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rast2solr.pl
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rast2solr.pl
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#!/usr/bin/env perl
###########################################################
#
# rast2solr.pl:
#
# Script to parse RASTtk genome object and input genbank file
# and prepare separate JSON files for each of the Solr cores.
#
# Input:
# - JSON file containing RASTtk genome object
# - Optional Original GenBank file used as input to RASTtk job
#
# Output: Six JSON files each correspodning to a Solr core
# - genome.json
# - genome_sequence.json
# - genome_feature.json
# - pathway.json
# - sp_gene.json
# - genome_amr.json
#
###########################################################
use strict;
use FindBin qw($Bin);
use Getopt::Long::Descriptive;
use POSIX;
use JSON;
use Data::Dumper;
use Digest::MD5 qw(md5 md5_hex md5_base64);
use Bio::SeqIO;
use Bio::SeqFeature::Generic;
use Date::Parse;
use XML::Simple;
our $have_config;
eval
{
require Bio::KBase::AppService::AppConfig;
$have_config = 1;
};
use lib "$Bin";
use SolrAPI;
my ($data_api_url, $reference_data_dir);
if ($have_config)
{
$data_api_url = Bio::KBase::AppService::AppConfig->data_api_url;
$reference_data_dir = Bio::KBase::AppService::AppConfig->reference_data_dir;
}else{
$data_api_url = $ENV{PATRIC_DATA_API};
$reference_data_dir = $ENV{PATRIC_REFERENCE_DATA};
}
my $json = JSON->new->allow_nonref;
my ($opt, $usage) = describe_options("%c %o",
[],
["genomeobj-file=s", "RASTtk annotations as GenomeObj.json file"],
["genbank-file=s", "Original GenBank file that was used as input to RASTtk"],
["public", "public, default is private"],
["data-api-url=s", "Data API URL", { default => $data_api_url }],
["reference-data-dir=s", "Data API URL", { default => $reference_data_dir }],
[],
["help|h", "Print usage message and exit"] );
print($usage->text), exit 0 if $opt->help;
die($usage->text) unless $opt->genomeobj_file;
my $solrh = SolrAPI->new($opt->data_api_url, $opt->reference_data_dir);
my $genomeobj_file = $opt->genomeobj_file;
my $genbank_file = $opt->genbank_file;
my $outfile = $genomeobj_file;
$outfile=~s/(.gb|.gbf|.json)$//;
print "Processing $genomeobj_file\n";
# Read GenomeObj
open GOF, $genomeobj_file or die "Can't open input RASTtk GenomeObj JSON file: $genomeobj_file\n";
my @json_array = <GOF>;
my $json_str = join "", @json_array;
close GOF;
my $genomeObj = $json->decode($json_str);
# Set global parameters
my $public = $opt->public? 1 : 0;
my $annotation = "PATRIC";
# Get EC, pathway, and spgene reference dictionaries
my $ecRef = $solrh->getECRef();
my $pathwayRef = $solrh->getPathwayRef();
my $spgeneRef = $solrh->getSpGeneRef();
# Initialize global arrays to hold genome data
my %seq=();
my $genome;
my @sequences = ();
my @features = ();
my @pathwaymap = ();
my @spgenemap = ();
my @taxonomy = ();
my @genome_amr = ();
my $featureIndex;
# Process GenomeObj
getGenomeInfo();
# Get additional genome metadata
getMetadataFromGenBankFile($genbank_file) if -f $genbank_file;
getMetadataFromBioProject($genome->{bioproject_accession}) if $genome->{bioproject_accession};
getMetadataFromBioSample($genome->{biosample_accession}) if $genome->{biosample_accession};
# Get predicted AMR phenotypes
getAMRPhenotypes();
# Get genome sequences
getGenomeSequences();
# Get Genome features from genome obj
getGenomeFeatures();
# Get additional features from the GenBank file
getGenomeFeaturesFromGenBankFile($genbank_file) if -f $genbank_file;
# write to json files
writeJson();
sub writeJson {
print "Preparing JSON files ...\n";
my $genome_json = $json->pretty->encode($genome);
my $sequence_json = $json->pretty->encode(\@sequences);
my $feature_json = $json->pretty->encode(\@features);
my $pathwaymap_json = $json->pretty->encode(\@pathwaymap);
my $spgenemap_json = $json->pretty->encode(\@spgenemap);
my $taxonomy_json = $json->pretty->encode(\@taxonomy);
my $genome_amr_json = $json->pretty->encode(\@genome_amr);
open FH, ">genome.json" or die "Cannot write genome.json: $!";
print FH "[".$genome_json."]";
close FH;
open FH, ">genome_sequence.json" or die "Cannot write genome_sequence.json: $!";
print FH $sequence_json;
close FH;
open FH, ">genome_feature.json" or die "Cannot write genome_feature.json: $!";
print FH $feature_json;
close FH;
open FH, ">pathway.json" or die "Cannot write pathway.json: $!";
print FH $pathwaymap_json;
close FH;
open FH, ">sp_gene.json" or die "Cannot write sp_gene.json: $!";
print FH $spgenemap_json;
close FH;
open FH, ">taxonomy.json" or die "Cannot write taxonomy.json: $!";
print FH $taxonomy_json;
close FH;
