tilelib.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "io"
   7         "strings"
   8         "sync"
   9
  10         log "github.com/sirupsen/logrus"
  11         "golang.org/x/crypto/blake2b"
  12 )
  13
  14 type tileVariantID uint16 // 1-based
  15
  16 type tileLibRef struct {
  17         tag     tagID
  18         variant tileVariantID
  19 }
  20
  21 type tileSeq map[string][]tileLibRef
  22
  23 func (tseq tileSeq) Variants() []tileVariantID {
  24         maxtag := 0
  25         for _, refs := range tseq {
  26                 for _, ref := range refs {
  27                         if maxtag < int(ref.tag) {
  28                                 maxtag = int(ref.tag)
  29                         }
  30                 }
  31         }
  32         vars := make([]tileVariantID, maxtag+1)
  33         for _, refs := range tseq {
  34                 for _, ref := range refs {
  35                         vars[int(ref.tag)] = ref.variant
  36                 }
  37         }
  38         return vars
  39 }
  40
  41 type tileLibrary struct {
  42         skipOOO bool
  43         taglib  *tagLibrary
  44         variant [][][blake2b.Size256]byte
  45         // count [][]int
  46         // seq map[[blake2b.Size]byte][]byte
  47         variants int
  48
  49         mtx sync.Mutex
  50 }
  51
  52 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
  53         ret := tileSeq{}
  54         type jobT struct {
  55                 label string
  56                 fasta []byte
  57         }
  58         todo := make(chan jobT)
  59         scanner := bufio.NewScanner(rdr)
  60         go func() {
  61                 defer close(todo)
  62                 var fasta []byte
  63                 var seqlabel string
  64                 for scanner.Scan() {
  65                         buf := scanner.Bytes()
  66                         if len(buf) == 0 || buf[0] == '>' {
  67                                 todo <- jobT{seqlabel, fasta}
  68                                 seqlabel, fasta = string(buf[1:]), nil
  69                                 log.Debugf("%s %s reading fasta", filelabel, seqlabel)
  70                         } else {
  71                                 fasta = append(fasta, bytes.ToLower(buf)...)
  72                         }
  73                 }
  74                 todo <- jobT{seqlabel, fasta}
  75         }()
  76         type foundtag struct {
  77                 pos    int
  78                 tagid  tagID
  79                 taglen int
  80         }
  81         found := make([]foundtag, 2000000)
  82         path := make([]tileLibRef, 2000000)
  83         totalPathLen := 0
  84         skippedSequences := 0
  85         for job := range todo {
  86                 if len(job.fasta) == 0 {
  87                         continue
  88                 } else if strings.Contains(job.label, "_") {
  89                         skippedSequences++
  90                         continue
  91                 }
  92                 log.Debugf("%s %s tiling", filelabel, job.label)
  93
  94                 found = found[:0]
  95                 tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
  96                         found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
  97                 })
  98                 path = path[:0]
  99                 last := foundtag{tagid: -1}
 100                 for i, f := range found {
 101                         log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
 102                         if tilelib.skipOOO {
 103                                 if f.tagid < last.tagid+1 {
 104                                         // e.g., last=B, this=A
 105                                         log.Debugf("%s %s skipped out-of-order tag %d (found at %d) because it follows tag %d (found at %d)", filelabel, job.label, f.tagid, f.pos, last.tagid, last.pos)
 106                                         continue
 107                                 }
 108                                 if f.tagid > last.tagid+1 && i+1 < len(found) && found[i+1].tagid <= f.tagid {
 109                                         // e.g., last=A, this=C, next=B
 110                                         log.Debugf("%s %s skipped out-of-order tag %d (found at %d) because it appears between tag %d (found at %d) and %d (found at %d)", filelabel, job.label, f.tagid, f.pos, last.tagid, last.pos, found[i+1].tagid, found[i+1].pos)
 111                                         continue
 112                                 }
 113                         }
 114                         if last.taglen > 0 {
 115                                 path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen]))
 116                         }
 117                         last = f
 118                 }
 119                 if last.taglen > 0 {
 120                         path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:]))
 121                 }
 122
 123                 pathcopy := make([]tileLibRef, len(path))
 124                 copy(pathcopy, path)
 125                 ret[job.label] = pathcopy
 126                 log.Debugf("%s %s tiled with path len %d", filelabel, job.label, len(path))
 127                 totalPathLen += len(path)
 128         }
 129         log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name)", filelabel, totalPathLen, len(ret), skippedSequences)
 130         return ret, scanner.Err()
 131 }
 132
 133 func (tilelib *tileLibrary) Len() int {
 134         tilelib.mtx.Lock()
 135         defer tilelib.mtx.Unlock()
 136         return tilelib.variants
 137 }
 138
 139 // Return a tileLibRef for a tile with the given tag and sequence,
 140 // adding the sequence to the library if needed.
 141 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
 142         for _, b := range seq {
 143                 if b != 'a' && b != 'c' && b != 'g' && b != 't' {
 144                         // return "tile not found" if seq has any
 145                         // no-calls
 146                         return tileLibRef{tag: tag}
 147                 }
 148         }
 149         tilelib.mtx.Lock()
 150         defer tilelib.mtx.Unlock()
 151         // if tilelib.seq == nil {
 152         //      tilelib.seq = map[[blake2b.Size]byte][]byte{}
 153         // }
 154         if tilelib.variant == nil {
 155                 tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
 156         }
 157         seqhash := blake2b.Sum256(seq)
 158         for i, varhash := range tilelib.variant[tag] {
 159                 if varhash == seqhash {
 160                         return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
 161                 }
 162         }
 163         tilelib.variants++
 164         tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
 165         // tilelib.seq[seqhash] = append([]byte(nil), seq...)
 166         return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
 167 }