├── tests
    ├── nim.cfg
    ├── test_transcript.nim
    └── test_translate.nim
├── package.json
├── .gitignore
├── CHANGES.md
├── seqcover.nimble
├── src
    ├── seqcoverpkg
    │   ├── seqcover_html.nim
    │   ├── typeenum.nim
    │   ├── background.nim
    │   ├── seqcover.html
    │   ├── transcript.js
    │   ├── transcript.nim
    │   ├── utils.nim
    │   └── seqcover.js
    └── seqcover.nim
├── LICENSE
├── .github
    └── workflows
    │   └── main.yaml
├── README.md
└── test
    ├── transcript-test.js
    └── data.js


/tests/nim.cfg:
--------------------------------------------------------------------------------
1 | path = "$projectPath/../src"
2 | 


--------------------------------------------------------------------------------
/package.json:
--------------------------------------------------------------------------------
1 | {
2 | "scripts": {
3 |   "test": "mocha"
4 | }
5 | }
6 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | o.js
 2 | tests/test_translate
 3 | tests/test_transcript
 4 | src/seqcover
 5 | src/seqcoverpkg/background
 6 | src/seqcoverpkg/transcript
 7 | src/seqcoverpkg/typeenum
 8 | src/seqcoverpkg/utils
 9 | seqcover_report.html
10 | 
11 | 


--------------------------------------------------------------------------------
/CHANGES.md:
--------------------------------------------------------------------------------
 1 | v0.0.5
 2 | ======
 3 | + handle more chrMT namings
 4 | + allow extending introns
 5 | + fix bug where sample names were converted to dates
 6 | 
 7 | v0.0.4
 8 | ============
 9 | + plot aesthetics (#23)
10 | + add sub-command `seqcover save-transcripts`
11 | 
12 | v0.0.3
13 | ======
14 | + fix bug for overlapping exons (#21)
15 | + prefer "22" over "22_KI270879v1_alt"
16 | + fix bug for no exons (#22 and thanks @oyvindbusk for reporting this and other issues)
17 | + report e.g. "exon 1 / 6" when hovering.
18 | + show genomic position next to gene
19 | 


--------------------------------------------------------------------------------
/seqcover.nimble:
--------------------------------------------------------------------------------
 1 | import os
 2 | 
 3 | version       = "0.0.5"
 4 | author        = "Brent Pedersen"
 5 | description   = "find depth support for DUP/DEL/CNV calls that use PE/SR"
 6 | license       = "MIT"
 7 | 
 8 | 
 9 | # Dependencies
10 | 
11 | requires "https://github.com/brentp/d4-nim >= 0.0.1", "argparse >= 0.7.0 & < 1.0", "binaryheap", "hts"
12 | srcDir = "src"
13 | installExt = @["nim"]
14 | 
15 | bin = @["seqcover"]
16 | 
17 | 
18 | skipDirs = @["tests"]
19 | 
20 | 
21 | #task test, "run the tests":
22 | #  exec "nim c --lineDir:on --debuginfo -r --threads:on tests/all"
23 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/seqcover_html.nim:
--------------------------------------------------------------------------------
 1 | import strutils
 2 | import ./utils
 3 | import json
 4 | 
 5 | const TOKEN = "SEQCOVER_JAVASCRIPT"
 6 | 
 7 | const html = staticRead("./seqcover.html")
 8 | const seqcover_js = staticRead("./seqcover.js")
 9 | const transcript_js = staticRead("./transcript.js")
10 | 
11 | 
12 | proc write_html*(path:string, plot_data:seq[GenePlotData]) =
13 | 
14 | 
15 |   var pieces = html.split(TOKEN)
16 | 
17 |   pieces = @[pieces[0], "<script>", transcript_js, seqcover_js, "XX", "</script>", pieces[1]]
18 | 
19 |   var fh:File
20 |   if not fh.open(path, fmWrite):
21 |     quit "could not open file:" & path
22 |   discard
23 | 
24 |   #pieces[3] = $(%(plot_data))
25 |   for p in pieces:
26 |     if p == "XX":
27 |       fh.write("var plot_data = ")
28 |       fh.write_line($(%(plot_data)))
29 |     else:
30 |       fh.write_line(p)
31 | 
32 |   fh.close
33 | 
34 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | MIT License
 2 | 
 3 | Copyright (c) 2020 Brent Pedersen, Joe Brown, Mike Cormier
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/typeenum.nim:
--------------------------------------------------------------------------------
 1 | import d4
 2 | import hts
 3 | import strutils
 4 | 
 5 | type CoverType* {.pure.} = enum
 6 |   D4
 7 |   BED
 8 | 
 9 | type Cover* = object
10 |   case kind:CoverType
11 |   of CoverType.D4:
12 |     d4*: D4
13 |   of CoverType.BED:
14 |     bed*: BGZI
15 | 
16 | type iv = object
17 |   start:int32
18 |   stop:int32
19 |   depth:int32
20 | 
21 | proc open_dp*(path:string): Cover =
22 |   if path.endsWith(".d4"):
23 |     result = Cover(kind:CoverType.D4)