open FH, ">genome_amr.json" or die "Cannot write genome_amr.json: $!";
print FH $genome_amr_json;
close FH;
}
sub getGenomeInfo {
print "Getting genome metadata ...\n";
my ($chromosomes, $plasmids, $contigs, $sequences, $cds, $genome_length, $gc_count, $taxon_lineage_ranks);
$genome->{owner} = $genomeObj->{owner}? $genomeObj->{owner} : "PATRIC";
$genome->{public} = $public;
$genome->{genome_id} = $genomeObj->{id};
$genome->{genome_name} = $genomeObj->{scientific_name};
$genome->{common_name} = $genomeObj->{scientific_name};
$genome->{common_name}=~s/\W+/_/g;
$genome->{taxon_id} = $genomeObj->{ncbi_taxonomy_id};
($genome->{taxon_lineage_ids}, $genome->{taxon_lineage_names}, $taxon_lineage_ranks) = $solrh->getTaxonLineage($genome->{taxon_id});
prepareTaxonomy($genome->{taxon_lineage_ids}) if $public;
my $i=0;
for my $rank (@{$taxon_lineage_ranks}){
$genome->{kingdom} = $genome->{taxon_lineage_names}[$i] if $rank=~/kingdom/i;
$genome->{phylum} = $genome->{taxon_lineage_names}[$i] if $rank=~/phylum/i;
$genome->{class} = $genome->{taxon_lineage_names}[$i] if $rank=~/class/i;
$genome->{order} = $genome->{taxon_lineage_names}[$i] if $rank=~/order/i;
$genome->{family} = $genome->{taxon_lineage_names}[$i] if $rank=~/family/i;
$genome->{genus} = $genome->{taxon_lineage_names}[$i] if $rank=~/genus/i;
$genome->{species} = $genome->{taxon_lineage_names}[$i] if $rank=~/species/i;
$i++;
}
foreach my $type (@{$genomeObj->{typing}}){
$genome->{mlst} .= "," if $genome->{mlst};
$genome->{mlst} .= $type->{typing_method}.".".$type->{database}.".".$type->{tag};
#$genome->{mlst} .= "," if $genome->{mlst};
#$genome->{mlst} .= @{$type}[0].".".@{$type}[1].".".@{$type}[2];
}
foreach my $seqObj (@{$genomeObj->{contigs}}) {
if ($seqObj->{genbank_locus}->{definition}=~/chromosome|complete genome/i){
$chromosomes++;
}elsif ($seqObj->{genbank_locus}->{definition}=~/plasmid/i){
$plasmids++;
}else{
$contigs++;
}
$sequences++;
$genome_length += length($seqObj->{dna});
$gc_count += $seqObj->{dna}=~tr/GCgc//;
if ($sequences == 1){
foreach my $dblink (@{$seqObj->{genbank_locus}->{dblink}}){
$genome->{bioproject_accession} = $1 if $dblink=~/BioProject:\s*(.*)/;
$genome->{biosample_accession} = $1 if $dblink=~/BioSample:\s*(.*)/;
}
$genome->{assembly_accession} = getAssemblyAccession($seqObj->{genbank_locus}->{locus}) if $seqObj->{genbank_locus}->{locus};
foreach my $reference (@{$seqObj->{genbank_locus}->{references}}){
$genome->{publication} .= $reference->{PUBMED}."," unless $genome->{publication}=~/$reference->{PUBMED}/;
}
$genome->{publication}=~s/,*$//g;
$genome->{completion_date} = strftime "%Y-%m-%dT%H:%M:%SZ", localtime str2time($seqObj->{genbank_locus}->{date}) if $seqObj->{genbank_locus}->{date};
}
if ($seqObj->{genbank_locus}->{accession}[1]=~/^([A-Z]{4})\d+00000$/){ # wgs, capture only master accession
$genome->{genbank_accessions} = $seqObj->{genbank_locus}->{accession}[1];
}else{
$genome->{genbank_accessions} .= $seqObj->{genbank_locus}->{accession}[0]."," unless length($genome->{genbank_accessions}) > 100 ;
}
}
$genome->{genbank_accessions}=~s/,*$//g;
$genome->{chromosomes} = $chromosomes if $chromosomes;
$genome->{plasmids} = $plasmids if $plasmids;
$genome->{contigs} = $contigs if $contigs ;
$genome->{sequences} = $sequences;
$genome->{genome_length} = $genome_length;
$genome->{gc_content} = sprintf("%.2f", ($gc_count*100/$genome_length));
$genome->{genome_status} = ($contigs > 0)? "WGS": "Complete";
}
sub getAMRPhenotypes {
foreach my $amr1 (@{$genomeObj->{classifications}}){
my $amr;
next if $amr1->{name}=~/combined/;
$amr->{owner} = $genome->{owner};
$amr->{public} = $public;
$amr->{genome_id} = $genome->{genome_id};
$amr->{genome_name} = $genome->{genome_name};
$amr->{taxon_id} = $genome->{taxon_id};
$amr->{antibiotic} = lc $amr1->{name};
$amr->{resistant_phenotype} = ucfirst $amr1->{sensitivity};
$amr->{resistant_phenotype} = "Susceptible" if $amr->{resistant_phenotype}=~/sensitive/i;
$amr->{laboratory_typing_method} = "Computational Prediction";
$amr->{laboratory_typing_platform} = "AdaBoost Classifier";
$amr->{vendor} = "PATRIC";
$amr->{laboratory_typing_method_version} = "Accuracy:$amr1->{accuracy}, F1 score:$amr1->{f1_score}, AUC:$amr1->{area_under_roc_curve}";
push @{$genome->{antimicrobial_resistance}}, ucfirst $amr->{resistant_phenotype} unless (grep {$_ eq ucfirst $amr->{resistant_phenotype}} @{$genome->{antimicrobial_resistance}});
$genome->{antimicrobial_resistance_evidence} = "Computational Prediction";
push @genome_amr, $amr;
}
}
sub getGenomeSequences {
print "Getting genome sequences ...\n";
my $count=0;
foreach my $seqObj (@{$genomeObj->{contigs}}){
$count++;
