/
parseCrass.go
228 lines (197 loc) · 4.47 KB
/
parseCrass.go
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package main
import (
"database/sql"
"encoding/csv"
"fmt"
_ "github.com/mattn/go-sqlite3"
"io"
"io/ioutil"
"log"
"os"
"regexp"
"strconv"
"strings"
"sync"
)
func main() {
//stick into database
dbName := "./crass.db3"
os.Remove(dbName)
db, err := sql.Open("sqlite3", dbName)
if err != nil {
log.Fatal(err)
}
defer db.Close()
fmt.Println("Creating the database")
createTable(db)
fmt.Println("parsing out the files...")
ReadFiles(db)
fmt.Println("querying the data and writing output...")
QueryAndStore(db)
fmt.Println("Done")
}
func createTable(db *sql.DB) {
sqlStmt := `
create table sample (pos int, val text, sampName text);
delete from sample;
create index indx_samp on sample(pos,sampName);
create table masterSample(pos int, val text);
create index indx_master on masterSample(pos);
delete from masterSample;
create table sampleName(name text);
create index indx_sampName on sampName(name);
delete from sampleName;
`
_, err := db.Exec(sqlStmt)
if err != nil {
log.Printf("%q: %s\n", err, sqlStmt)
return
}
}
func ReadFiles(db *sql.DB) {
var wg sync.WaitGroup
tx, err := db.Begin()
if err != nil {
log.Fatal(err)
}
stmt, err := tx.Prepare("insert into sample(pos, val, sampName) values(?, ?, ?)")
if err != nil {
log.Fatal(err)
}
defer stmt.Close()
//read all csv files in dir
files, _ := ioutil.ReadDir("./")
for _, f := range files {
if !strings.HasSuffix(f.Name(), "pos") {
continue
}
//fmt.Println(f.Name())
wg.Add(1)
go parseFileFnc(f.Name(), stmt, &wg)
}
wg.Wait()
tx.Commit()
//select distinct samples into sample table
sqlInsStmt := `insert into sampleName select distinct sampName from sample;`
_, err = db.Exec(sqlInsStmt)
if err != nil {
log.Fatal(err)
return
}
//read in master table
txMas, err := db.Begin()
if err != nil {
log.Fatal(err)
}
stmtInsMaster, err := txMas.Prepare("insert into masterSample(pos, val) values(?, ?)")
if err != nil {
log.Fatal(err)
}
file, err := os.Open("crass.gen.var")
if err != nil {
log.Fatal(err)
}
defer file.Close()
reader := csv.NewReader(file)
fmt.Println("parsing the master file")
reader.Comma = '\t'
for {
//parse out into needed fields
record, err := reader.Read()
if err == io.EOF {
break
} else if err != nil {
log.Fatal(err)
}
//fmt.Println(record[0], record[1])
_, err = stmtInsMaster.Exec(record[0], record[1])
if err != nil {
log.Fatal(err)
}
}
txMas.Commit()
}
func parseFileFnc(fName string, stmt *sql.Stmt, wg *sync.WaitGroup) {
defer wg.Done()
fmt.Println("parsing file", fName)
file, err := os.Open(fName)
if err != nil {
log.Fatal(err)
}
defer file.Close()
reader := csv.NewReader(file)
reader.Comma = '\t'
for {
//parse out into needed fields
record, err := reader.Read()
if err == io.EOF {
break
} else if err != nil {
log.Fatal(err)
}
//fmt.Println(record[0], record[1])
_, err = stmt.Exec(record[0], record[2], fName)
if err != nil {
log.Fatal(err)
}
}
}
func QueryAndStore(db *sql.DB) {
rows, err := db.Query(`
select ms.pos, ms.val, sn.name, s.val
from mastersample ms, sampleName sn
left join sample s on s.pos = ms.pos and sn.name = s.sampName
order by ms.pos, sn.name;
`)
if err != nil {
log.Fatal(err)
}
defer rows.Close()
csvfile, err := os.Create("output.csv")
if err != nil {
//fmt.Println("Error:", err)
return
}
defer csvfile.Close()
writer := csv.NewWriter(csvfile)
writer.Comma = '\t'
priorPos := 0
headerRow := []string{""}
var rowToWrite []string
outputArr := [][]string{}
hasWrittenHeader := false
for rows.Next() {
var pos int
var mVal, name string
var sVal sql.NullString
rows.Scan(&pos, &mVal, &name, &sVal)
//capture all the header rows
if hasWrittenHeader == false && (pos == priorPos || priorPos == 0) {
reItem := regexp.MustCompile(".pos$")
headerRow = append(headerRow, reItem.ReplaceAllString(name, ""))
}
if pos != priorPos {
if priorPos != 0 {
if hasWrittenHeader == false {
outputArr = append(outputArr, headerRow)
hasWrittenHeader = true
}
outputArr = append(outputArr, rowToWrite)
}
priorPos = pos
posStr := strconv.Itoa(pos)
rowToWrite = []string{posStr}
}
if sVal.Valid {
rowToWrite = append(rowToWrite, sVal.String)
} else {
rowToWrite = append(rowToWrite, mVal)
}
}
if rowToWrite != nil {
outputArr = append(outputArr, rowToWrite)
}
fmt.Println("finished querrying and building, now writing to file")
writer.WriteAll(outputArr)
writer.Flush()
}