Mercurial > repos > iuc > gemini_actionable_mutations
view test-data/util/build-gemini-testdata.sh @ 7:142d95ab942e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author | iuc |
---|---|
date | Tue, 10 Mar 2020 06:18:46 -0400 |
parents | 712aa8283200 |
children |
line wrap: on
line source
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