tilelib.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "crypto/md5"
   7         "io"
   8         "log"
   9         "sync"
  10 )
  11
  12 type tileVariantID int32 // 1-based
  13
  14 type tileLibRef struct {
  15         tag     tagID
  16         variant tileVariantID
  17 }
  18
  19 type tileSeq map[string][]tileLibRef
  20
  21 type tileLibrary struct {
  22         taglib  *tagLibrary
  23         variant [][][md5.Size]byte
  24         // count [][]int
  25         // seq map[[md5.Size]byte][]byte
  26
  27         mtx sync.Mutex
  28 }
  29
  30 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
  31         ret := tileSeq{}
  32         type jobT struct {
  33                 label string
  34                 fasta []byte
  35         }
  36         todo := make(chan jobT)
  37         scanner := bufio.NewScanner(rdr)
  38         go func() {
  39                 defer close(todo)
  40                 var fasta []byte
  41                 var seqlabel string
  42                 for scanner.Scan() {
  43                         buf := scanner.Bytes()
  44                         if len(buf) == 0 || buf[0] == '>' {
  45                                 todo <- jobT{seqlabel, fasta}
  46                                 seqlabel, fasta = string(buf[1:]), nil
  47                                 log.Printf("%s %s reading fasta", filelabel, seqlabel)
  48                         } else {
  49                                 fasta = append(fasta, bytes.ToLower(buf)...)
  50                         }
  51                 }
  52                 todo <- jobT{seqlabel, fasta}
  53         }()
  54         for job := range todo {
  55                 if len(job.fasta) == 0 {
  56                         continue
  57                 }
  58                 log.Printf("%s %s tiling", filelabel, job.label)
  59                 var path []tileLibRef
  60                 tilestart := -1        // position in fasta of tile that ends here
  61                 tiletagid := tagID(-1) // tag id starting tile that ends here
  62                 tilelib.taglib.FindAll(job.fasta, func(id tagID, pos int) {
  63                         if tilestart >= 0 {
  64                                 path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:pos]))
  65                         }
  66                         tilestart = pos
  67                         tiletagid = id
  68                 })
  69                 if tiletagid >= 0 {
  70                         path = append(path, tilelib.getRef(tiletagid, job.fasta[tilestart:]))
  71                 }
  72                 ret[job.label] = path
  73                 log.Printf("%s %s tiled with path len %d", filelabel, job.label, len(path))
  74         }
  75         return ret, scanner.Err()
  76 }
  77
  78 // Return a tileLibRef for a tile with the given tag and sequence,
  79 // adding the sequence to the library if needed.
  80 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
  81         tilelib.mtx.Lock()
  82         defer tilelib.mtx.Unlock()
  83         // if tilelib.seq == nil {
  84         //      tilelib.seq = map[[md5.Size]byte][]byte{}
  85         // }
  86         if len(tilelib.variant) <= int(tag) {
  87                 tilelib.variant = append(tilelib.variant, make([][][md5.Size]byte, int(tag)-len(tilelib.variant)+1)...)
  88         }
  89         seqhash := md5.Sum(seq)
  90         for i, varhash := range tilelib.variant[tag] {
  91                 if varhash == seqhash {
  92                         return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
  93                 }
  94         }
  95         tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
  96         // tilelib.seq[seqhash] = append([]byte(nil), seq...)
  97         return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
  98 }