_id (@{$pheno_id2subtypes{$pheno_id}}){ if(not exists $matched_pheno_ids{$sub_type_id}){ $matched_pheno_ids{$sub_type_id} = $matched_pheno_ids{$pheno_id}; push @matched_pheno_ids, $sub_type_id; } } } $/="\n"; # record separator my %human2mouse; # example line: # WNT3A 89780 Wnt3a MGI:98956 MP:0003012 MP:0003631 ... MP:0010768 open(HUMAN2MOUSE, $human_mouse_file) or die "Cannot open $human_mouse_file for reading: $!\n"; while(<HUMAN2MOUSE>){ my @F = split /\t/, $_; $human2mouse{$F[0]} = $F[2]; } close(HUMAN2MOUSE); my %gene2pheno_ids; # example line: # Rbpj<tm1Kyo>/Rbpj<tm1Kyo> Rbpj<tm1Kyo> involves: 129S2/SvPas * C57BL/6 MP:0001614 15466160 MGI:96522 open(PHENO, $geno_pheno_file) or die "Cannot open $geno_pheno_file for reading: $!\n"; while(<PHENO>){ chomp; my @F = split /\t/, $_; next unless $#F > 2; # does it have the phenotype id field? my $knockout = $F[0]; next if $knockout =~ /,/; # ignore double knockouts etc. $knockout =~ s/^(\S+?)<.*/$1/; # keep only first gene name bit of knockout description my $pheno_id = $F[3]; $gene2pheno_ids{$knockout} = [] unless exists $gene2pheno_ids{$knockout}; push @{$gene2pheno_ids{$knockout}}, [$pheno_id,$F[4]]; } # remove genes if they don't have a matching phenotype for my $gene (keys %gene2pheno_ids){ my $keep = 0; for my $pheno_id (@{$gene2pheno_ids{$gene}}){ if(exists $matched_pheno_ids{$pheno_id->[0]}){ $keep = 1; last; } } delete $gene2pheno_ids{$gene} unless $keep; } #print STDERR "Found ", scalar(keys %gene2pheno_ids), " genes with knockout phenotype 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\tMouse Knockout Phenotypes (matching $orig_query)\tMouse Phenotypes (other)\n"; # Check if any of the variants in the annotated HGVS table are in knockout genes matching the target phenotypes list while(<HGVS>){ chomp; my @F = split /\t/, $_, -1; my (%target_phenos, %other_phenos); for my $gene_name (split /\s*;\s*/, $F[$gene_name_column]){ next unless exists $human2mouse{$gene_name}; next unless exists $gene2pheno_ids{$human2mouse{$gene_name}}; for my $pheno_id (@{$gene2pheno_ids{$human2mouse{$gene_name}}}){ my ($id, $pmid) = @$pheno_id; if(exists $matched_pheno_ids{$id}){ $target_phenos{$pmid} = [] unless exists $target_phenos{$pmid}; push @{$target_phenos{$pmid}}, $pheno_id2name{$id}."($matched_pheno_ids{$id})"; } else{ $other_phenos{$pmid} = [] unless exists $other_phenos{$pmid}; push @{$other_phenos{$pmid}}, $pheno_id2name{$id}; } } } if(%target_phenos){ print OUT join("\t", @F); print OUT "\t"; my $count = 0; for my $pmid (keys %target_phenos){ print OUT " // " if $count++; print OUT "PubMed $pmid: ", join("; ", @{$target_phenos{$pmid}}); } print OUT "\t"; $count = 0; for my $pmid (keys %other_phenos){ print OUT " // " if $count++; print OUT "PubMed $pmid: ", join("; ", @{$other_phenos{$pmid}}); } print OUT "\n"; } else{ print OUT join("\t", @F, "", ""), "\n"; } } close(HGVS); close(OUT);