my $sequence;
$sequence->{owner} = $genome->{owner};
$sequence->{public} = $public;
$sequence->{genome_id} = $genome->{genome_id};
$sequence->{genome_name} = $genome->{genome_name};
$sequence->{taxon_id} = $genome->{taxon_id};
$sequence->{sequence_id} = $sequence->{genome_id}.".con.".sprintf("%04d", $count);
my $seq_id = $seqObj->{id};
$sequence->{gi} = $seqObj->{genbank_locus}->{gi};
if($seqObj->{genbank_locus}->{locus}){
$sequence->{accession} = $seqObj->{genbank_locus}->{locus};
}elsif($seq_id=~/gi\|(\d+)\|(ref|gb)\|([\w\.]+)/){
$sequence->{gi} = $1;
$sequence->{accession} = $3;
}elsif($seq_id=~/accn\|([\w\.]+)/){
$sequence->{accession} = $1;
}else{
$sequence->{accession} = $sequence->{sequence_id};
}
$sequence->{topology} = $seqObj->{genbank_locus}->{geometry};
$sequence->{description} = $seqObj->{genbank_locus}->{definition};
$sequence->{description} .= $seqObj->{id}; # Copy original contig id as description
if ($sequence->{description}=~/chromosome|complete genome/i){
$sequence->{sequence_type} = "chromosome";
}elsif ($sequence->{description}=~/plasmid/i){
$sequence->{sequence_type} = "plasmid";
}else{
$sequence->{sequence_type} = "contig";
}
$sequence->{chromosome} = $1 if $sequence->{description}=~/chromosome (\S*)\s*,/i;
$sequence->{plasmid} = $1 if $sequence->{description}=~/plasmid (\S*)\s*,/i;
$sequence->{gc_content} = sprintf("%.2f", ($seqObj->{dna}=~tr/GCgc//)*100/length($seqObj->{dna}));
$sequence->{length} = length($seqObj->{dna});
$sequence->{sequence} = lc($seqObj->{dna});
$sequence->{version} = $1 if $seqObj->{genbank_locus}->{version}[0]=~/^.*\.(\d+)$/;
$sequence->{release_date} = strftime "%Y-%m-%dT%H:%M:%SZ", localtime str2time($seqObj->{genbank_locus}->{date});
# look up hash
$seq{$seq_id}{sequence_id} = $sequence->{sequence_id};
$seq{$seq_id}{accession} = $sequence->{accession};
$seq{$seq_id}{sequence} = $sequence->{sequence};
push @sequences, $sequence;
}
}
sub getGenomeFeatures{
print "Getting genome features ...\n";
foreach my $featObj (@{$genomeObj->{features}}){
my ($feature, $sequence, $pathways, $ecpathways);
my (@segments, @go, @ec_no, @ec, @pathways, @ecpathways, @spgenes, @uniprotkb_accns, @ids);
$feature->{owner} = $genome->{owner};
$feature->{public} = $public;
$feature->{annotation} = $annotation;
$feature->{genome_id} = $genome->{genome_id};
$feature->{genome_name} = $genome->{genome_name};
$feature->{taxon_id} = $genome->{taxon_id};
$feature->{patric_id} = $featObj->{id};
$feature->{feature_type} = $featObj->{type};
$feature->{feature_type} = $1 if ($featObj->{type} eq "rna" && $featObj->{function}=~/(rRNA|tRNA)/);
$feature->{feature_type} = 'misc_RNA' if ($featObj->{type} eq "rna" && !($featObj->{function}=~/rRNA|tRNA/));
$feature->{feature_type} = 'repeat_region' if ($featObj->{type} eq "repeat");
$feature->{product} = $featObj->{function};
$feature->{product} = "hypothetical protein" if ($feature->{feature_type} eq 'CDS' && !$feature->{product});
$feature->{product}=~s/\"/''/g;
$feature->{product}=~s/^'* *| *'*$//g;
foreach my $locObj (@{$featObj->{location}}){
my ($seq_id, $pstart, $start, $end, $strand, $length);
($seq_id, $pstart, $strand, $length) = @{$locObj};
if ($strand eq "+"){
$start = $pstart;
$end = $start+$length-1;
}else{
$end = $pstart;
$start = $pstart-$length+1;
}
push @segments, $start."..". $end;
$feature->{sequence_id} = $seq{$seq_id}{sequence_id};
$feature->{accession} = $seq{$seq_id}{accession};
$feature->{start} = $start if ($start < $feature->{start} || !$feature->{start});
$feature->{end} = $end if ($end > $feature->{end} || !$feature->{end});
$feature->{strand} = $strand;
$sequence .= substr($seq{$seq_id}{sequence}, $start-1, $length);
}
$sequence =~tr/ACGTacgt/TGCAtgca/ if $feature->{strand} eq "-";
$sequence = reverse($sequence) if $feature->{strand} eq "-";
$feature->{segments} = \@segments;
$feature->{location} = $feature->{strand} eq "+"? join(",", @segments): "complement(".join(",", @segments).")";
$feature->{pos_group} = "$feature->{sequence_id}:$feature->{end}:+" if $feature->{strand} eq '+';
$feature->{pos_group} = "$feature->{sequence_id}:$feature->{start}:-" if $feature->{strand} eq '-';
$feature->{na_sequence} = $sequence;
$feature->{na_length} = length($sequence) unless $feature->{feature_type} eq "source";
$feature->{aa_sequence} = $featObj->{protein_translation};
$feature->{aa_length} = length($feature->{aa_sequence}) if ($feature->{aa_sequence});
$feature->{aa_sequence_md5} = md5_hex($feature->{aa_sequence}) if ($feature->{aa_sequence});
my $strand = ($feature->{strand} eq '+')? 'fwd':'rev';
$feature->{feature_id} = "$annotation.$feature->{genome_id}.$feature->{accession}.".
