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patric2uniprot.pl
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patric2uniprot.pl
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#!/usr/bin/perl
###############################################################################
# Script to update genome_name. Input is a tab delimited file containing
# genome_id and new_genome_name for each genome on a separate line. The
# script queries all relevant solr cores containing genome data and updates
# genome names using atomic updates.
#
# Usage: updateGenomeName.pl new_names.tab
#
# #############################################################################
use strict;
use warnings;
use Getopt::Long;
$0 =~ m/([^\/]+)$/;
my $self = $1;
my $usage = $self. qq( --genome_list genome_list.tab --help);
my $solrServer = $ENV{PATRIC_SOLR};
my $solrFormat="&wt=csv&csv.separator=%09&csv.mv.separator=;";
my ($help, $genome_list, $genome_id, $outfile);
my @genome_ids = ();
my $opts = GetOptions(
"help" => \$help,
"genome_list=s" => \$genome_list,
"genome_id=s" => \$genome_id,
"outfile=s" => \$outfile
);
if (!$opts || $help || !($genome_list || $genome_id)){
warn qq(\n usage: $usage\n\n);
exit(0);
}
if ($genome_list){
open LIST, $genome_list;
@genome_ids = <LIST>;
close LIST;
}
if ($genome_id){
push @genome_ids, $genome_id;
}
foreach my $genome_id (@genome_ids){
chomp $genome_id;
next if $genome_id=~/genome_id/;
my %gis;
my %gene_ids;
my %protein_ids;
my $core = "/genome_feature";
my $query = "/select?q=genome_id:$genome_id AND annotation:PATRIC AND feature_type:CDS AND refseq_locus_tag:*";
my $fields = "&fl=patric_id,refseq_locus_tag,gi,gene_id,protein_id";
my $rows = "&rows=100000";
my $sort = "";
my $solrQuery = $solrServer.$core.$query.$fields.$rows.$sort.$solrFormat;
my @results = `wget -q -O - "$solrQuery" | grep -v patric_id`;
next unless scalar @results > 0;
print "Genome_id:$genome_id\tFeatures:". scalar @results. "\n";
foreach my $result (@results){
chomp $result;
my ($patric_id, $refseq_locus_tag, $gi, $gene_id, $protein_id) = split /\t/, $result;
$gis{$gi} = $patric_id;
$gene_ids{$gene_id} = $patric_id;
$protein_ids{$protein_id} = $patric_id;
}
my %patric2uniprot = ();
my $url1 = $solrServer."/id_ref/select/";
my $query1 = "q=id_type:GeneID AND id_value:(". join (" OR ", keys %gene_ids).")";
$query1 .= "&fl=uniprotkb_accession,id_value&rows=100000";
$query1 .= $solrFormat;
my @rows1 = `wget -q -O - "$url1" --post-data="$query1" | grep -v "uniprotkb_accession"`;
foreach my $row1 (@rows1){
my ($uniprotkb_accession, $gene_id) = $row1=~/(.*)\t(.*)/;
my $patric_id = $gene_ids{$gene_id};
$patric2uniprot{$patric_id} = $uniprotkb_accession;
print "$uniprotkb_accession\t$patric_id\t$gene_id\n";
}
my $url2 = $solrServer."/id_ref/select/";
my $query2 = "q=id_type:RefSeq AND id_value:(". join (" OR ", keys %protein_ids).")";
$query2 .= "&fl=uniprotkb_accession,id_value&rows=100000";
$query2 .= $solrFormat;
my @rows2 = `wget -q -O - "$url2" --post-data="$query2" | grep -v "uniprotkb_accession"`;
foreach my $row2 (@rows2){
my ($uniprotkb_accession, $protein_id) = $row2=~/(.*)\t(.*)/;
my $patric_id = $protein_ids{$protein_id};
$patric2uniprot{$patric_id} = $uniprotkb_accession;
print "$uniprotkb_accession\t$patric_id\t$protein_id\n";
}
my $url3 = $solrServer."/id_ref/select/";
my $query3 = "q=id_type:GI AND id_value:(". join (" OR ", keys %gis).")";
$query3 .= "&fl=uniprotkb_accession,id_value&rows=100000";
$query3 .= $solrFormat;
my @rows3 = `wget -q -O - "$url3" --post-data="$query3" | grep -v "uniprotkb_accession"`;
foreach my $row3 (@rows3){
my ($uniprotkb_accession, $gi) = $row3=~/(.*)\t(.*)/;
my $patric_id = $gis{$gi};
$patric2uniprot{$patric_id} = $uniprotkb_accession;
print "$uniprotkb_accession\t$patric_id\t$gi\n";
}
next unless scalar (keys %patric2uniprot) > 0;
open MAP, ">$genome_id.map";
foreach my $patric_id (keys %patric2uniprot){
print MAP "$patric2uniprot{$patric_id}\t$patric_id\n";
}
close MAP;
}