24 |     doAssert result.d4.open(path), "seqcover: error opening d4 file:" & path
25 |   else:
26 |     result = Cover(kind:CoverType.BED)
27 |     doAssert result.bed.open(path), "seqcover: error opening bed.gz file:" & path
28 | 
29 | proc close*(c:var Cover) =
30 |   case c.kind
31 |   of CoverType.D4:
32 |     c.d4.close()
33 |   of CoverType.BED:
34 |     discard c.bed.close
35 | 
36 | proc parse(s:string): iv {.noInit.} =
37 |   var i = -1
38 |   for tok in s.split('\t', maxsplit=4):
39 |     i.inc
40 |     if i == 0: continue
41 |     if i == 1:
42 |       result.start = parseInt(tok).int32
43 |     if i == 2:
44 |       result.stop = parseInt(tok).int32
45 |     if i == 3:
46 |       result.depth = parseInt(tok).int32
47 |       break
48 | 
49 | proc values*(c:var Cover, chrom:string, start:uint32, values: var seq[int32]) =
50 |   case c.kind
51 |   of CoverType.D4:
52 |     c.d4.values(chrom, start, values)
53 |   of CoverType.BED:
54 |     zeroMem(values[0].addr, values.len * sizeof(int32))
55 |     for s in c.bed.query(chrom, start.int64, start.int64 + values.len.int64):
56 |       let iv = s.parse
57 |       for p in max(0, iv.start - start.int32)..<(min(values.len.int32, iv.stop)):
58 |         values[p] = iv.depth
59 | 
60 | proc chromosomes*(c:var Cover, fai:Fai): OrderedTableRef[string, uint32] =
61 |   case c.kind
62 |   of CoverType.D4:
63 |     result = c.d4.chromosomes
64 |   of CoverType.BED:
65 |     result = newOrderedTable[string, uint32]()
66 |     if fai == nil:
67 |       raise newException(OSError, "--fasta index required when .bed.gz files are given")
68 |     for i in 0..<fai.len:
69 |       var cname = fai[i]
70 |       result[cname] = fai.chrom_len(cname).uint32
71 | 
72 | when isMainModule:
73 |   import os
74 | 
75 |   var x = paramStr(1)
76 | 
77 |   let y = if x == "bed":
78 |     Cover(kind:CoverType.BED)
79 |   else:
80 |     Cover(kind:CoverType.D4)
81 | 
82 |   echo y
83 | 


--------------------------------------------------------------------------------
/.github/workflows/main.yaml:
--------------------------------------------------------------------------------
 1 | name: tests
 2 | 
 3 | # Controls when the action will run. Triggers the workflow on push or pull request
 4 | # events but only for the master branch
 5 | on:
 6 |   push:
 7 |     branches: [ master, dev]
 8 |   pull_request:
 9 |     branches: [ master ]
10 | 
11 | 
12 | 
13 | 
14 | # A workflow run is made up of one or more jobs that can run sequentially or in parallel
15 | jobs:
16 |   # This workflow contains a single job called "build"
17 |   build:
18 |     # The type of runner that the job will run on
19 |     runs-on: ubuntu-latest
20 |     strategy:
21 |       matrix:
22 |         version:
23 |         - 1.2.8
24 | 
25 |     # Steps represent a sequence of tasks that will be executed as part of the job
26 |     steps:
27 |     - name: ACTIONS_ALLOW_UNSECURE_COMMANDS
28 |       id: ACTIONS_ALLOW_UNSECURE_COMMANDS
29 |       run: echo 'ACTIONS_ALLOW_UNSECURE_COMMANDS=true' >> $GITHUB_ENV
30 |     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
31 |     - uses: actions/checkout@v2
32 |     - uses: actions/setup-node@v2-beta
33 |       with:
34 |         node-version: '12'
35 | 
36 |     - uses: iffy/install-nim@v3
37 |       with:
38 |         version: ${{ matrix.version }}
39 | 
40 |     - uses: actions-rs/toolchain@v1
41 |       with:
42 |         toolchain: stable
43 |     - uses: actions-rs/cargo@v1
44 | 
45 |     - name : install htslib
46 |       run: |
47 |         sudo apt-get update
48 |         sudo apt-get install git llvm curl wget libcurl4-openssl-dev autoconf
49 |         wget https://github.com/samtools/htslib/archive/1.11.tar.gz
50 |         tar xzf 1.11.tar.gz
51 |         cd htslib-1.11/
52 |         autoheader && autoconf && ./configure --disable-libcurl
53 |         sudo make -j4 install
54 | 
55 |     #export HTSLIB=system
56 |     #sudo ln -s /usr/bin/gcc /usr/bin/musl-gcc
57 |     # rustup target add x86_64-unknown-linux-musl
58 |     - name : install d4
59 |       run: |
60 |         git clone https://github.com/38/d4-format
61 |         cd d4-format
62 |         cargo build --release --all #--target=x86_64-unknown-linux-musl
63 |         ls target/release
64 |         sudo cp target/release/libd4binding.* /usr/local/lib
65 |         sudo cp ./d4binding/include/d4.h /usr/local/include/
66 | 
67 |     # Runs a single command using the runners shell
68 |     - name: test nim stuff
69 |       run: |
