first commit

LICENCE

@@ -0,0 +1,24 @@
+opyright (c) 2013, Jeongbin Park
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list
+of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation and/or other
+materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -0,0 +1,4 @@
+Cas-Analyzer
+==
+
+Updated soon

core/compile_core.sh

@@ -0,0 +1,4 @@
+cp jbfilereader/jbfilereader.coffee .
+coffee --bare --compile jbfilereader.coffee
+coffee --bare --compile fastq-join.coffee
+coffee --bare --compile miseq-analyzer.coffee

core/fastq-join-sync.coffee

@@ -0,0 +1,220 @@
+###
+fastq-join.coffee
+(Based on Fastq-join 1.01 by Expression Analysis / Erik Aronesty)
+
+Copyright (c) 2015 Jeongbin Park
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+###
+
+dev = 0
+joins = []
+#un1s = []
+#un2s = []
+
+class _line
+    constructor: ->
+        this.s = ''
+        this.n = 0
+
+class _fq
+    constructor: ->
+        this.id = new _line
+        this.seq = new _line
+        this.com = new _line
+        this.qual = new _line
+
+comp = (l) ->
+    for i in [0...l.length] by 1
+        if l[i] == 'A'
+            l[i] = 'T'
+        else if l[i] == 'T'
+            l[i] = 'A'
+        else if l[i] == 'G'
+            l[i] = 'C'
+        else if l[i] == 'C'
+            l[i] = 'G'
+        else if l[i] == 'a'
+            l[i] = 't'
+        else if l[i] == 't'
+            l[i] = 'a'
+        else if l[i] == 'g'
+            l[i] = 'c'
+        else if l[i] == 'c'
+            l[i] = 'g'
+    return l
+
+revcomp = (fq) ->
+    fq.seq.s = comp(fq.seq.s).reverse() # Non-unicode aware!
+    fq.qual.s = fq.qual.s.reverse() # Again, non-unicode aware!
+    return fq
+
+min = (a, b) ->
+    if a > b
+        return b
+    else
+        return a
+
+max = (a, b) ->
+    if a < b
+        return b
+    else
+        return a
+
+hd = (a, s, b, n) ->
+    d = 0
+    i = 0
+    while n > 0
+        if a[s+i] != b[i]
+            d++
+        n--
+        i++
+    return d+n
+
+# Third mate file is not supported yet
+run_fastq_join = (files, donecallback, pgcallback, chunkcallback, joinsonly = false, mino = 6, pctdiff = 8) ->
+    dev = 0
+    joincnt = 0
+    tlen = 0
+    tlensq = 0
+    nline = [0, 0]
+    joins = []
+    un1s = []
+    un2s = []
+    fq = [new _fq, new _fq]
+    nrec = 0
+    prevfpos = 0
+    steprec = 50
+
+    readers = [0, 0]
+    for nfin in [0..1] by 1
+        entries = files[nfin].name.split('.')
+        if entries[entries.length-1] == 'gz'
+            gzipped = 1
+        readers[nfin] = new jbfilereader(files[nfin], gzipped)
+
+    read_line = (nfin, l, opt) ->
+        readers[nfin].readline( (line) -> 
+            if readers[0].eof or line == ""
+                readers[1].readline( (line2) ->
+                    if readers[1].eof or line2 == ""
+                        post_loop()
+                    else
+                        self.postMessage({msgtype: 1, error: "# of rows in mate file doesn't match primary file!"})
+                )
+            else if readers[1].eof and !readers[0].eof
+                self.postMessage({msgtype: 1, error: "# of rows in mate file doesn't match primary file!"})
+            else
+                l.s = line.split("") # To array, because strings are immutable, note that this is not unicode aware!
+                l.n = l.s.length
+                opt++
+                read_fq(opt)
+        )
+        return
+
+    post_loop = ->
+        chunkcallback(joins)
+        pgcallback(100)
+        donecallback()
+        return
+
