TASK-5388 - Add AlphaMissense predictions

cellbase-app/app/scripts/ensembl-scripts/DB_CONFIG.pm

@@ -134,10 +134,10 @@ our $ENSEMBL_GENOMES_PORT = "4157";
 our $ENSEMBL_GENOMES_USER = "anonymous";
 
 ## Vertebrates
-our $HOMO_SAPIENS_CORE = "homo_sapiens_core_110_38";
-our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_110_38";
-our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_110_38";
-our $HOMO_SAPIENS_COMPARA = "homo_sapiens_compara_110_38";
+our $HOMO_SAPIENS_CORE = "homo_sapiens_core_111_38";
+our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_111_38";
+our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_111_38";
+our $HOMO_SAPIENS_COMPARA = "homo_sapiens_compara_111_38";
 #our $HOMO_SAPIENS_CORE = "homo_sapiens_core_78_38";
 #our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_78_38";
 #our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_78_38";

cellbase-app/app/scripts/ensembl-scripts/protein_function_prediction_matrices.pl

@@ -6,6 +6,10 @@
 use Digest::MD5 qw(md5 md5_hex md5_base64);
 use JSON;
 
+#use lib "~/appl/cellbase/build/scripts/ensembl-scripts/";
+#use lib "~/soft/ensembl-variation/modules/";
+#use lib "~/soft/ensembl/modules/";
+
 use DB_CONFIG;
 
 my $species = 'Homo sapiens';
@@ -87,6 +91,37 @@
 #}
 #print join("=", $polyphen2->get_prediction(1, 'G'))."\n";
 
+##################################################################
+
+# Get the current time
+my ($sec, $min, $hour, $mday, $mon, $year) = localtime();
+# Adjust the year and month values (year is years since 1900, and month is 0-based)
+
+$year += 1900;
+$mon += 1;
+
+# Format the date and time
+my $formatted_date = sprintf("%04d%02d%02d_%02d%02d%02d", $year, $mon, $mday, $hour, $min, $sec);
+
+my $jsonVersion = {};
+$jsonVersion->{"date"} = $formatted_date;
+$jsonVersion->{"data"} = "protein_substitution_predictions";
+$jsonVersion->{"version"} = "Ensembl 104";
+my @urls = ();
+push @urls, "ensembldb.ensembl.org:3306";
+$jsonVersion->{"url"} = \@urls;
+
+print "Generating the JSON file for the Sift version.\n";
+$jsonVersion->{"name"} = "sift";
+open(FILE, ">".$outdir."/siftVersion.json") || die "error opening file\n";
+print FILE to_json($jsonVersion) . "\n";
+close(FILE);
+
+print "Generating the JSON file for the PolyPhen version\n";
+$jsonVersion->{"name"} = "polyphen";
+open(FILE, ">".$outdir."/polyphenVersion.json") || die "error opening file\n";
+print FILE to_json($jsonVersion) . "\n";
+close(FILE);
 
 my ($translation, $seq, $md5seq, @preds, @all_predictions);
 #my @transcripts = @{$transcript_adaptor->fetch_all_by_biotype('protein_coding')};
@@ -126,42 +161,56 @@
 
 	        ## HASH ##
 			my $effect = {};
+			$effect->{"chromosome"} = $trans->seq_region_name;
 	        $effect->{"transcriptId"} = $trans->stable_id;
-	        $effect->{"checksum"} = $md5seq;
-	        $effect->{"size"} = length($seq);
 
 	        foreach my $u (@{ $trans->get_all_xrefs('Uniprot/SWISSPROT') }){
 		        $effect->{"uniprotId"} = $u->display_id();
 	        }
 
+			$effect->{"source"} = "polyphen";
 	        my $polyphen2 = $prot_function_adaptor->fetch_polyphen_predictions_by_translation_md5($md5seq);
-			for(my $i=1; $i<=length($seq); $i++) {
-				foreach (my $j=0; $j < @aa_code; $j++) {
-					if(defined $polyphen2) {
+			if(defined $polyphen2) {
+				for(my $i=1; $i<=length($seq); $i++) {
+					$effect->{"aaPosition"} = $i;
+					my @scores = ();
+					foreach (my $j=0; $j < @aa_code; $j++) {
 						@preds = $polyphen2->get_prediction($i, $aa_code[$j]);
-						$effect->{"aaPositions"}->{$i}->{$aa_code[$j]}->{"pe"} = $effect_code{$preds[0]};
-						$effect->{"aaPositions"}->{$i}->{$aa_code[$j]}->{"ps"} = $preds[1];
+						if(defined $preds[0] || defined $preds[1]) {
+							push @scores, {"aaAlternate" => $aa_code[$j], "score" => $preds[1], "effect" => $preds[0]};
+							$effect->{"scores"} = \@scores;
+						}
+					}
+					if(@scores) {
+						print FILE to_json($effect)."\n";
 					}
 				}
 			}
 