70 |         export LD_LIBRARY_PATH=/usr/local/lib/
71 |         nimble build -y
72 |         nimble test
73 | 
74 |     # Runs a set of commands using the runners shell
75 |     - name: test javascript stuff
76 |       run: |
77 |         npm install mocha
78 |         npm test
79 | 
80 | 
81 | 


--------------------------------------------------------------------------------
/tests/test_transcript.nim:
--------------------------------------------------------------------------------
 1 | import unittest
 2 | import seqcoverpkg/transcript
 3 | import seqcoverpkg/utils
 4 | import hts/fai
 5 | import seqcoverpkg/typeenum
 6 | import tables
 7 | import json
 8 | 
 9 | suite "transcript suite":
10 |   test "simple plot exon coords":
11 | 
12 |     #exon_plot_coords*(tr:Transcript, dps:TableRef[string, D4], extend:uint32=10): tuple[x:seq[uint32], depths: TableRef[string, seq[int32]], g: seq[uint32]] =
13 |     var tr = Transcript(txStart: 10, txEnd: 100, cdsStart: 15, cdsEnd: 95, position: @[[15, 25], [85, 91]])
14 |     var dps = newTable[string, Cover]()
15 |     var bgs = newTable[string, Cover]()
16 |     var fa:Fai
17 |     var res = tr.exon_plot_coords(dps, bgs, 10, 10, fa)
18 |     check res.x.len == res.g.len
19 |     for name, depth in res.depths.pairs:
20 |       check res.x.len == depth.len
21 | 
22 |   test "translate":
23 | 
24 |     var u = Transcript(txstart:55, cdsstart:85, position: @[[85, 96], [122, 137]], cdsend: 137, txend: 152)
25 |     var o = u #Transcript(txstart:55, cdsstart:85, position: @[[85, 96], [122, 137]], cdsend: 137, txend: 152)
26 | 
27 | 
28 |     var t = u.translate(o, 10, 100)
29 |     check t.position == @[[40, 51], [77, 92]]
30 | 
31 |     check t.txstart == 10
32 |     check t.txend == 107
33 | 
34 |     o = Transcript(txstart:55, cdsstart:85, position: @[[89, 94], [132, 137]], cdsend: 137, txend: 152)
35 |     t = u.translate(o, 10, 100)
36 |     check t.position ==   @[[44, 49], [87, 92]]
37 |     check t.txstart == 10
38 |     check t.txend == 107
39 | 
40 |   test "spanning exon":
41 |     var g = Gene(symbol: "HNRNPA1", description: "heterogeneous nuclear ribonucleoprotein A1", transcripts: @[
42 |     Transcript(cdsstart: 74591, cdsend: 78097, chr: "12", position: @[[78041, 78101], [78332, 80871]], strand: 1, transcript: "NM_002136", txstart: 74509, txend: 80871),
43 |     Transcript(cdsstart: 80871, cdsend: 80871, chr: "12", position: @[[77595, 77751], [78041, 78101], [80445, 80516],  [80736, 80871]], strand: 1, transcript: "NR_135167", txstart: 74509, txend: 80871)
44 |     #Transcript(cdsstart: 80871, cdsend: 80871, chr: "12", position: @[[77595, 77751], [78041, 78101], [80445, 80516], [80736, 80871]], strand: 1, transcript: "NR_135167", txstart: 74509, txend: 80871)
45 |     ])
46 | 
47 |     var u = g.transcripts.union
48 | 
49 |     var tr = u.translate(g.transcripts[0], 10, 100)
50 | 
51 |     check tr == Transcript(cdsstart: 92, cdsend: 3428, chr: "12", position: @[[3372, 3432], [3552, 6091]], strand: 1, transcript: "NM_002136", txstart: 10, txend: 6091)
52 | 
53 |   test "no exons":
54 | 
55 |     var g = Gene(symbol: "CCDC39", description: "coiled-coil domain containing 39", transcripts: @[Transcript(cdsstart: 180614920, cdsend: 180679380, chr: "3", position: @[[180614007, 180615077], [180616280, 180616363], [180616515, 180616695], [180616825, 180616966], [180619258, 180619365], [180619810, 180619970], [180631468, 180631592], [180641992, 180642201], [180644119, 180644257], [180647078, 180647243], [180648164, 180648359], [180651400, 180651533], [180652162, 180652266], [180654761, 180654953], [180659451, 180659580], [180659676, 180659769], [180660569, 180660728], [180661860, 180662007], [180663866, 180663986], [180679290, 180679489]], strand: -1, transcript: "NM_181426", txstart: 180614007, txend: 180679489)])
56 |     var u = g.transcripts.union
57 | 
58 |     for t in g.transcripts:
59 |       var v = u.translate(t, 10, 100)
60 |       check v.`chr` == g.transcripts[0].`chr`
61 | 
62 | 


--------------------------------------------------------------------------------
/tests/test_translate.nim:
--------------------------------------------------------------------------------
 1 | import unittest
 2 | import json
 3 | import tables
 4 | import hts/fai
 5 | import seqcoverpkg/transcript
 6 | import seqcoverpkg/typeenum
 7 | import seqcoverpkg/utils
 8 | 
 9 | var extend = 10
10 | var max_gap = 100
11 | 
12 | suite "translate suite":
13 |   test "bug case":
