zcat CHR_*/hs_ref_GRCh37.p2_*.gbs.gz | \
intron_exon_loader| \
- psql snp -c "COPY mrna FROM STDIN WITH DELIMITER ' ' NULL AS 'NULL'";
+ psql snp -c "COPY mrna FROM STDIN WITH DELIMITER ' ' NULL AS 'NULL'";
zcat CHR_*/hs_ref_GRCh37.p2_*.gbs.gz | \
intron_exon_loader --output cds| \
- psql snp -c "COPY cds FROM STDIN WITH DELIMITER ' ' NULL AS 'NULL'";
+ psql snp -c "COPY cds FROM STDIN WITH DELIMITER ' ' NULL AS 'NULL'";
=cut
--- /dev/null
+#!/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'";
#!/bin/sh
rsync -rvP -m --include '**GRCh37.p*_*.gbs.gz' --include '**GRCh37.p*_*.fa.gz' --include '**/' --exclude '*' rsync://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/CHR* .
-rsync -rvP rsync://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.gbff.gz .
\ No newline at end of file
+rsync -rvP rsync://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.gbff.gz .
+rsync -LvP rsync://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/mapview/seq_contig.md.gz .