-			my $sift = $prot_function_adaptor->fetch_sift_predictions_by_translation_md5($md5seq);
-			for(my $i=1; $i<=length($seq); $i++) {
-	            foreach (my $j=0; $j < @aa_code; $j++) {
-	            	if(defined $sift) {
-	            		@preds = $sift->get_prediction($i, $aa_code[$j]);
-						$effect->{"aaPositions"}->{$i}->{$aa_code[$j]}->{"se"} = $effect_code{$preds[0]};
-						$effect->{"aaPositions"}->{$i}->{$aa_code[$j]}->{"ss"} = $preds[1];
-	            	}
-	            }
-	        }
-			print FILE to_json($effect)."\n";
+			$effect->{"source"} = "sift";
+	        my $sift = $prot_function_adaptor->fetch_sift_predictions_by_translation_md5($md5seq);
+			if(defined $sift) {
+				for(my $i=1; $i<=length($seq); $i++) {
+					$effect->{"aaPosition"} = $i;
+					my @scores = ();
+					foreach (my $j=0; $j < @aa_code; $j++) {
+						@preds = $sift->get_prediction($i, $aa_code[$j]);
+						if(defined $preds[0] || defined $preds[1]) {
+							push @scores, {"aaAlternate" => $aa_code[$j], "score" => $preds[1], "effect" => $preds[0]};
+							$effect->{"scores"} = \@scores;
+						}
+					}
+					if(@scores) {
+						print FILE to_json($effect)."\n";
+					}
+				}
+			}
 		}
 	}
 	close(FILE);
 
 	## GZip output to save space in Amazon AWS
-#	exec("gzip prot_func_pred_chr_".$chrom->seq_region_name);
+	exec("gzip " . $outdir . "/prot_func_pred_chr_" . $chr->seq_region_name . ".json");
 }
 
 sub print_parameters {

cellbase-app/app/scripts/mirtarbase/fix-gene-symbol.sh

@@ -0,0 +1,60 @@
+#!/bin/bash
+
+# The original MirTarBase hsa_MTI.xlsx contains invalid Gene Symbols in 793 lines.
+# To fix it, that file has to be converted to a CSV file, i.e.: hsa_MTI.csv
+#
+# After converting to CSV file, we can see the errors from the original file for the Gene Symbols (column 4),
+# e.g.: 06-mar:
+# MIRT050267,hsa-miR-25-3p,Homo sapiens,06-mar,10299,Homo sapiens,CLASH,Functional MTI (Weak),23622248
+# MIRT051174,hsa-miR-16-5p,Homo sapiens,06-mar,10299,Homo sapiens,CLASH,Functional MTI (Weak),23622248
+#
+# This script fix those lines and convert the column 4 for a vaild Gene Symbol:
+#
+# MIRT050267,hsa-miR-25-3p,Homo sapiens,MARCHF6,10299,Homo sapiens,CLASH,Functional MTI (Weak),23622248
+# MIRT051174,hsa-miR-16-5p,Homo sapiens,MARCHF6,10299,Homo sapiens,CLASH,Functional MTI (Weak),23622248
+
+# Check the parameters number
+if [ "$#" -ne 1 ]; then
+    echo "Usage: $0 <csv_file>"
+    exit 1
+fi
+
+# Check CSV file
+csv_file="$1"
+if [ ! -f "$csv_file" ]; then
+    echo "CSV file '$csv_file' does not exist."
+    exit 1
+fi
+
+# Fix gene-symbol
+while IFS=$'\t' read -r c1 c2 c3 c4 c5 c6 c7 c8 c9 || [[ -n "$c1" ]]; do
+    # Aplica las condiciones
+    if [ "$c5" = "10299" ]; then
+        c4="MARCHF6"
+    elif [ "$c5" = "51257" ]; then
+        c4="MARCHF2"
+    elif [ "$c5" = "54708" ]; then
+        c4="MARCHF5"
+    elif [ "$c5" = "54996" ]; then
+        c4="MTARC2"
+    elif [ "$c5" = "55016" ]; then
+        c4="MARCHF1"
+    elif [ "$c5" = "57574" ]; then
+        c4="MARCHF4"
+    elif [ "$c5" = "64757" ]; then
+        c4="MTARC1"
+    elif [ "$c5" = "64844" ]; then
+        c4="MARCHF7"
+    elif [ "$c5" = "92979" ]; then
+        c4="MARCHF9"
+    elif [ "$c5" = "115123" ]; then
+        c4="MARCHF3"
+    elif [ "$c5" = "220972" ]; then
+        c4="MARCHF8"
+    elif [ "$c5" = "441061" ]; then
+        c4="MARCHF11"
+    fi
+
+    # Print line
+    echo -e "$c1\t$c2\t$c3\t$c4\t$c5\t$c6\t$c7\t$c8\t$c9"
+done < "$csv_file"

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminCliOptionsParser.java

@@ -19,11 +19,14 @@
 import com.beust.jcommander.*;
 import org.opencb.cellbase.app.cli.CliOptionsParser;
 import org.opencb.cellbase.core.api.key.ApiKeyQuota;
+import org.opencb.cellbase.lib.EtlCommons;
 