14 |     var u = Transcript(cdsstart: 21505, cdsend: 31930, chr: "X", position: @[[19450, 21772], [24664, 24871], [25019, 25152]], strand: -1, transcript: "union", txstart: 19450, txend: 35554)
15 |     var t = Transcript(cdsstart: 21505, cdsend: 31930, chr: "X", position: @[[19450, 21772], [24664, 24871], [25019, 25152]], strand: -1, transcript: "NM_002641", txstart: 19450, txend: 35554)
16 |     var tr = u.translate(t, extend.uint32, max_gap.uint32)
17 |     check tr.position == @[[10, 2332], [2452, 2659], [2779, 2912]]
18 | 
19 | 
20 |   test "offset first exon":
21 |     var u = Transcript(cdsstart: 21505, cdsend: 31930, chr: "X", position: @[[19450, 21772], [24664, 24871], [25019, 25152], [25913, 26046], [31215, 31992], [35500, 35554]], strand: -1, transcript: "union", txstart: 19450, txend: 35554)
22 | 
23 |     var l = u.find_offset(u.position[0][1], extend, max_gap)
24 |     check l == 2322
25 |     var r = u.find_offset(u.position[1][0], extend, max_gap)
26 |     check r == l + 2 * extend + max_gap
27 | 
28 |   test "weird kcnq2":
29 | 
30 |     var o = Transcript(cdsstart: 33744, cdsend: 33900, chr: "20", position: @[[33677, 33903]], strand: -1, transcript: "NM_172109", txstart: 33677, txend: 72655)
31 |     var u = Transcript(cdsstart: 06643, cdsend: 72463, chr: "20", position:
32 |        @[[207, 7375],
33 |          [8412, 8536],
34 |          [13449, 13581],
35 |          [14087, 14193],
36 |          [14902, 15126],
37 |          [19618, 19672],
38 |          [24176, 24206],
39 |          [28366, 28435],
40 |          [31339, 31369],
41 |          [33677, 33903],
42 |          [38624, 38720],
43 |          [39597, 39708],
44 |          [42405, 42531],
45 |          [44658, 44834], [45237, 45364], [46746, 46837], [72167, 72655]], strand: -1, transcript: "union", txstart: 207, txend: 72655)
46 | 
47 |     var ot = u.translate(o, extend.uint32, max_gap.uint32)
48 |     var ut = u.translate(u, extend.uint32, max_gap.uint32)
49 | 
50 |     check ot.position[0] == ut.position[9]
51 |     check ot.position[0][1] == ot.cdsend + 3
52 |     check ot.position[0][0] - ot.cdsstart == o.position[0][0] - o.cdsstart
53 | 
54 |   test "translation doesn't change exon length and adjusts intron length correctly":
55 | 
56 |     var u = Transcript(cdsstart: 9551, cdsend: 26688, chr: "20", position: @[[8675, 9033], [9497, 9617], [13168, 13226], [13257, 13383], [13984, 14058], [15280, 15312], [18516, 18632]], strand: 1, transcript: "union", txstart: 8675, txend: 27449)
57 | 
58 |     var ut = u.translate(u, extend.uint32, max_gap.uint32)
59 | 
60 |     for i, e in ut.position:
61 |       check e[1] - e[0] == u.position[i][1] - u.position[i][0]
62 | 
63 |       if i > 0:
64 |         var l = ut.position[i-1]
65 |         var r = e
66 |         check r[0] - l[1] == min(2 * extend + max_gap, u.position[i][0] - u.position[i - 1][1])
67 | 
68 |   test "translation matches depth coords":
69 |     var u = Transcript(cdsstart: 9551, cdsend: 26688, chr: "20", position: @[[8675, 9033], [9497, 9617], [13168, 13226], [13257, 13383], [13984, 14058], [15280, 15312], [18516, 18632]], strand: 1, transcript: "union", txstart: 8675, txend: 27449)
70 |     var ut = u.translate(u, extend.uint32, max_gap.uint32)
71 | 
72 |     var g = Gene(transcripts: @[u])
73 |     var fa:Fai
74 | 
75 |     #stderr.write_line u
76 |     #stderr.write_line ut
77 |     var t = newTable[string, Cover]()
78 |     var b = newTable[string, Cover]()
79 |     #var gpt = ut.exon_plot_coords(t, extend.uint32, max_gap.uint32)
80 |     var gpt = @[g.plot_data(t, b, extend.uint32, max_gap.uint32, fa)]
81 |     check gpt[0].transcripts[0].transcript == "union"
82 |     #echo $(%gpt)
83 | 
84 | 
85 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | [![Build Status](https://github.com/brentp/seqcover/workflows/tests/badge.svg?branch=master)](https://github.com/brentp/seqcover/actions)
 2 | 
 3 | seqcover is a tool for viewing and evaluating depth-of-coverage with the following aims. It should:
 4 | 
 5 |  - show a global view where it's easy to see problematic samples and genes
 6 |  - offer an interactive gene-wise view to explore coverage characteristics of individual samples within each gene
 7 |  - **not** require a server (single html page)
 8 |  - be responsive for up to 20 samples * 200 genes and be useful for a single-sample [see how we do this](#how-it-works)
 9 |  - highlight outlier samples based on any number of (summarized) background samples
10 | 
11 | It is available as a static linux binary.