"$feature->{feature_type}.$feature->{start}.$feature->{end}.$strand";
foreach my $alias (@{$featObj->{alias_pairs}}){
my ($alias_type, $alias_value) = @{$alias};
$feature->{refseq_locus_tag} = $alias_value if ($alias_type eq "locus_tag");
#$feature->{refseq_locus_tag} = $alias_value if ($alias_type eq "old_locus_tag");
$feature->{protein_id} = $alias_value if ($alias_type eq "");
$feature->{gene_id} = $alias_value if ($alias_type eq "GeneID");
$feature->{gi} = $alias_value if ($alias_type eq "GI");
$feature->{gene} = $alias_value if ($alias_type eq "gene");
}
foreach my $family (@{$featObj->{family_assignments}}){
my ($family_type, $family_id, $family_function) = @{$family};
$feature->{figfam_id} = $family_id if ($family_id=~/^FIG/);
$feature->{plfam_id} = $family_id if ($family_id=~/^PLF/);
$feature->{pgfam_id} = $family_id if ($family_id=~/^PGF/);
}
@ec_no = $feature->{product}=~/\( *EC[: ]([\d-\.]+) *\)/g if $feature->{product}=~/EC[: ]/;
foreach my $ec_number (@ec_no){
my $ec_description = $ecRef->{$ec_number}->{ec_description};
push @ec, $ec_number.'|'.$ec_description unless (grep {$_ eq $ec_number.'|'.$ec_description} @ec);
foreach my $go_term (@{$ecRef->{$ec_number}->{go}}){
push @go, $go_term unless (grep {$_ eq $go_term} @go);
}
foreach my $pathway (@{$pathwayRef->{$ec_number}->{pathway}}){
my ($pathway_id, $pathway_name, $pathway_class) = split(/\t/, $pathway);
push @pathways, $pathway_id.'|'.$pathway_name unless (grep {$_ eq $pathway_id.'|'.$pathway_name} @pathways);
my $ecpathway = "$ec_number\t$ec_description\t$pathway_id\t$pathway_name\t$pathway_class";
push @ecpathways, $ecpathway unless (grep {$_ eq $ecpathway} @ecpathways);
}
}
$feature->{ec} = \@ec if scalar @ec;
$feature->{go} = \@go if scalar @go;
$feature->{pathway} = \@pathways if scalar @pathways;
push @pathwaymap, preparePathways($feature, \@ecpathways);
@spgenes = @{$featObj->{similarity_associations}} if $featObj->{similarity_associations};
push @spgenemap, prepareSpGene($feature, $_) foreach(@spgenes);
# Prepare PATRIC AMR genes for matching functions
push @spgenemap, prepareSpGene($feature, ()) if $spgeneRef->{$feature->{product}};
push @features, $feature unless $feature->{feature_type} eq 'gene';
$genome->{lc($annotation).'_cds'}++ if $feature->{feature_type} eq 'CDS';
}
}
sub prepareSpGene {
my ($feature, $spgene_match) = @_;
my $spgene;
my ($property, $locus_tag, $organism, $function, $classification, $antibiotics_class, $antibiotics, $pmid, $assertion);
my ($source, $source_id, $qcov, $scov, $identity, $evalue);
if($spgene_match){ # All specialty genes from external sources
($source, $source_id, $qcov, $scov, $identity, $evalue) = @$spgene_match;
$source_id=~s/^\S*\|//;
($property, $locus_tag, $organism, $function, $classification, $antibiotics_class, $antibiotics, $pmid, $assertion)
= split /\t/, $spgeneRef->{$source.'_'.$source_id} if ($source && $source_id);
}elsif($spgeneRef->{$feature->{product}}){ # PATRIC AMR genes, match by functional role
($property, $locus_tag, $organism, $function, $classification, $antibiotics_class, $antibiotics, $pmid, $assertion)
= split /\t/, $spgeneRef->{$feature->{product}};
$source = "PATRIC";
}
return unless $property && $source;
my ($qgenus) = $feature->{genome_name}=~/^(\S+)/;
my ($qspecies) = $feature->{genome_name}=~/^(\S+ +\S+)/;
my ($sgenus) = $organism=~/^(\S+)/;
my ($sspecies) = $organism=~/^(\S+ +\S+)/;
my ($same_genus, $same_species, $same_genome, $evidence);
$same_genus = 1 if ($qgenus eq $sgenus && $sgenus ne "");
$same_species = 1 if ($qspecies eq $sspecies && $sspecies ne "");
$same_genome = 1 if ($feature->{genome} eq $organism && $organism ne "") ;
$evidence = ($source && $source_id)? 'BLAT' : "K-mer Search";
$spgene->{owner} = $feature->{owner};
$spgene->{public} = $public;
$spgene->{genome_id} = $feature->{genome_id};
$spgene->{genome_name} = $feature->{genome_name};
$spgene->{taxon_id} = $feature->{taxon_id};
$spgene->{feature_id} = $feature->{feature_id};
$spgene->{patric_id} = $feature->{patric_id};
$spgene->{alt_locus_tag} = $feature->{alt_locus_tag};
$spgene->{refseq_locus_tag} = $feature->{refseq_locus_tag};
$spgene->{gene} = $feature->{gene};
$spgene->{product} = $feature->{product};
$spgene->{property} = $property;
$spgene->{source} = $source;
