Add hack script to update existing core meta table sample example genes

scripts/misc_scripts/GenerateExampleGenes.sh

@@ -0,0 +1,143 @@
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#!/usr/bin/env bash
+
+INPUT_CORES=$1
+MODE=${2^^}
+PATCH_OUTFILE="${PWD}/$3"
+HOST=$4
+OUTPUT_TSV_SUMMARY="${PWD}/New_EG_Genes_Selected.tsv"
+COMPARA_DB=""
+
+if [[ -z $INPUT_CORES ]] || [[ -z $MODE ]] || [[ -z $PATCH_OUTFILE ]] || [[ -z $HOST ]] || [[ -z "$COMPARA_DB" ]]; then
+    echo "Usage: sh GenerateExampleGenes.sh <INPUT FILE> <auto|manual> <PATCH_OUTFILE_NAME> <CORE HOST>"
+    echo "Input file format"
+    echo "Manual mode: core_db_name<'\n'>"
+    echo "Auto mode: core_db_name<'\t'>manually_selected_stable_id<'\n'>"
+    echo "Make sure to alter script and add the appropriate compara DB!! Line: 22."
+    exit 0;
+fi
+META_OUTDIR=$PWD/GENE_META
+mkdir -p $META_OUTDIR
+
+# Some different filters to search for a sub sample of core stable_ids
+BIOTYPE="protein_coding" # Not, this really can't be changed as e.g genes are related to peptide compara
+STABLE_ID_SQL_FILTER="and description NOT LIKE '%uncharacterized%' and description IS NOT NULL " # SUGGEST TO USE THIS FILTER ON GENE RANDOM SAMPLE 
+# STABLE_ID_SQL_FILTER="and description NOT LIKE '%uncharacterized%' "
+# STABLE_ID_SQL_FILTER="and description IS NOT NULL "
+
+# Get meta data on core + selected stable_id
+gather_gene_meta () {
+    local PROD=$1
+    local INPUT_STABLE_ID=$2
+
+    echo "Gathering meta data on stable_id: $INPUT_STABLE_ID"
+    $HOST -D $CORE -Ne "select stable_id, seq_region_id, seq_region_start, seq_region_end, description from gene where stable_id=\"$INPUT_STABLE_ID\";" \
+        > $META_OUTDIR/gene_${PROD}_meta_${INPUT_STABLE_ID}.tmp
+    $HOST -D $CORE -Ne "select t.stable_id, t.seq_region_id, t.seq_region_start, t.seq_region_end from transcript t join gene g where t.gene_id = g.gene_id and g.stable_id = \"$INPUT_STABLE_ID\" and g.canonical_transcript_id = t.transcript_id;" \
+        > $META_OUTDIR/transcript_${PROD}_meta_${INPUT_STABLE_ID}.tmp
+    $HOST -D $CORE -Ne "select s.name from seq_region s join gene g where g.seq_region_id = s.seq_region_id and g.stable_id=\"$INPUT_STABLE_ID\";" \
+        > $META_OUTDIR/seq_region_${PROD}_meta_${INPUT_STABLE_ID}.tmp
+    $HOST -D $CORE -Ne "select x.display_label from xref x join gene g where x.xref_id = g.display_xref_id and g.stable_id=\"$INPUT_STABLE_ID\";" \
+        > $META_OUTDIR/xref_display_${PROD}_meta_${INPUT_STABLE_ID}.tmp
+
+    return
+}
+
+if [[ -e $PWD/$OUTPUT_TSV_SUMMARY ]]; then echo "Removing old summary TSV"; rm $OUTPUT_TSV_SUMMARY; fi
+echo -e -n "DB Name\tNew Example Gene\tGeneDescription\n" > $OUTPUT_TSV_SUMMARY
+
+if [[ -e $PATCH_OUTFILE ]]; then echo "Removing old PATCH SQL"; rm $PATCH_OUTFILE; fi
+
+while read LINE
+do
+    CORE=`echo "$LINE" | cut -d $'\t' -f1`
+    PROD_NAME=`echo $CORE | sed -E 's/_core.+$//g'`
+
+    if [[ "$MODE" == "AUTO" ]]; then
+        echo -e -n "\nAuto patching : $CORE\n"
+        $HOST -D $CORE -Ne  "select stable_id from gene where biotype = \"$BIOTYPE\" ${STABLE_ID_SQL_FILTER} order by RAND() limit 25;" \
+            | tr "\n" " " >> $META_OUTDIR/rand_genes_${CORE}.txt
+
+        NEW_GENE=""
+
+        for NEW_GENE_CHECK in $(tail -n 1 $META_OUTDIR/rand_genes_${CORE}.txt);