12 | 
13 | ## Example Output
14 | 
15 | https://brentp.github.io/seqcover/
16 | 
17 | ### Usage
18 | 
19 | `seqcover` can accept per-base coverage files in [d4](https://github.com/38/d4-format) or bgzipped bedgaph format. Either of
20 | these formats can be output by [mosdepth](https://github.com/brentp/mosdepth) but `d4` format will be much faster.
21 | 
22 | Generate a report:
23 | ```
24 | # generate per base depth files if you don't have them. can also parallize this...
25 | mkdir -p samples/
26 | for b in *.bam; do
27 |   n=$(basename $b .bam)
28 |   mosdepth -x -t 4 samples/$n $b
29 | done
30 | seqcover report --genes PIGA,KCNQ2,ARX,DNM1,SLC25A22,CDKL5,GABRA1,CAD,MDH2,SCN1B,CNPY3,CPLX1,NEB,HNRNPA1,CCDC39,AIFM1,CHCHD10 \
31 | 		 --background seqcover/seqcover_p5.d4 \
32 | 		 --fasta $fasta samples/*.bed.gz \
33 | 		 -r my_genes_report.html
34 | ```
35 | 
36 | Generate a background level:
37 | ```
38 | seqcover generate-background --percentile 5 -f $fasta -o seqcover/ d4s/HG00*.d4
39 | ```
40 | Once generated, this can be sent to `seqcover report` to give a metric for each sample
41 | of the number of bases below the 5th percentile of the backgrounds, which is a nice quality-control
42 | value. 
43 | 
44 | These backgounds should be specific to the samples of interest, so if you are using exome data
45 | the backgrounds should be generated from samples from the same exome capture kit (and prefereably
46 | from the same sequencing center).
47 | 
48 | Generate a transcript file:
49 | ```
50 | # generate a transcripts file that can be used as input to the report option with the --transcripts-file option
51 | # this is useful if running on servers with restricted internet access
52 | 
53 | seqcover save-transcripts --genes PIGA,KCNQ2,ARX,DNM1,SLC25A22,CDKL5,GABRA1,CAD,MDH2,SCN1B,CNPY3,CPLX1,NEB,HNRNPA1,CCDC39,AIFM1,CHCHD10 \
54 | 		 --output-path transcripts.json \
55 | 		 --hg19
56 | 
57 | # use the file as input to report with the --transcripts-file option
58 | seqcover report --genes PIGA,KCNQ2,ARX,DNM1,SLC25A22,CDKL5,GABRA1,CAD,MDH2,SCN1B,CNPY3,CPLX1,NEB,HNRNPA1,CCDC39,AIFM1,CHCHD10 \
59 | 		 --background seqcover/seqcover_p5.d4 \
60 | 		 --fasta $fasta samples/*.bed.gz \
61 | 		 -r my_genes_report.html \
62 | 		 --transcripts-file transcripts.json
63 | ```
64 | 
65 | ## How It Works
66 | 
67 | ### Performance
68 | 
69 | `seqcover` is a command-line tool that extracts depth information for requested genes and generates a terse report.
70 | This is possible because we **excise introns** which are often the majority of bases in the gene. The user can specify to extend
71 | into the intron beyond the default of 10 bases. As that extension increases, `seqcover` will show more and more of the intronic space.
72 | But it's possible to display 20 samples * 100 genes in html because we remove introns and use webGL (via plotly) for rendering.
73 | 
74 | ### Outliers
75 | 
76 | An outlier is data-dependent. Every exome will appear as an outlier given a set of genomes and every 30X genome will
77 | appear as an outlier given a set of 60X genomes. Therefore, `seqcover` let's the user extract a depth percentile from a set
78 | of chosen backgrounds. For example, the default is to extract the 5th percentile from a set of samples. This percentile can then
79 | be shown in the report and used as a metric: **how many bases in each sample are below the 5th percentile**.
