func doFillRsids(c *cli.Context) {
arg_bucket := c.String("bucket")
arg_setup := c.Bool("setup")
arg_overwrite := c.Bool("overwrite")
arg_strict := c.Bool("strict")
if len(c.Args()) <= 2 {
fmt.Fprintln(os.Stderr)
fmt.Fprintln(os.Stderr, "[FATAL] too few arguments")
fmt.Fprintln(os.Stderr)
cli.ShowCommandHelp(c, "fill-rsids")
os.Exit(1)
} else if !arg_overwrite && arg_strict {
fmt.Fprintln(os.Stderr)
fmt.Fprintln(os.Stderr, "[FATAL] -strict option is only effective with -overwrite option")
fmt.Fprintln(os.Stderr)
cli.ShowCommandHelp(c, "fill-rsids")
os.Exit(1)
} else if arg_bucket == "" {
fmt.Fprintln(os.Stderr)
fmt.Fprintln(os.Stderr, "[FATAL] -bucket is required")
fmt.Fprintln(os.Stderr)
cli.ShowCommandHelp(c, "fill-rsids")
os.Exit(1)
}
databaseName := "bolt.db"
bucketName := []byte(path.Base(arg_bucket))
// Store chrpos <=> rsid mappings into bolt.db
db, err := bolt.Open(databaseName, 0600, nil)
if err != nil {
panic(err)
}
defer db.Close()
if arg_setup {
f, err := os.Open(arg_bucket)
if err != nil {
panic(err)
}
defer f.Close()
gz, err := gzip.NewReader(f)
if err != nil {
panic(err)
}
defer gz.Close()
// TODO: workaround for non-uniq chrpos. skip high rs numbers?
err = db.Batch(func(tx *bolt.Tx) error {
bucket, err := tx.CreateBucketIfNotExists(bucketName)
if err != nil {
return err
}
map_reader := bufio.NewReaderSize(gz, 128*1024)
map_line, err := lib.Readln(map_reader)
for err == nil {
// chrom/pos to rs id mapping resource file ([TAB] delimited)
//
// | rs id | chrom | pos |
// |--------|--------|--------|
// | xxxxx | xx | xxxxx |
//
records := strings.Split(map_line, "\t")
rsId := strings.Replace(records[0], "rs", "", 1)
rsChr := records[1]
rsPos, _ := strconv.ParseInt(records[2], 10, 64)
if rsChr != "" && rsChr != "NotOn" && rsChr != "Multi" && rsChr != "Un" && rsChr != "PAR" {
// | chrom id | 0-filled pos |
// |------------|----------------|
// | xx | xxxxxxxxx |
// | (2 digits) | (9 digits) |
chrpos := lib.ChrPos(rsChr, rsPos)
key := lib.Itob(chrpos)
val := []byte(rsId) // TODO: put/get rsId as byte(int)
err = bucket.Put(key, val)
}
map_line, err = lib.Readln(map_reader)
}
if err != nil && err != io.EOF {
return err
}
return nil
})
if err != nil {
panic(err)
}
//
os.Exit(0)
}
// Parse VCF header lines
reader := bufio.NewReaderSize(os.Stdin, 64*1024)
line, err := lib.Readln(reader)
for err == nil {
if strings.HasPrefix(line, "##") {
fmt.Println(line)
} else if strings.HasPrefix(line, "#CHROM") {
fmt.Println(line)
break
} else {
err = errors.New("Invalid VCF header")
break
}
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
// Parse VCF body lines
pattern := regexp.MustCompile(`rs(\d+)`)
line, err = lib.Readln(reader)
for err == nil {
records := strings.Split(line, "\t")
chrom := records[0]
pos, _ := strconv.ParseInt(records[1], 10, 64)
snpId := records[2]
rsIdFound := pattern.FindStringSubmatch(snpId)
// Skip or fill rs id. Switch by '-overwrite' option.
