add extra data loader; update intron exon loader and add util to retreive human refse...

[dbsnp.git] / utils / load_extra_data.sh

diff --git a/utils/load_extra_data.sh b/utils/load_extra_data.sh
new file mode 100644 (file)
index 0000000..182ffc0
--- /dev/null
+++ b/utils/load_extra_data.sh
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+DATA_DIR=/srv/ncbi/refseq/
+SCHEMA_DIR=/srv/ncbi/db_snp_utils/schema
+UTIL_DIR=${SCHEMA_DIR}/../utils/
+
+
+psql snp < ${SCHEMA_DIR}/extra_schema/mrna_cds_table.sql
+psql snp < ${SCHEMA_DIR}/extra_schema/intron_exon_schema.sql
+
+zcat ${DATA_DIR}/human.rna.gbff.gz | \
+    ${UTIL_DIR}/human_mrna_cds_insert.pl | \
+    psql snp -c "COPY mrna_cds_table FROM STDIN WITH DELIMITER '       ' NULL AS 'NULL'";
+
+zcat ${DATA_DIR}/seq_contig.md.gz | \
+    ${UTIL_DIR}/import_seq_component_md.pl | \
+    psql snp -c "COPY contigs FROM STDIN WITH DELIMITER '      ' NULL AS 'NULL'";
+
+zcat ${DATA_DIR}/CHR_*/hs_ref_GRCh37.p*_*.gbs.gz | \
+    ${UTIL_DIR}/intron_exon_loader.pl --type mrna| \
+    psql snp -c "COPY mrna FROM STDIN WITH DELIMITER ' ' NULL AS 'NULL'";
+
+zcat ${DATA_DIR}/CHR_*/hs_ref_GRCh37.p*_*.gbs.gz | \
+    ${UTIL_DIR}/intron_exon_loader.pl --type cds| \
+    psql snp -c "COPY cds FROM STDIN WITH DELIMITER '  ' NULL AS 'NULL'";