80 | 
81 | 


--------------------------------------------------------------------------------
/test/transcript-test.js:
--------------------------------------------------------------------------------
  1 | var assert = require('assert');
  2 | let data = require("./data.js")
  3 | let transcript = require("../src/seqcoverpkg/transcript.js")
  4 | 
  5 | let tr = new transcript.Transcript(data.tr_data)
  6 | 
  7 | describe('Transcript', function () {
  8 |   describe('cdsstart', function () {
  9 |     it('should equal cdsstart', function () {
 10 |         assert.equal(tr.cdsstart, data.tr_data.cdsstart)
 11 |     });
 12 |   });
 13 | 
 14 |   describe('transcript tests', function () {
 15 |       it('inferred genomic coords should match actual', function () {
 16 |           let parts = tr.parts()
 17 |           parts.forEach((p, i) => {
 18 |               //  u:Transcript(cdsstart: 15321505, cdsend: 15335554, chr: "X", position: @[[15319450, 15321772], [15324664, 15324871], [15325019, 15325152], [15325913, 15326046], [15331215, 15331992], [15335500, 15335554]], strand: -1, transcript: "union", txstart: 15319450, txend: 15335554)
 19 |               let s = p.hoverinfo(data.xs, data.gs)
 20 |               if(i == 0){
 21 |                   assert.equal(s.start, 15319450)
 22 |                   assert.equal(s.stop, 15321505)
 23 |               } else if (i == parts.length) {
 24 |                   assert.equal(s.start, 15335554)
 25 |                   assert.equal(s.stop, 15335554)
 26 | 
 27 |               } else {
 28 | 
 29 |                   if(s.type == transcript.FeatureType.CDS) {
 30 |                       assert(s.start >= 15321505, s.start.toString() + " " + i.toString())
 31 |                       assert(s.stop <= 15335554, s.stop.toString() + " " + i.toString())
 32 |                   }
 33 |                   if(s.type == transcript.FeatureType.EXON) {
 34 |                       assert(s.start >= 15319450, s.start.toString() + " " + i.toString())
 35 |                       assert(s.stop <= 15335554, s.stop.toString() + " " + i.toString())
 36 |                   }
 37 |               }
 38 | 
 39 |           })
 40 | 
 41 |       });
 42 |       it('traces should work', function () {
 43 |           let traces = tr.traces(0, data.xs, data.gs)
 44 |           assert.equal(traces.length, 3)
 45 |           assert.equal(traces[0].x.length, 2, "only need start and end")
 46 |           assert.equal(traces[0].y[0], 0, "y offset should be 0")
 47 |           assert.equal(traces[0].genome_x.length, 2, "only need start and end")
 48 | 
 49 |           assert.equal(traces[0].name, tr.name)
 50 | 
 51 | 
 52 |           var trace = traces[traces.length - 1]; // get a CDS trace
 53 |           assert(trace.text[0].startsWith("exon 6 / 6"))
 54 |           assert(trace.text[trace.text.length - 1].startsWith("exon 1 / 6"))
 55 | 
 56 | 
 57 |       })
 58 | 
 59 |       it('stats returns expected values', function() {
 60 |           var depths = {
 61 |               "sampleA": Array(60).fill(10),
 62 |               "sampleB": Array(60).fill(0),
 63 |           }
 64 |           var background_depths = {
 65 |               "p10": Array(60).fill(5),
 66 |               "p90": Array(60).fill(90),
 67 |           }
 68 | 
 69 |           background_depths.p10[4] = 500;
 70 |           //{ sampleA: { lt_background: 0, low: 0, mean: 10, median: 10 },
 71 |           //  sampleB: { lt_background: 20, low: 20, mean: 0, median: 0 } }
 72 | 
 73 |           let stats = tr.stats([{start:20, stop:40}], depths, background_depths, 5);
 74 |           assert.equal(stats.sampleA.median, 10)
 75 |           assert.equal(stats.sampleB.median, 0)
 76 | 
 77 |           assert.equal(stats.sampleA.low, 0)
 78 |           assert.equal(stats.sampleB.low, 20)
 79 | 
 80 |           assert.equal(stats.sampleA["lt-background"], 0)
 81 |           assert.equal(stats.sampleB["lt-background"], 20)
 82 | 
 83 | 
 84 | 
 85 |       })
 86 |   });
 87 |   describe('zscore tests', function () {
 88 |       it('should return correct zscore', function (){
 89 |           var vals = [2, 4, 6,7,8,9]
 90 |           var expected = [-1.6803361 , -0.84016805,  0.        ,  0.42008403,  0.84016805,
 91 |         1.26025208]
 92 | 
 93 |           let zs = transcript.z_transform(vals)
 94 |           for(var i=0; i <vals.length; i++){
 95 |               assert(Math.abs(zs[i] - expected[i]) < 0.0001, "expected:" + expected[i] + " obs:" + zs[i])
 96 |           }
 97 | 
 98 |       })
 99 | 
100 |   })
101 | });
102 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/background.nim:
--------------------------------------------------------------------------------
  1 | import argparse
  2 | import strformat
  3 | import os
  4 | import d4
  5 | import hts
  6 | import tables
  7 | import ./utils
  8 | import ./typeenum
  9 | import algorithm
 10 | import times
 11 | 
 12 | 
 13 | proc summarize_block(d4s: var seq[Cover], chrom:string, start:uint32, stop:uint32, percentiles: seq[float], outs:var seq[D4], vals: var seq[seq[int32]], out_vals: var seq[seq[int32]]) =
 14 |   # extract data for each sample from start to stop, calculate per-base
 15 |   # percentiles and write to outs.