//
// | input | overwrite = t | overwrite = f |
// |-----------|---------------|---------------|
// | "rsxxxx" | fill | skip |
// | "." | fill | fill |
if rsIdFound != nil && !arg_overwrite {
// Skip
fmt.Println(line)
} else if (rsIdFound != nil && arg_overwrite) || rsIdFound == nil {
// Fill
result := []string{}
result = append(result, records[0:2]...)
err = db.View(func(tx *bolt.Tx) error {
bucket := tx.Bucket(bucketName)
if bucket == nil {
return fmt.Errorf("Bucket %q not found!", bucketName)
}
val := bucket.Get(lib.Itob(lib.ChrPos(chrom, pos)))
if val != nil {
// Fill rs id if locus is found.
result = append(result, "rs"+string(val))
} else {
if arg_strict {
// Fill '.' if locus in not found ('-strict' option).
result = append(result, ".")
} else {
// Keep original record (including '.') if locus is not found.
result = append(result, snpId)
}
}
return nil
})
if err != nil {
panic(err)
}
result = append(result, records[3:]...)
fmt.Println(strings.Join(result, "\t"))
}
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
}
func doFilter(c *cli.Context) {
arg_keep_ids := c.String("keep-ids")
arg_keep_pos := c.String("keep-pos")
arg_keep_only_pass := c.Bool("keep-only-pass")
pattern := regexp.MustCompile(`rs(\d+)`)
keep_ids := make(map[int]bool)
keep_pos := make(map[int64]bool)
// Get SNP IDs to be kept if exists
if arg_keep_ids != "" {
var ids_fp *os.File
var err error
ids_fp, err = os.Open(arg_keep_ids)
if err != nil {
panic(err)
}
defer ids_fp.Close()
ids_reader := bufio.NewReaderSize(ids_fp, 128*1024)
ids_line, err := lib.Readln(ids_reader)
for err == nil {
id_found := pattern.FindStringSubmatch(ids_line)
if id_found != nil {
keep_id, _ := strconv.Atoi(id_found[1])
keep_ids[keep_id] = true
}
ids_line, err = lib.Readln(ids_reader)
}
if err != nil && err != io.EOF {
panic(err)
}
}
// Get loci to be kept if exists
if arg_keep_pos != "" {
var pos_fp *os.File
var err error
pos_fp, err = os.Open(arg_keep_pos)
if err != nil {
panic(err)
}
defer pos_fp.Close()
pos_reader := bufio.NewReaderSize(pos_fp, 128*1024)
pos_line, err := lib.Readln(pos_reader)
for err == nil {
records := strings.Split(pos_line, "\t")
chrom := records[0]
pos, _ := strconv.ParseInt(records[1], 10, 64)
chrpos := lib.ChrPos(chrom, pos)
keep_pos[chrpos] = true
pos_line, err = lib.Readln(pos_reader)
}
if err != nil && err != io.EOF {
panic(err)
}
}
// Parse header lines
reader := bufio.NewReaderSize(os.Stdin, 128*1024)
line, err := lib.Readln(reader)
for err == nil {
if strings.HasPrefix(line, "##") {
fmt.Println(line)
} else if strings.HasPrefix(line, "#CHROM") {
fmt.Println(line)
break
} else {
err = errors.New("Invalid VCF header")
break
}
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
// Parse body lines
line, err = lib.Readln(reader)
for err == nil {
records := strings.Split(line, "\t")
var is_pass bool
// Filter by id
if arg_keep_ids != "" {
id_found := pattern.FindStringSubmatch(records[2])
if id_found != nil {
id, _ := strconv.Atoi(id_found[1])
if keep_ids[id] {
is_pass = true
}
}
}
// Filter by loci
if arg_keep_pos != "" {
chrom := records[0]
pos, _ := strconv.ParseInt(records[1], 10, 64)
chrpos := lib.ChrPos(chrom, pos)
if keep_pos[chrpos] {
is_pass = true
}
}
// Filter by FILTER = PASS
if arg_keep_only_pass {
if records[6] == "PASS" {
is_pass = true
} else {
is_pass = false
}
}
if is_pass {
fmt.Println(line)
}
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
}