diff test-data/util/build-gemini-testdata.sh @ 4:246ad1a7ff20 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/util/build-gemini-testdata.sh	Fri Dec 14 12:42:37 2018 -0500
@@ -0,0 +1,72 @@
+cd "$(dirname "$0")"
+
+export GEMINI_CONFIG=../test-cache
+OUT_PTH=$GEMINI_CONFIG/gemini/data
+GENOMIC_REGION=3:187000000-187500000
+
+
+if [ -n "$1" ]; then
+
+IN_PTH="$1"
+# downsample all vcf and bed annotation files to the region of interest and reindex
+for vcf in `ls $IN_PTH/*.gz | grep -v hprd_interaction_edges.gz -`
+do
+    python ./shrink_tabix.py $vcf -r $GENOMIC_REGION -o $OUT_PTH/`basename $vcf`
+done
+
+# downsample gene_table files to the region of interest
+echo "$IN_PTH/summary_gene_table_v75 -> $OUT_PTH/summary_gene_table_v75"
+python ./shrink_simple_tab.py $IN_PTH/summary_gene_table_v75 -r chr$GENOMIC_REGION -c 0 8 9 -n 1 -o $OUT_PTH/summary_gene_table_v75
+
+echo "$IN_PTH/detailed_gene_table_v75 -> $OUT_PTH/detailed_gene_table_v75"
+python ./shrink_simple_tab.py $IN_PTH/detailed_gene_table_v75 -r chr$GENOMIC_REGION -c 0 11 12 -n 1 -o $OUT_PTH/detailed_gene_table_v75
+
+# filter kegg_pathway files to retain only records of the genes listed
+# in the downsampled summary_gene_table
+for kegg in `ls $IN_PTH/kegg_pathways_*`
+do
+    echo "$kegg -> $OUT_PTH/`basename $kegg`"
+    cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Fwf - $kegg > $OUT_PTH/`basename $kegg`
+done
+
+# filter hprd_interaction file to retain only records of the genes listed
+# in the downsampled summary_gene_table
+echo "$IN_PTH/hprd_interaction_edges.gz -> $OUT_PTH/hprd_interaction_edges.gz"
+bgzip -dc $IN_PTH/hprd_interaction_edges.gz > $OUT_PTH/hprd_interaction_edges
+cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Ff - $OUT_PTH/hprd_interaction_edges | bgzip > $OUT_PTH/hprd_interaction_edges.gz
+rm $OUT_PTH/hprd_interaction_edges
+
+# filter cancer_gene_census file to retain only records of the genes listed
+# in the downsampled summary_gene_table;
+# TO DO: make the filter stricter by looking for matches only in the first
+# column of the cancer_gene_census file (but the file is relatively small anyway)
+echo "$IN_PTH/cancer_gene_census.20140120.tsv -> $OUT_PTH/cancer_gene_census.20140120.tsv"
+cut -f2 $OUT_PTH/summary_gene_table_v75 | grep -Fv None | grep -Fwf - $IN_PTH/cancer_gene_census.20140120.tsv > $OUT_PTH/cancer_gene_census.20140120.tsv
+
+else
+    echo "no path to gemini annotation files provided - only building test databases"
+fi
+
+
+# now use gemini load to build the test databases
+echo "Building gemini test databases"
+echo "Test databases for gemini_load"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/gemini_load_input.vcf -t snpEff ../gemini_load_result1.db
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/gemini_load_input.vcf -t snpEff --skip-gene-tables --no-load-genotypes ../gemini_load_result2.db
+echo "Test database for gemini_amend"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_rec.vcf -t snpEff ../gemini_amend_input.db
+echo "Test database for gemini_annotate"
+bgzip -c build-data anno.bed > build-data/anno.bed.gz
+tabix --force -p bed build-data/anno.bed.gz
+cp ../gemini_load_result1.db ../gemini_annotate_result.db
+gemini --annotation-dir $OUT_PTH annotate -f build-data/anno.bed.gz -c anno5 -a count ../gemini_annotate_result.db
+echo "Test database for gemini_set_somatic"
+cp ../gemini_load_result1.db ../gemini_is_somatic_result.db
+gemini set_somatic --min-somatic-score 5.65 ../gemini_is_somatic_result.db
+echo "Test database for gemini_de_novo and gemini_mendel_errors"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.de_novo.vcf -p build-data/test.de_novo.ped -t snpEff ../gemini_de_novo_input.db
+echo "Test database for gemini_comp_hets"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.comp_het.vcf -p build-data/test.comp_het.ped -t snpEff ../gemini_comphets_input.db
+echo "Test databases for gemini_autosomal"
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_rec.vcf -p build-data/test.auto_rec.ped -t snpEff ../gemini_auto_rec_input.db
+gemini --annotation-dir $OUT_PTH load --skip-cadd --skip-gerp-bp -v build-data/test.auto_dom.vcf -p build-data/test.auto_dom.ped -t snpEff ../gemini_auto_dom_input.db