 16 |   # vals and out_vals just let us avoid allocations
 17 |   for i in 0..vals.high:
 18 |     if vals[i].len != int(stop) - int(start):
 19 |       vals[i].setLen(int(stop) - int(start))
 20 |       echo "changing length:", vals[i].len, " start:", start, " stop:", stop
 21 | 
 22 |     d4s[i].values(chrom, start, vals[i])
 23 | 
 24 |   if out_vals[0].len != vals[0].len:
 25 |     for i in 0..<out_vals.len:
 26 |       out_vals[i].setLen(vals[0].len)
 27 | 
 28 |   let n_samples = d4s.len.float
 29 | 
 30 |   # we just keep here which sample we'll stop at when getting to each
 31 |   # percentile
 32 |   var int_sample = newSeqUninitialized[uint32](percentiles.len)
 33 |   for i, p in percentiles:
 34 |     int_sample[i] = uint32(max(0, int(n_samples * p - 0.5)))
 35 | 
 36 |   var H : array[1024, uint32]
 37 |   for i in 0..vals[0].high:
 38 |     zeroMem(H[0].addr.pointer, sizeof(H[0]) * H.len)
 39 |     # fill the histogram
 40 |     for j in 0..d4s.high:
 41 |       H[min(H.high, vals[j][i])].inc
 42 | 
 43 |     var cutoff_index = 0
 44 |     var isamp = int_sample[cutoff_index]
 45 | 
 46 |     # extract the percentiles from the histogram.
 47 |     # this is faster than doing binary search for each value as we iterate over
 48 |     # array only once and most values are near the left end.
 49 |     var high_set = false
 50 |     block cumsum_block:
 51 |       var cumsum:uint32
 52 |       for k, n in H:
 53 |         cumsum += n
 54 |         # use while in case we had a chunk of samples that span some percentiles.
 55 |         while cumsum > isamp:
 56 |           out_vals[cutoff_index][i] = k
 57 |           cutoff_index += 1
 58 |           if cutoff_index > int_sample.high:
 59 |             high_set = true
 60 |             break cumsum_block
 61 |           isamp = int_sample[cutoff_index]
 62 |     # if we ran out of samples, just set it to highest value.
 63 |     if not high_set:
 64 |       out_vals[^1][i] = H.len.int32
 65 | 
 66 |   for i in 0..out_vals.high:
 67 |     outs[i].write(chrom, start, out_vals[i])
 68 | 
 69 | 
 70 | proc generate_backgrounds(dps: var seq[Cover], output_dir: string, percentiles: seq[int], fai:Fai) =
 71 |   let block_size = 1_000_000'u32
 72 |   let info = dps[0].chromosomes(fai)
 73 |   var chroms = newSeqOfCap[tuple[name:string, length:int]](info.len)
 74 |   for k, v in info: chroms.add((k, v.int))
 75 | 
 76 |   discard outputDir.existsOrCreateDir
 77 |   var percentiles = sorted(percentiles)
 78 | 
 79 |   var pctiles = newSeq[float](percentiles.len)
 80 |   for i, p in percentiles:
 81 |     pctiles[i] = p.float / 100.0
 82 | 
 83 |   var outs = newSeq[D4](percentiles.len)
 84 |   for i in 0..<percentiles.len:
 85 |     doAssert outs[i].open(&"{outputDir}/seqcover_p{percentiles[i]}.d4", mode="w")
 86 |     outs[i].set_chromosomes(chroms)
 87 |   var vals = newSeq[seq[int32]](dps.len)
 88 |   for v in vals.mitems: v.setLen(block_size)
 89 | 
 90 |   var out_vals = newSeq[seq[int32]](outs.len)
 91 |   for i in 0..outs.high:
 92 |     out_vals[i] = newSeqUninitialized[int32](vals[0].len)
 93 | 
 94 | 
 95 |   for (chrom, length) in info.pairs:
 96 |     dps.check_same_lengths(chrom, length, fai)
 97 |     let t0 = cpuTime()
 98 |     var j = 0
 99 |     for i in countup(0'u32, length, block_size):
100 |       if j mod 10 == 0 and i > 0:
101 |         echo &"{chrom}:{min(i + blocksize, length)} time:{cpuTime() - t0:.2f} bases/second: {min(i + blocksize, length).float / (cpuTime() - t0):.0f}"
102 |       dps.summarize_block(chrom, i, min(i + block_size, length), pctiles, outs, vals, out_vals)
103 |       j.inc
104 | 
105 |   for o in outs.mitems:
106 |     o.close()
107 | 
108 | proc generate_background_main*() =
109 |   let p = newParser("seqcover generate-background"):
110 |     option("-o", "--output-dir", help="directory for output", default="seqcover-backgrounds")
111 |     option("-f", "--fasta", help="indexed fasta required for bed.gz files")
112 |     option("-p", "--percentile", default="5", help="percentile to extract from backgrounds")
113 |     arg("samples", nargs= -1, help="per-base bed.gz files or d4 files or a glob of either to generate background")
114 | 
115 |   var argv = commandLineParams()
116 |   if len(argv) > 0 and argv[0] == "generate-background":
117 |     argv = argv[1..argv.high]
118 |   if len(argv) == 0:
119 |     argv.add("--help")
120 | 
121 |   var fai:Fai
122 | 
123 |   var opts = p.parse(argv)
124 |   if opts.help:
125 |     quit 0
126 | 
127 |   let percentiles = @[parseInt(opts.percentile)]
128 | 
129 |   if opts.fasta != "":
130 |     doAssert fai.open(opts.fasta), "[seqcover] error opening fasta file:" & opts.fasta
131 | 
132 |   let paths = get_glob_samples(opts.samples)
133 |   echo paths
134 |   if paths.len < 4:
135 |     quit "[seqcover] need at least 4 samples to generate a background"
136 |   if paths.len < 10:
137 |     stderr.write_line "[seqcover] warning: creating background with fewer than 10 samples might give unexpected results"
138 | 
139 |   var covers = read_dps(paths)
140 |   covers.generate_backgrounds(opts.output_dir, percentiles, fai)
141 | 
142 |   echo opts
143 | 
144 | 
145 | when isMainModule:
146 |   generate_background_main()
