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get_fills_net.go
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get_fills_net.go
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// extract fills from net files, min ref size is 10
// Reuben
// need to see what is happening with the stacking
package fills
import (
"bufio"
"fmt"
"log"
"os"
"strconv"
"strings"
)
type fill struct {
RefChr string
RefStart int
RefEnd int
QueChr string
QueStart int
QueEnd int
Strand string
id int
//Type string
}
type gap struct {
RefChr string
RefStart int
RefEnd int
QueStart int
QueEnd int
Strand string
}
type doubleStack struct {
ref int
que int
}
type net struct {
Chr string
Len int
}
func main() {
var newFill fill
var newGap gap
var chrStack []string
var netElem net
var fillStartStack []doubleStack
var fillEndStack []doubleStack
var strandStack []string
var fillPrint fill
var chainStack []int
fillFile, err := os.Open(os.Args[1])
if err != nil {
log.Fatalf("reading file: %v", err)
}
defer fillFile.Close()
scFill := bufio.NewScanner(fillFile)
scFill.Split(bufio.ScanLines)
for scFill.Scan() {
var refLen int
line := scFill.Text()
line = strings.TrimSpace(line)
words := strings.Split(line, " ")
switch words[0] {
case "net":
//flush the stack before starting the next chr
for i := len(fillStartStack) - 1; i > -1; i-- {
// send fill info to print
fillPrint.RefStart = fillStartStack[len(fillStartStack)-1].ref
fillPrint.RefEnd = fillEndStack[len(fillEndStack)-1].ref
fillPrint.QueStart = fillStartStack[len(fillStartStack)-1].que
fillPrint.QueEnd = fillEndStack[len(fillEndStack)-1].que
fillPrint.RefChr = netElem.Chr
fillPrint.QueChr = chrStack[len(chrStack)-1]
fillPrint.Strand = strandStack[len(strandStack)-1]
fillPrint.id = chainStack[len(chainStack)-1]
// if fillPrint.RefEnd-fillPrint.RefStart > 8 {
fmt.Println(strings.Trim(fmt.Sprintf("%v", fillPrint), "{}"))
// }
// remove from stack
fillStartStack = fillStartStack[0 : len(fillStartStack)-1]
fillEndStack = fillEndStack[0 : len(fillEndStack)-1]
chrStack = chrStack[0 : len(chrStack)-1]
strandStack = strandStack[0 : len(strandStack)-1]
chainStack = chainStack[0 : len(chainStack)-1]
}
netElem.Chr = words[1]
netElem.Len, err = strconv.Atoi(words[2])
case "gap":
// get information for next gap
refLen, err = strconv.Atoi(words[2])
//if refLen <= 9 {
// continue
//}
newGap.RefStart, err = strconv.Atoi(words[1])
newGap.RefStart = newGap.RefStart + 1
newGap.RefEnd = newGap.RefStart + refLen - 1
refLen, err = strconv.Atoi(words[6])
newGap.QueStart, err = strconv.Atoi(words[5])
newGap.QueStart = newGap.QueStart
newGap.QueEnd = newGap.QueStart + refLen
newGap.Strand = words[4]
if newGap.Strand == "-" {
newGap.QueStart, newGap.QueEnd = newGap.QueEnd+1, newGap.QueStart-1
}
newGap.QueStart = newGap.QueStart + 1
newGap.QueEnd = newGap.QueEnd
//fmt.Println(newGap, "newFILL")
// if the gap is totaly left of our stack, we should print it
// after that we find we have the fill thats interupted
if len(fillStartStack) > 0 && len(fillEndStack) > 0 {
for i := len(fillStartStack) - 1; i > -1; i-- {
if fillEndStack[i].ref < newGap.RefStart {
// send fill info to print
fillPrint.RefStart = fillStartStack[len(fillStartStack)-1].ref
fillPrint.RefEnd = fillEndStack[len(fillEndStack)-1].ref
fillPrint.QueStart = fillStartStack[len(fillStartStack)-1].que
fillPrint.QueEnd = fillEndStack[len(fillEndStack)-1].que
fillPrint.RefChr = netElem.Chr
fillPrint.QueChr = chrStack[len(chrStack)-1]
fillPrint.Strand = strandStack[len(strandStack)-1]
fillPrint.id = chainStack[len(chainStack)-1]
// if fillPrint.RefEnd-fillPrint.RefStart > 8 {
fmt.Println(strings.Trim(fmt.Sprintf("%v", fillPrint), "{}"))
// }
// remove from stack
fillStartStack = fillStartStack[0 : len(fillStartStack)-1]
fillEndStack = fillEndStack[0 : len(fillEndStack)-1]
chrStack = chrStack[0 : len(chrStack)-1]
strandStack = strandStack[0 : len(strandStack)-1]
chainStack = chainStack[0 : len(chainStack)-1]
}
}
}
if len(fillEndStack) > 0 && newGap.RefStart <= fillEndStack[len(fillEndStack)-1].ref {
fillPrint.RefStart = fillStartStack[len(fillStartStack)-1].ref
