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, int, int) {
  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         var kept, dropped int
  34         for _, refs := range tseq {
  35                 for _, ref := range refs {
  36                         if vars[int(ref.tag)] != 0 {
  37                                 dropped++
  38                         } else {
  39                                 kept++
  40                         }
  41                         vars[int(ref.tag)] = ref.variant
  42                 }
  43         }
  44         return vars, kept, dropped
  45 }
  46
  47 type tileLibrary struct {
  48         skipOOO bool
  49         taglib  *tagLibrary
  50         variant [][][blake2b.Size256]byte
  51         // count [][]int
  52         // seq map[[blake2b.Size]byte][]byte
  53         variants int
  54
  55         mtx sync.Mutex
  56 }
  57
  58 func (tilelib *tileLibrary) TileFasta(filelabel string, rdr io.Reader) (tileSeq, error) {
  59         ret := tileSeq{}
  60         type jobT struct {
  61                 label string
  62                 fasta []byte
  63         }
  64         todo := make(chan jobT)
  65         scanner := bufio.NewScanner(rdr)
  66         go func() {
  67                 defer close(todo)
  68                 var fasta []byte
  69                 var seqlabel string
  70                 for scanner.Scan() {
  71                         buf := scanner.Bytes()
  72                         if len(buf) == 0 || buf[0] == '>' {
  73                                 todo <- jobT{seqlabel, fasta}
  74                                 seqlabel, fasta = string(buf[1:]), nil
  75                                 log.Debugf("%s %s reading fasta", filelabel, seqlabel)
  76                         } else {
  77                                 fasta = append(fasta, bytes.ToLower(buf)...)
  78                         }
  79                 }
  80                 todo <- jobT{seqlabel, fasta}
  81         }()
  82         type foundtag struct {
  83                 pos    int
  84                 tagid  tagID
  85                 taglen int
  86         }
  87         found := make([]foundtag, 2000000)
  88         path := make([]tileLibRef, 2000000)
  89         totalFoundTags := 0
  90         totalPathLen := 0
  91         skippedSequences := 0
  92         for job := range todo {
  93                 if len(job.fasta) == 0 {
  94                         continue
  95                 } else if strings.Contains(job.label, "_") {
  96                         skippedSequences++
  97                         continue
  98                 }
  99                 log.Debugf("%s %s tiling", filelabel, job.label)
 100
 101                 found = found[:0]
 102                 tilelib.taglib.FindAll(job.fasta, func(tagid tagID, pos, taglen int) {
 103                         found = append(found, foundtag{pos: pos, tagid: tagid, taglen: taglen})
 104                 })
 105                 totalFoundTags += len(found)
 106
 107                 path = path[:0]
 108                 last := foundtag{tagid: -1}
 109                 for i, f := range found {
 110                         log.Tracef("%s %s found[%d] == %#v", filelabel, job.label, i, f)
 111                         if tilelib.skipOOO {
 112                                 if f.tagid < last.tagid+1 {
 113                                         log.Debugf("%s %s skipped out-of-order tag %d (found at %d) because it appears after tag %d (found at %d)", filelabel, job.label, f.tagid, f.pos, last.tagid, last.pos)
 114                                         continue
 115                                 }
 116                                 if f.tagid > last.tagid+1 && // accepting this tag would mean skipping some tags
 117                                         i+1 < len(found) && // there is a "next" found tag after this one
 118                                         found[i+1].tagid > last.tagid && // next found tag is usable (we haven't already passed it in accepted sequence)
 119                                         found[i+1].tagid <= f.tagid { // next found tag is expected before this one (so we can't use both)
 120                                         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)
 121                                         continue
 122                                 }
 123                         }
 124                         if last.taglen > 0 {
 125                                 path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:f.pos+f.taglen]))
 126                         }
 127                         last = f
 128                 }
 129                 if last.taglen > 0 {
 130                         path = append(path, tilelib.getRef(last.tagid, job.fasta[last.pos:]))
 131                 }
 132
 133                 pathcopy := make([]tileLibRef, len(path))
 134                 copy(pathcopy, path)
 135                 ret[job.label] = pathcopy
 136                 log.Debugf("%s %s tiled with path len %d, skipped %d", filelabel, job.label, len(path), len(found)-len(path))
 137                 totalPathLen += len(path)
 138         }
 139         log.Printf("%s tiled with total path len %d in %d sequences (skipped %d sequences with '_' in name, skipped %d out-of-order tags)", filelabel, totalPathLen, len(ret), skippedSequences, totalFoundTags-totalPathLen)
 140         return ret, scanner.Err()
 141 }
 142
 143 func (tilelib *tileLibrary) Len() int {
 144         tilelib.mtx.Lock()
 145         defer tilelib.mtx.Unlock()
 146         return tilelib.variants
 147 }
 148
 149 // Return a tileLibRef for a tile with the given tag and sequence,
 150 // adding the sequence to the library if needed.
 151 func (tilelib *tileLibrary) getRef(tag tagID, seq []byte) tileLibRef {
 152         for _, b := range seq {
 153                 if b != 'a' && b != 'c' && b != 'g' && b != 't' {
 154                         // return "tile not found" if seq has any
 155                         // no-calls
 156                         return tileLibRef{tag: tag}
 157                 }
 158         }
 159         tilelib.mtx.Lock()
 160         defer tilelib.mtx.Unlock()
 161         // if tilelib.seq == nil {
 162         //      tilelib.seq = map[[blake2b.Size]byte][]byte{}
 163         // }
 164         if tilelib.variant == nil {
 165                 tilelib.variant = make([][][blake2b.Size256]byte, tilelib.taglib.Len())
 166         }
 167         seqhash := blake2b.Sum256(seq)
 168         for i, varhash := range tilelib.variant[tag] {
 169                 if varhash == seqhash {
 170                         return tileLibRef{tag: tag, variant: tileVariantID(i + 1)}
 171                 }
 172         }
 173         tilelib.variants++
 174         tilelib.variant[tag] = append(tilelib.variant[tag], seqhash)
 175         // tilelib.seq[seqhash] = append([]byte(nil), seq...)
 176         return tileLibRef{tag: tag, variant: tileVariantID(len(tilelib.variant[tag]))}
 177 }