+    read_fq = (opt) ->
+        for nfin in [0..1] by 1
+            if opt == 0+nfin*4
+                read_line(nfin, fq[nfin].id, opt)
+                return
+            else if opt == 1+nfin*4
+                read_line(nfin, fq[nfin].seq, opt)
+                return
+            else if opt == 2+nfin*4
+                read_line(nfin, fq[nfin].com, opt)
+                return
+            else if opt == 3+nfin*4
+                read_line(nfin, fq[nfin].qual, opt)
+                return
+        if opt == 8
+            #if fq[nfin].id.s[0] == '>'
+            #    alert('Input is FASTA!')
+            #    return 1
+            if (fq[0].id.n == 0 or (fq[0].id.n != 0 and fq[0].id.s[0] != '@')) or
+               (fq[1].id.n == 0 or (fq[1].id.n != 0 and fq[1].id.s[0] != '@'))
+                self.postMessage({msgtype: 1, error: 'Input file is not FASTQ!'})
+                return 1
+            main_loop()
+            return
+        return
+
+    main_loop = ->
+        nrec++
+        rc = revcomp(fq[1])
+        maxo = min(fq[0].seq.n, rc.seq.n)
+        bestscore = 2147483647 # INT_MAX of C
+        besto = -1
+        for i in [mino..maxo] by 1
+            mind = (pctdiff * i) // 100
+            d = hd(fq[0].seq.s, fq[0].seq.n-i, rc.seq.s, i)
+            if d <= mind
+                score = (1000*(d*d+1)) // i
+                if (score < bestscore)
+                    bestscore = score
+                    besto = i
+        hasex = 0
+        olen = besto - hasex
+        if besto > 0
+            joincnt++
+
+            tlen += olen
+            tlensq += olen**2
+
+            #joins.push(fq[0].id.s.join("") + "\n")
+            for i in [0...besto] by 1
+                li = fq[0].seq.n-besto+i
+                ri = i
+                if fq[0].seq.s[li] == rc.seq.s[ri]
+                    fq[0].qual.s[li] = String.fromCharCode(max(fq[0].qual.s[li].charCodeAt(0), rc.qual.s[ri].charCodeAt(0)))
+                else
+                    if fq[0].qual.s[li].charCodeAt(0) > rc.qual.s[ri].charCodeAt(0)
+                        fq[0].qual.s[li] = String.fromCharCode(33+min(fq[0].qual.s[li].charCodeAt(0),max(fq[0].qual.s[li].charCodeAt(0)-rc.qual.s[ri].charCodeAt(0),3)))
+                    else
+                        fq[0].seq.s[li] = rc.seq.s[ri]
+                        fq[0].qual.s[li] = String.fromCharCode(33+min(rc.qual.s[ri].charCodeAt(0),max(rc.qual.s[ri].charCodeAt(0)-fq[0].qual.s[li].charCodeAt(0),3)))
+            joins.push(fq[0].seq.s.join("") + rc.seq.s[besto..].join("") + "\n")
+            #joins.push(fq[0].com.s.join("") + "\n")
+            #joins.push(fq[0].qual.s.join("") + rc.qual.s[besto..].join("") + "\n")
+        #else if !joinsonly
+        #    un1s.push(fq[0].id.s.join("") + "\n")
+        #    un1s.push(fq[0].seq.s.join("") + "\n")
+        #    un1s.push(fq[0].com.s.join("") + "\n")
+        #    un1s.push(fq[0].qual.s.join("") + "\n")
+        #    un2s.push(fq[1].id.s.join("") + "\n")
+        #    un2s.push(fq[1].seq.s.join("") + "\n")
+        #    un2s.push(fq[1].com.s.join("") + "\n")
+        #    un2s.push(fq[1].qual.s.join("") + "\n")
+        if nrec %% steprec == 0
+            if prevfpos != readers[0].fpos
+                pgcallback(readers[0].fpos*100/files[0].size)
+                chunkcallback(joins)
+                joins = []
+                prevfpos = readers[0].fpos
+            setTimeout( ( -> read_fq(0)), 0)
+        else
+            read_fq(0)
+        return
+    setTimeout( ( -> read_fq(0)), 0)
+    return