$spgene->{property_source} = $property.': '.$source;
$spgene->{source_id} = $source_id;
$spgene->{organism} = $organism;
$spgene->{function} = $function;
$spgene->{classification} = $classification;
$spgene->{antibiotics_class} = $antibiotics_class if $antibiotics_class;
$spgene->{antibiotics} = [split /[,;]/, $antibiotics] if $antibiotics;
$spgene->{pmid} = [split /[,;]/, $pmid] if $pmid;
$spgene->{assertion} = $assertion;
$spgene->{query_coverage} = $qcov;
$spgene->{subject_coverage} = $scov;
$spgene->{identity} = $identity;
$spgene->{e_value} = $evalue;
$spgene->{same_genus} = $same_genus;
$spgene->{same_species} = $same_species;
$spgene->{same_genome} = $same_genome;
$spgene->{evidence} = $evidence;
return $spgene;
}
sub preparePathways {
my ($feature, $ecpathways) = @_;
my @pathways = ();
foreach my $ecpathway (@$ecpathways){
my $pathway;
my ($ec_number, $ec_description, $pathway_id, $pathway_name, $pathway_class) = split /\t/, $ecpathway;
$pathway->{owner} = $feature->{owner};
$pathway->{public} = $public;
$pathway->{genome_id} = $feature->{genome_id};
$pathway->{genome_name} = $feature->{genome_name};
$pathway->{taxon_id} = $feature->{taxon_id};
$pathway->{sequence_id} = $feature->{sequence_id};
$pathway->{accession} = $feature->{accession};
$pathway->{annotation} = $feature->{annotation};
$pathway->{feature_id} = $feature->{feature_id};
$pathway->{patric_id} = $feature->{patric_id};
$pathway->{alt_locus_tag} = $feature->{alt_locus_tag};
$pathway->{refseq_locus_tag} = $feature->{refseq_locus_tag};
$pathway->{gene} = $feature->{gene};
$pathway->{product} = $feature->{product};
$pathway->{ec_number} = $ec_number;
$pathway->{ec_description} = $ec_description;
$pathway->{pathway_id} = $pathway_id;
$pathway->{pathway_name} = $pathway_name;
$pathway->{pathway_class} = $pathway_class;
$pathway->{genome_ec} = $feature->{genome_id}.'_'.$ec_number;
$pathway->{pathway_ec} = $pathway_id.'_'.$ec_number;
push @pathways, $pathway;
}
return @pathways;
}
sub getMetadataFromGenBankFile {
my ($genbak_file) = @_;
print "Getting genome metadata from genbank file: $genbank_file ...\n";
open GB, "<$genbank_file" || return "Can't open genbank file: $genbank_file\n";
my @gb = <GB>;
my $gb = join "", @gb;
close GB;
my $strain = $2 if $gb=~/\/(strain|isolate)="([^"]*)"/;
$strain =~s/\n */ /g;
$genome->{strain} = $strain unless $strain=~/^ *(-|missing|na|n\/a|not available|not provided|not determined|nd|unknown) *$/i;
$genome->{genome_name} .= " strain $genome->{strain}" if ($genome->{strain} && (not $genome->{genome_name}=~/$genome->{strain}/i));
$genome->{geographic_location} = $1 if $gb=~/\/country="([^"]*)"/;
$genome->{geographic_location} =~s/\n */ /g;
$genome->{isolation_country} = $1 if $genome->{geographic_location}=~/^([^:]*):.*/;
$genome->{host_name} = $1 if $gb=~/\/host="([^"]*)"/;
$genome->{host_name} =~s/\n */ /g;
$genome->{isolation_source} = $1 if $gb=~/\/isolation_source="([^"]*)"/;
$genome->{isolation_source} =~s/\n */ /g;
$genome->{collection_date} = $1 if $gb=~/\/collection_date="([^"]*)"/;
$genome->{collection_date} =~s/\n */ /g;
$genome->{collection_year} = $1 if $genome->{collection_date}=~/(\d\d\d\d)/;
$genome->{culture_collection} = $1 if $gb=~/\/culture_collection="([^"]*)"/;
$genome->{culture_collection} =~s/\n */ /g;
$genome->{assembly_method} = $1 if $gb=~/Assembly Method\s*:: (.*)/;
$genome->{assembly_method} =~s/\n */ /g;
$genome->{sequencing_depth} = $1 if $gb=~/Genome Coverage\s*:: (.*)/;
$genome->{sequencing_depth} =~s/\n */ /g;
$genome->{sequencing_platform} = $1 if $gb=~/Sequencing Technology\s*:: (.*)/;
$genome->{sequencing_platform} =~s/\n */ /g;
}
sub getAssemblyAccession {
my ($accn) = @_;
my $xml = `wget -q -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=$accn"`;
$xml=~s/\n//;
my ($gi) = $xml=~/<Id>(\d+)<\/Id>/;
my $xml = `wget -q -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nuccore&db=assembly&id=$gi"`;
$xml=~s/\n//;
my ($assembly_id) = $xml=~/<Link>\s*<Id>(\d+)<\/Id>/;
my $xml = `wget -q -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=assembly&id=$assembly_id"`;
my ($assembly_accession) = $xml=~/<Genbank>(\S*)<\/Genbank>/;
return $assembly_accession;
}
sub getMetadataFromBioProject {
my($bioproject_accn) = @_;
print "Getting genome metadata from BioProject: $bioproject_accn...\n";
