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#!/bin/sh | |
if [ ! -e gene_info ]; then | |
curl -O ftp://ftp.hgc.jp/pub/mirror/ncbi/gene/DATA/gene_info.gz | |
gunzip gene_info.gz | |
fi | |
function importtax() { | |
SUFFIX=$1 | |
TAXID=$2 | |
echo $1 $2 | |
if [ ! -e gene_info-$SUFFIX ];then | |
egrep "^$TAXID " gene_info > gene_info-$SUFFIX | |
fi | |
rm gene_info-$SUFFIX.sqlite3 2> /dev/null | |
sqlite3 gene_info-$SUFFIX.sqlite3 'CREATE TABLE gene_info(tax_id INTEGER,GeneID INTEGER,Symbol TEXT,LocusTag TEXT,Synonyms TEXT,dbXrefs TEXT,chromosome TEXT,map_location TEXT,description TEXT,type_of_gene TEXT,Symbol_from_nomenclature_authority TEXT,Full_name_from_nomenclature_authority TEXT,Nomenclature_status TEXT,Other_designations TEXT,Modification_date INTEGER);' | |
sqlite3 gene_info-$SUFFIX.sqlite3 <<EOF | |
.separator " " | |
.import gene_info-$SUFFIX gene_info | |
CREATE INDEX gene_info__tax_id__index on gene_info(tax_id); | |
CREATE INDEX gene_info__GeneID__index on gene_info(GeneID); | |
CREATE INDEX gene_info__Symbol__index on gene_info(Symbol); | |
CREATE INDEX gene_info__LocusTag__index on gene_info(LocusTag); | |
CREATE INDEX gene_info__chromosome__index on gene_info(chromosome); | |
CREATE INDEX gene_info__map_location__index on gene_info(map_location); | |
CREATE INDEX gene_info__type_of_gene__index on gene_info(type_of_gene); | |
CREATE INDEX gene_info__Symbol_from_nomenclature_authority__index on gene_info(Symbol_from_nomenclature_authority); | |
CREATE INDEX gene_info__Nomenclature_status__index on gene_info(Nomenclature_status); | |
CREATE INDEX gene_info__Modification_date__index on gene_info(Modification_date); | |
EOF | |
rm gene_info-$SUFFIX.zip 2> /dev/null | |
7z a gene_info-$SUFFIX.zip gene_info-$SUFFIX.sqlite3 | |
} | |
# taxonomy ids | |
# 9606 Human | |
# 10090 Mouse | |
# 7227 Drosophila melanogaster | |
# 3702 Arabidopsis thaliana | |
# 4577 Zea mays (Maize) | |
# 7955 Danio rerio (Zebra fish) | |
# 6239 Caenorhabditis elegans | |
# 4932 Saccharomyces cerevisiae | |
importtax hsa 9606 | |
importtax mmu 10090 | |
importtax dme 7227 | |
importtax ath 3702 | |
importtax dre 1955 | |
importtax cel 6239 | |