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import static org.opencb.cellbase.lib.EtlCommons.*;
+
 /**
  * Created by imedina on 03/02/15.
  */
@@ -87,12 +90,15 @@ public class DownloadCommandOptions {
         @ParametersDelegate
         public SpeciesAndAssemblyCommandOptions speciesAndAssemblyOptions = speciesAndAssemblyCommandOptions;
 
-        @Parameter(names = {"-d", "--data"}, description = "Comma separated list of data to download: genome, gene, "
-                + "variation, variation_functional_score, regulation, protein, conservation, "
-                + "clinical_variants, repeats, svs, pubmed and 'all' to download everything", required = true, arity = 1)
+        @Parameter(names = {"-d", "--data"}, description = "Comma separated list of data to download: " + GENOME_DATA + "," + GENE_DATA
+                + "," + VARIATION_FUNCTIONAL_SCORE_DATA + "," + REGULATION_DATA + "," + PROTEIN_DATA + "," + CONSERVATION_DATA + ","
+                + CLINICAL_VARIANT_DATA + "," + REPEATS_DATA + "," + ONTOLOGY_DATA + "," + PUBMED_DATA + "," + PHARMACOGENOMICS_DATA
+                + "," + PGS_DATA + "," + REVEL_DATA + "," + ALPHAMISSENSE_DATA + "; or use 'all' to download everything", required = true,
+                arity = 1)
         public String data;
 
-        @Parameter(names = {"-o", "--outdir"}, description = "Downloaded files will be saved in this directory.", required = true, arity = 1)
+        @Parameter(names = {"-o", "--outdir"}, description = "Downloaded files will be saved in this directory.", required = true,
+                arity = 1)
         public String outputDirectory;
     }
 
@@ -102,9 +108,11 @@ public class BuildCommandOptions {
         @ParametersDelegate
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
-        @Parameter(names = {"-d", "--data"}, description = "Comma separated list of data to build: genome, genome_info, "
-                + "gene, variation, variation_functional_score, regulation, protein, ppi, conservation, drug, "
-                + "clinical_variants, repeats, svs, splice_score, pubmed. 'all' builds everything.", required = true, arity = 1)
+        @Parameter(names = {"-d", "--data"}, description = "Comma separated list of data to build: " + GENOME_DATA + "," + GENE_DATA + ","
+                + VARIATION_FUNCTIONAL_SCORE_DATA + "," + REGULATION_DATA + "," + PROTEIN_DATA + "," + CONSERVATION_DATA + ","
+                + CLINICAL_VARIANT_DATA + "," + REPEATS_DATA + "," + ONTOLOGY_DATA + "," + SPLICE_SCORE_DATA + "," + PUBMED_DATA + ","
+                + PHARMACOGENOMICS_DATA + "," + PGS_DATA + "," + REVEL_DATA + "," + ALPHAMISSENSE_DATA + "; or use 'all' to build"
+                + " everything", required = true, arity = 1)
         public String data;
 
         @Parameter(names = {"-s", "--species"}, description = "Name of the species to be built, valid formats include 'Homo sapiens' or 'hsapiens'", required = false, arity = 1)
@@ -190,8 +198,9 @@ public class LoadCommandOptions {
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
         @Parameter(names = {"-d", "--data"}, description = "Data model type to be loaded: genome, gene, variation,"
-                + " conservation, regulation, protein, clinical_variants, repeats, regulatory_pfm, splice_score, pubmed, pharmacogenomics."
-                + " 'all' loads everything", required = true, arity = 1)
+                + " conservation, regulation, protein, clinical_variants, repeats, regulatory_pfm, splice_score, pubmed, pharmacogenomics,"
+                + " protein_functional_prediction, missense_variation_functional_score, alphamissense; and 'all' loads everything",
+                required = true, arity = 1)
         public String data;
 
         @Parameter(names = {"-i", "--input"}, required = true, arity = 1,
@@ -237,8 +246,8 @@ public class ExportCommandOptions {
         public CommonCommandOptions commonOptions = commonCommandOptions;
 
         @Parameter(names = {"-d", "--data"}, description = "Data model type to be loaded: genome, gene, variation, "
-                + "conservation, regulation, protein, clinical_variants, repeats, regulatory_pfm, splice_score, pubmed. 'all' "
-                + " loads everything", required = true, arity = 1)
+                + EtlCommons.PROTEIN_SUBSTITUTION_PREDICTION_DATA + ", conservation, regulation, protein, clinical_variants, repeats,"
+                + " regulatory_pfm, splice_score, pubmed. 'all' export everything", required = true, arity = 1)
         public String data;
 
         @Parameter(names = {"--db", "--database"}, description = "Database name, e.g., cellbase_hsapiens_grch38_v5", required = true,

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/AdminMain.java

@@ -98,10 +98,10 @@ public static void main(String[] args) {
                     commandExecutor.execute();
                 } catch (IOException | URISyntaxException | CellBaseException e) {
                     commandExecutor.getLogger().error("Error: " + e.getMessage());
+                    e.printStackTrace();
                     System.exit(1);
                 }
             }
         }
     }
-
 }