my $xml = `wget -q -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=bioproject&term=$bioproject_accn"`;
$xml=~s/\n//;
my ($bioproject_id) = $xml=~/<Id>(\d+)<\/Id>/;
`wget -q -O "$outfile.bioproject.xml" "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=bioproject&retmode=xml&id=$bioproject_id"`;
return unless -f "$outfile.bioproject.xml";
my ($projID, $projDescription, $subgroup, $organism, $description, $var, $serovar, $biovar, $pathovar, $strain, $cultureCollection, $typeStrain);
my ($isolateComment, $source, $month, $year, $country, $method, $person, $epidemic, $location, $altitude, $depth);
my ($hostName, $hostGender, $hostAge, $hostHealth);
my ($publication, $taxonID, $epidemiology);
my $xml = XMLin("$outfile.bioproject.xml", ForceArray => ["Organization"]);
my $root = $xml->{DocumentSummary};
#print Dumper $xml;
$organism = $root->{Project}->{ProjectType}->{ProjectTypeSubmission}->{Target}->{Organism};
my $organization = $root->{Submission}->{Description}->{Organization};
if (ref($organization->[0]->{Name}) eq "HASH"){
$genome->{sequencing_centers} = $organization->[0]->{Name}->{content};
}else{
$genome->{sequencing_centers} = $organization->[0]->{Name};
}
$genome->{strain} = $organism->{Strain} if $organism->{Strain} && not $genome->{strain};
$genome->{genome_name} .= " strain $genome->{strain}" if ($genome->{strain} && (not $genome->{genome_name}=~/$genome->{strain}/) );
$genome->{disease} = $organism->{BiologicalProperties}->{Phenotype}->{Disease};
$genome->{temperature_range} = $1 if $organism->{BiologicalProperties}->{Environment}->{TemperatureRange}=~/^e*(.*)/;
$genome->{optimal_temperature} = $organism->{BiologicalProperties}->{Environment}->{OptimumTemperature};
$genome->{oxygen_requirement} = $1 if $organism->{BiologicalProperties}->{Environment}->{OxygenReq}=~/^e*(.*)/;
$genome->{habitat} = $1 if $organism->{BiologicalProperties}->{Environment}->{Habitat}=~/^e*(.*)/;
$genome->{cell_shape} = $1 if $organism->{BiologicalProperties}->{Morphology}->{Shape}=~/^e*(.*)/;
$genome->{motility} = $1 if $organism->{BiologicalProperties}->{Morphology}->{Motility}=~/^e*(.*)/;
$genome->{gram_stain} = $1 if $organism->{BiologicalProperties}->{Morphology}->{Gram}=~/^e*(.*)/;
if (ref($root->{Project}->{ProjectDescr}->{Publication}->{id}) eq "HASH"){
foreach my $pmid (keys %{$root->{Project}->{ProjectDescr}->{Publication}}){
$genome->{publication} .= ",$pmid" unless $genome->{publication}=~/$pmid/;
}
}else{
my $pmid = $root->{Project}->{ProjectDescr}->{Publication}->{id};
}
$genome->{publication}=~s/^,|,$//g;
$description = $root->{Project}->{ProjectDescr}->{Description};
$description=~s/<\/*.>|
|<\/*.>//g;
$description=~s/<.*?>|<.*?>//g;
$description=~s/^ *| *$//g;
$description=~s/\t+/ /g;
$description=~s/Dr\.\s*/Dr /g;
$typeStrain="Yes" if($description=~/type str/i);
my($var1, $var2) = "$organism $description"=~/(serovar|sv\.|sv|serotype|biovar|bv\.|bv|biotype|pathovar|pv\.|pv|pathotype)\s*([\w-]*)/i;
$var = "$var1 $var2" if($var2 && !($var2=~/^of|and$/i));
$var =~s/serovar|sv\.|sv|serotype/serovar/i;
$var =~s/biovar|bv\.|bv|biotype/biovar/i;
$var =~s/pathovar|pv\.|pv|pathotype/pathovar/i;
$var =~s/^\s*$//;
$serovar = $var if($var=~/serovar/);
$biovar = $var if($var=~/biovar/);
$pathovar = $var if($var=~/pathovar/);
my($cc1, $cc2) = $description=~/(ATCC|NCTC|CCUG|DSM|LMG|CIP|NCIB|BCCM|NRRL)\s*([\w-]*)/;
$cultureCollection = "$cc1 $cc2" if ($cc1 && $cc2);
#($isolateComment) = $description=~/(isolated\s*.*?\S\S\.)/i;
my ($com1, $com2) = $description=~/(isolated|isolate from|isolate obtained from|derived|is from|was from|came from|recovered from)\s+(.*?\S\S\.)/i;
$isolateComment = "$com1 $com2";
$isolateComment =~s/\s*$|\s*\.$//;
$isolateComment =~s/<|>//g;
$source = $1 if $isolateComment=~/from\s*(.*)/;
$source =~s/^(a|an)\s+//;
$source =~s/( in | by | and will | and is | and is |\s*\.).*//g;
($month, $year) = $isolateComment=~/in\s*([a-zA-Z]*)\s*,*\s+(\d\d\d\d)/;
($method) = $isolateComment=~/isolated by ([a-z].*)/;
$method =~s/ (from|in) .*//;
($person) = $isolateComment=~/isolated by ([A-Z].*)/;
$person =~s/ (at|in|during) .*//;
($epidemiology) = $isolateComment=~/(outbreak|epidemic|pandemic)/i;
$isolateComment=~/(^|\s)(in|in the|at|at the|near|near the)\s([A-Z]+.*)/;