fillPrint.RefEnd = newGap.RefStart - 1 //to get it in position
fillPrint.QueStart = fillStartStack[len(fillStartStack)-1].que
fillPrint.QueEnd = newGap.QueStart - 1 //to get it in position
fillPrint.RefChr = netElem.Chr
fillPrint.QueChr = chrStack[len(chrStack)-1]
fillPrint.Strand = strandStack[len(strandStack)-1]
fillPrint.id = chainStack[len(chainStack)-1]
// if fillPrint.RefEnd-fillPrint.RefStart > 8 {
fmt.Println(strings.Trim(fmt.Sprintf("%v", fillPrint), "{}"))
// }
fillStartStack = fillStartStack[0 : len(fillStartStack)-1]
fillStartStack = append(fillStartStack, doubleStack{newGap.RefEnd + 1, newGap.QueEnd + 1}) // to get it in position
}
//now we need to think what a gap interruption looks like
// mape our gap interuptions need to work recursivly
// this may be the problem
case "fill":
// get new fill information
// feed back on position
newFill.RefStart, err = strconv.Atoi(words[1])
newFill.RefStart = newFill.RefStart + 1
refLen, err = strconv.Atoi(words[2])
newFill.RefEnd = newFill.RefStart + refLen - 1
newFill.QueChr = words[3]
newFill.Strand = words[4]
newFill.QueStart, err = strconv.Atoi(words[5])
newFill.QueStart = newFill.QueStart
refLen, err = strconv.Atoi(words[6])
newFill.QueEnd = newFill.QueStart + refLen
newFill.id, err = strconv.Atoi(words[8])
if newFill.Strand == "-" {
newFill.QueStart, newFill.QueEnd = newFill.QueEnd-1, newFill.QueStart+1
}
newFill.QueStart = newFill.QueStart + 1
newFill.QueEnd = newFill.QueEnd
//fmt.Println(newFill, "newGAP")
// here we enter fill this means we got to the end of our last fill non interrupted
// here we need to think about our position a bit more
// If we can get to a start point that is beyond our end point we need to print
if len(fillStartStack) > 0 && len(fillEndStack) > 0 {
for i := len(fillStartStack) - 1; i > -1; i-- {
if fillEndStack[i].ref < newFill.RefStart {
// send fill info to print
fillPrint.RefStart = fillStartStack[len(fillStartStack)-1].ref
fillPrint.RefEnd = fillEndStack[len(fillEndStack)-1].ref
fillPrint.QueStart = fillStartStack[len(fillStartStack)-1].que
fillPrint.QueEnd = fillEndStack[len(fillEndStack)-1].que
fillPrint.RefChr = netElem.Chr
fillPrint.QueChr = chrStack[len(chrStack)-1]
fillPrint.Strand = strandStack[len(strandStack)-1]
fillPrint.id = chainStack[len(chainStack)-1]
// if fillPrint.RefEnd-fillPrint.RefStart > 8 {
fmt.Println(strings.Trim(fmt.Sprintf("%v", fillPrint), "{}"))
// }
// remove from stack
fillStartStack = fillStartStack[0 : len(fillStartStack)-1]
fillEndStack = fillEndStack[0 : len(fillEndStack)-1]
chrStack = chrStack[0 : len(chrStack)-1]
strandStack = strandStack[0 : len(strandStack)-1]
chainStack = chainStack[0 : len(chainStack)-1]
}
}
}
// add to stack
fillStartStack = append(fillStartStack, doubleStack{newFill.RefStart, newFill.QueStart})
fillEndStack = append(fillEndStack, doubleStack{newFill.RefEnd, newFill.QueEnd})
// we could add query start and end to these stacks too maybe?
// the start can be ref and query, if they both update the same way
chrStack = append(chrStack, newFill.QueChr)
strandStack = append(strandStack, newFill.Strand)
chainStack = append(chainStack, newFill.id)
}
if err != nil {
log.Fatalf("value assignment error", err)
}
//fmt.Println(fillStartStack, fillEndStack, "fillStacks")
}
for i := len(fillStartStack) - 1; i > -1; i-- {
// send fill info to print
fillPrint.RefStart = fillStartStack[len(fillStartStack)-1].ref
fillPrint.RefEnd = fillEndStack[len(fillEndStack)-1].ref
fillPrint.QueStart = fillStartStack[len(fillStartStack)-1].que
fillPrint.QueEnd = fillEndStack[len(fillEndStack)-1].que
fillPrint.RefChr = netElem.Chr
fillPrint.QueChr = chrStack[len(chrStack)-1]
fillPrint.Strand = strandStack[len(strandStack)-1]
fillPrint.id = chainStack[len(chainStack)-1]
// if fillPrint.RefEnd-fillPrint.RefStart > 8 {
fmt.Println(strings.Trim(fmt.Sprintf("%v", fillPrint), "{}"))
// }
// remove from stack
fillStartStack = fillStartStack[0 : len(fillStartStack)-1]
fillEndStack = fillEndStack[0 : len(fillEndStack)-1]
chrStack = chrStack[0 : len(chrStack)-1]
strandStack = strandStack[0 : len(strandStack)-1]
chainStack = chainStack[0 : len(chainStack)-1]
}
}