+            do
+            # Now check if compara DB contains homologies on randomly select gene stable_id
+            CHECK_COMPARA_HOMOLOGY=`$HOST -D $COMPARA_DB -Ne "SELECT count(*) FROM gene_member JOIN genome_db USING(genome_db_id) JOIN gene_member_hom_stats USING(gene_member_id) WHERE genome_db.name = \"${PROD_NAME}\" AND gene_trees > 0 and stable_id = \"${NEW_GENE_CHECK}\";"`
+
+            if [[ $CHECK_COMPARA_HOMOLOGY -ge 1 ]]; then
+
+                echo "Homologies for $NEW_GENE_CHECK located! [$CORE]"
+
+                CHECK_DESCRIPTION=`$HOST -D $CORE -Ne "SELECT COUNT(*) FROM gene WHERE stable_id = \"$NEW_GENE_CHECK\" $STABLE_ID_SQL_FILTER;"`
+
+                if [[ $CHECK_DESCRIPTION -eq 1 ]]; then
+                    NEW_GENE=$NEW_GENE_CHECK
+                    # Get meta on stable id:
+                    gather_gene_meta $PROD_NAME $NEW_GENE_CHECK
+                    break
+                fi
+            else
+                echo "Failed homology check: $CORE -> $NEW_GENE_CHECK" | tee -a Missing_homologies.txt
+            fi
+        done
+    elif [[ "$MODE" == "MANUAL" ]]; then
+
+        echo -e -n "\nManual patching : $CORE\n"
+        # Quickly take the gene stable_id from the input file 
+        NEW_GENE=`echo "$LINE" | cut -d $'\t' -f2`
+        gather_gene_meta $CORE $NEW_GENE
+
+    fi
+
+    GENE_METAFILE="$META_OUTDIR/gene_${PROD_NAME}_meta_${NEW_GENE}.tmp"
+    SEQR_METAFILE="$META_OUTDIR/seq_region_${PROD_NAME}_meta_${NEW_GENE}.tmp"
+    TRANSC_METAFILE="$META_OUTDIR/transcript_${PROD_NAME}_meta_${NEW_GENE}.tmp"
+    XREF_METAFILE="$META_OUTDIR/xref_display_${PROD_NAME}_meta_${NEW_GENE}.tmp"
+
+    GENE_DESCRIPTION=`cut -f5 "$GENE_METAFILE"`
+    echo -e -n "$CORE\t$NEW_GENE\t$GENE_DESCRIPTION\n" >> $OUTPUT_TSV_SUMMARY
+
+    # # gene info:
+    GENE_STABLE_ID=$NEW_GENE
+    SEQR_ID=`cut -f2 $GENE_METAFILE`
+    SEQR_NAME=`cut -f1 $SEQR_METAFILE`
+    GENE_SEQR_START=`cut -f3 $GENE_METAFILE`
+    GENE_SEQR_END=`cut -f4 $GENE_METAFILE`
+
+    # gene info:
+    TRANSCRIPT_STABLE_ID=`cut -f1 $TRANSC_METAFILE`
+    TRANSCRIPT_TEXT=$TRANSCRIPT_STABLE_ID
+    TRANSCRIPT_SEQR_START=`cut -f3 $TRANSC_METAFILE`
+    TRANSCRIPT_SEQR_END=`cut -f4 $TRANSC_METAFILE`
+
+    #XREF info:
+    XREF_DISPLAY=`cut -f1 $XREF_METAFILE`
+
+    if [[ "$XREF_DISPLAY" == "" ]]; then
+        XREF_DISPLAY=$GENE_STABLE_ID
+    fi
+
+    # Write new meta data to Patch sql outfile
+    echo "USE $CORE;" >> $PATCH_OUTFILE
+    echo "UPDATE meta SET meta_value = \"$NEW_GENE\" where meta_key = \"sample.gene_param\";" >> $PATCH_OUTFILE
+    echo "UPDATE meta SET meta_value = \"$XREF_DISPLAY\" where meta_key = \"sample.gene_text\";" >> $PATCH_OUTFILE
+    echo "UPDATE meta SET meta_value = \"${SEQR_NAME}:${GENE_SEQR_START}-${GENE_SEQR_END}\" where meta_key = \"sample.location_param\";" >> $PATCH_OUTFILE
+    echo "UPDATE meta SET meta_value = \"$TRANSCRIPT_STABLE_ID\" where meta_key = \"sample.transcript_param\";" >> $PATCH_OUTFILE
+    echo "UPDATE meta SET meta_value = \"${SEQR_NAME}:${TRANSCRIPT_SEQR_START}-${TRANSCRIPT_SEQR_END}\" where meta_key = \"sample.location_text\";" >> $PATCH_OUTFILE
+    echo -e -n "UPDATE meta SET meta_value = \"$TRANSCRIPT_TEXT\" where meta_key = \"sample.transcript_text\";\n\n" >> $PATCH_OUTFILE
+
+done < $INPUT_CORES