$location = $3;
$location =~s/\..*//;
$location =~s/\W+/ /g;
$location =~s/^\s*|\s*$|\s\s//g;
$location =~s/ [a-z0-9]+.*//g;
my ($num, $unit);
if ($isolateComment=~/depth of/i){
($num, $unit) = $isolateComment=~/depth of (\d+\s*[\.\-to]*\s*\d*)\s*(\w+)/;
$depth = "$num $unit";
}elsif($isolateComment=~/below the surface/i){
($num, $unit) = $isolateComment=~/(\d+\s*[\.\-to]*\s*\d*)\s*(\w+) below the surface/;
$depth = "$num $unit";
$depth =~s/\s$//;
}
$hostGender = $1 if $isolateComment=~/(male|female)/i; # man|woman
$hostAge = "$1 $2" if $isolateComment=~/(\d+).(year|years|month|months|day|days).old/; # month|months|day|days
$hostHealth = $2 if $isolateComment=~/(patient with |suffering from )(.*)/i; # suffered|diagnosed with
$hostHealth =~s/^(a|an)\s//;
$hostHealth =~s/\s+(and is|and will be|and has|and was|by|in|and contains)\s+.*//;
$hostName = $1 if $isolateComment=~/ (pig|sheep|goat|dog|cat |cattle|chicken|cow|mouse|rat|buffalo|tick|mosquito)/i;
$hostName ="Human, Homo sapiens" if ($isolateComment=~/ (human|man|woman|infant|child|patient|homo sapiens)/i);
# Organism Info
$genome->{serovar} = $serovar if $serovar;
$genome->{biovar} = $biovar if $biovar;
$genome->{pathovar} = $pathovar if $pathovar;
$genome->{type_strain} = $typeStrain if $typeStrain;
$genome->{culture_collection} = $cultureCollection if $cultureCollection;
push @{$genome->{comments}}, $description if $description;
$genome->{publication} = $publication if $publication;
# Isolate / Environmental Metadata
#$genome->{isolation_site} = ""; #$source;
$genome->{isolation_source} = $source if $source;
$genome->{isolation_comments} = $isolateComment if $isolateComment;
$genome->{collection_date} = $year if $year;
#$genome->{isolation_country} = ""; #$location;
$genome->{geographic_location} = $location if $location;
#$genome->{latitude} = "";
#$genome->{longitude} = "";
#$genome->{altitude} = "";
#$genome->{depth} = $depth;
# Host Metadata
$genome->{host_name} = $hostName if $hostName;
$genome->{host_gender} = $hostGender if $hostGender;
$genome->{host_age} = $hostAge if $hostAge ;
$genome->{host_health} = $hostHealth if $hostHealth;
#$genome->{body_sample_site} = "";
#$genome->{body_sample_substitute} = "";
}
sub getGenomeFeaturesFromGenBankFile {
my ($genbank_file) = @_;
print "Getting genome features from the genbank file: $genbank_file ...\n";
my $annotation = "RefSeq";
my $genomeObj = Bio::SeqIO->new( -file => "<$genbank_file", -format => 'GenBank');
while (my $seqObj = $genomeObj->next_seq){
my ($accession, $sequence_id);
$accession = $seqObj->accession_number;
for (my $i=0; $i < scalar @sequences; $i++){
next unless $sequences[$i]->{accession} eq $accession;
$sequence_id = $sequences[$i]->{sequence_id};
last;
}
for my $featObj ($seqObj->get_SeqFeatures){
my ($accn, $feature, $pathways, $ecpathways);
my (@go, @ec_no, @ec, @pathway, @ecpathways, @spgenes, @uniprotkb_accns, @ids);
$feature->{owner} = $genome->{owner};
$feature->{public} = $public;
$feature->{annotation} = $annotation;
$feature->{genome_id} = $genome->{genome_id};
$feature->{genome_name} = $genome->{genome_name};
$feature->{taxon_id} = $genome->{taxon_id};
$feature->{sequence_id} = $sequence_id;
$feature->{accession} = $accession;
$feature->{feature_type} = $featObj->primary_tag;
$featureIndex->{$feature->{feature_type}}++;
$feature->{start} = $featObj->start;
$feature->{end} = $featObj->end;
$feature->{strand} = ($featObj->strand==1)? '+':'-';
$feature->{location} = $featObj->location->to_FTstring;
my @segments;
if ($featObj->location->isa('Bio::Location::SplitLocationI')){
for my $location ($featObj->location->sub_Location){
push @segments, $location->start."..". $location->end;
}
}else{
push @segments, $featObj->start."..". $featObj->end;
}
$feature->{segments} = \@segments;
$feature->{pos_group} = "$feature->{sequence_id}:$feature->{end}:+" if $feature->{strand} eq '+';
$feature->{pos_group} = "$feature->{sequence_id}:$feature->{start}:-" if $feature->{strand} eq '-';
$feature->{na_length} = length($featObj->spliced_seq->seq);
$feature->{na_sequence} = $featObj->spliced_seq->seq unless $featObj->primary_tag eq "source";
my $strand = ($feature->{strand} eq '+')? 'fwd':'rev';
$feature->{feature_id} = "$annotation.$feature->{genome_id}.$feature->{accession}.".
"$feature->{feature_type}.$feature->{start}.$feature->{end}.$strand";
for my $tag ($featObj->get_all_tags){
for my $value ($featObj->get_tag_values($tag)){
$feature->{feature_type} = 'pseudogene' if ($tag eq 'pseudo' && $feature->{feature_type} eq 'gene');
$feature->{patric_id} = $1 if ($tag eq 'db_xref' && $value=~/SEED:(fig.*)/);
$feature->{refseq_locus_tag} = $value if ($tag eq 'locus_tag' && $annotation eq "RefSeq");
$feature->{refseq_locus_tag} = $1 if ($tag eq 'db_xref' && $value=~/Refseq_locus_tag:(.*)/i);
$feature->{protein_id} = $value if ($tag eq 'protein_id');
$feature->{protein_id} = $1 if ($tag eq 'db_xref' && $value=~/protein_id:(.*)/);
$feature->{gene_id} = $1 if ($tag eq 'db_xref' && $value=~/^GeneID:(\d+)/);
$feature->{gi} = $1 if ($tag eq 'db_xref' && $value=~/^GI:(\d+)/);
$feature->{aa_sequence} = $value if ($tag eq 'translation');
$feature->{aa_length} = length($value) if ($tag eq 'translation');
$feature->{aa_sequence_md5} = md5_hex($value) if ($tag eq 'translation');
$feature->{gene} = $value if ($tag eq 'gene');
$feature->{product} = $value if ($tag eq 'product');
$feature->{figfam_id} = $value if ($tag eq 'FIGfam');
if ($tag eq 'EC_number'){
my $ec_number = $value;
my $ec_description = $ecRef->{$ec_number}->{ec_description};
push @ec, $ec_number.'|'.$ec_description unless (grep {$_ eq $ec_number.'|'.$ec_description} @ec);
}
push @ids, $value if ($tag eq 'db_xref');
}
}
$feature->{ec} = \@ec if scalar @ec;
push @features, $feature unless ($feature->{feature_type} eq 'gene' && (grep {$_=~/Bacteria|Archaea/} @{$genome->{taxon_lineage_names}}));
$genome->{lc($annotation).'_cds'}++ if $feature->{feature_type} eq 'CDS'
}
}
$genomeObj->close();
}
sub getMetadataFromBioSample {
my($biosample_accn) = @_;
print "Getting genome metadata from BioSample: $biosample_accn ...\n";
my $xml = `wget -q -O - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=biosample&term=$biosample_accn"`;
$xml=~s/\n//;
my ($biosample_id) = $xml=~/<Id>(\d+)<\/Id>/;
`wget -q -O "$outfile.biosample.xml" "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=biosample&retmode=xml&id=$biosample_id"`;
return unless -f "$outfile.biosample.xml";
my $xml = XMLin("$outfile.biosample.xml", ForceArray => ["Row"]);
return unless ref $xml->{BioSample}->{Attributes}->{Attribute} eq 'ARRAY';
foreach my $attrib (@{$xml->{BioSample}->{Attributes}->{Attribute}}){
my $attrib_name = $attrib->{harmonized_name};
my $attrib_value = $attrib->{content};
if ($attrib_name=~/lat_lon/i){
my ($latitude, $longitude) = $attrib=~/(\d+\.*\d* [NS])\s+(\d+\.*\d* [EW])/;
$genome->{latitude} = $latitude;
$genome->{longitude} = $longitude;
}else{
my $patric_attrib_name = biosample2patricAttrib($attrib_name);
next unless ($patric_attrib_name && $attrib_value && not $attrib_value=~/^ *(-|missing|na|n\/a|not available|not provided|not determined|nd|unknown) *$/i);
if ($patric_attrib_name=~/other|additional/i){
my ($attrib1, $attrib2) = $patric_attrib_name=~/^([^:]*):(.*)/;
push @{$genome->{$attrib1}}, "$attrib2:$attrib_value";
}elsif ($patric_attrib_name=~/comments/i){
push @{$genome->{$patric_attrib_name}}, $attrib_value;