147 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/seqcover.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html>
  3 | 
  4 | <head>
  5 |     <meta charset="utf-8" />
  6 |     <meta name="author" content="Brent Pedersen" />
  7 |     <meta name="author" content="Mike Cormier" />
  8 |     <meta name="author" content="Joe Brown" />
  9 | 
 10 |     <link href="https://fonts.googleapis.com/css2?family=Raleway:wght@900&display=swap" rel="stylesheet">
 11 |     <link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.14.0/css/all.min.css" rel="stylesheet">
 12 |     <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css" rel="stylesheet">
 13 | 
 14 |     <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
 15 |     <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.5.2/js/bootstrap.bundle.min.js"></script>
 16 |     <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
 17 | 
 18 |     <style>
 19 |         body {
 20 |             height: 100%;
 21 |             margin: 0px;
 22 |             padding: 0px;
 23 |         }
 24 | 
 25 |         .container-fluid {
 26 |             font-size: .875rem;
 27 |         }
 28 | 
 29 |         .brand {
 30 |             font-size: 1.2rem;
 31 |             font-family: 'Raleway', sans-serif;
 32 |         }
 33 | 
 34 |         .meta-info {
 35 |             font-weight: 800;
 36 |         }
 37 | 
 38 |         .yaxislayer-above {
 39 |             cursor: pointer;
 40 |             pointer-events: all;
 41 |         }
 42 | 
 43 |         .xaxislayer-above {
 44 |             cursor: pointer;
 45 |             pointer-events: all;
 46 |         }
 47 | 
 48 |         .selected_label {
 49 |             font-weight: 800;
 50 |             text-decoration: underline;
 51 |         }
 52 | 
 53 |         .unselected_label {
 54 |             font-weight: 400;
 55 |         }
 56 | 
 57 |         .unselected_label:hover {
 58 |             text-decoration: underline;
 59 |             font-weight: 700;
 60 |         }
 61 | 
 62 |         .popover{
 63 |             max-width: 40%;
 64 |         }
 65 | 
 66 |         .fa-question-circle {
 67 |             padding-left: .30em;
 68 |         }
 69 | 
 70 |     </style>
 71 | </head>
 72 | 
 73 | <body>
 74 |     <!-- nav -->
 75 |     <div class="row bg-dark mx-0 p-1">
 76 |         <div class="col-sm-3 col-md-2 col-lg-2 pl-1"><a class="brand text-white
 77 |                 text-decoration-none" href="https://github.com/brentp/seqcover">seqcover</a>
 78 |         </div>
 79 |         <div class="col-sm-9 col-md-10 col-lg-10 d-flex align-items-center justify-content-end" id="meta-header">
 80 |             <div class="font-weight-light text-light">
 81 |                 <span class="meta-info" id="sample-count">__</span> samples;
 82 |                 <span class="meta-info" id="gene-count">__</span> genes
 83 |                 <!-- lower percentile threshold -->
 84 |                 <!-- genome build -->
 85 |             </div>
 86 |         </div>
 87 |     </div>
 88 |     <main role="main" class="container-fluid">
 89 | 
 90 |         <div class="row pt-2 bg-light">
 91 |             <div class="col-md-6 col-lg-6">
 92 |                 <h5>Coverage summary <span id="navigation-popover" data-toggle="popover"><i class="far fa-question-circle fa-sm"></i></span></h5>
 93 |             </div>
 94 |             <div class="col-sm-12 col-lg-6 d-flex align-items-center">
 95 |                 <div class="col-auto my-1">
 96 |                     <div class="form-check form-check-inline">
 97 |                         <input class="form-check-input z_scale" type="checkbox" value="" id="z_scale_samples">
 98 |                         <label class="form-check-label pr-3" for="z_scale_samples" title="Scale values within each sample" data-toggle="tooltip">
 99 |                             Sample Scaling
100 |                         </label>
101 |                         <input class="form-check-input z_scale" type="checkbox" value="" id="z_scale_genes">
102 |                         <label class="form-check-label" for="z_scale_genes" title="Scale values within each gene" data-toggle="tooltip">
103 |                             Gene Scaling
104 |                         </label>
105 |                     </div>
106 |                 </div>
107 |                 <div class="input-group input-group-sm">
108 |                     <div class="input-group-prepend">
109 |                         <span class="input-group-text">Summary metric</span>
110 |                     </div>
111 |                     <select class="form-control" id="metric_select">
112 |                         <option value="cds_mean">Mean CDS depth</option>
113 |                         <option value="transcript_mean">Mean transcript depth</option>
114 |                         <option value="cds_low">CDS Bases below <span id="cds-bases-below">7</span></option>
115 |                         <option id="cds_lt_bg" value="cds_lt-background">CDS Bases below lower background percentile</option>
116 |                     </select>
117 |                 </div>
118 |             </div>
119 |             <div class="col-12">
120 |                 <div id="heatmap_plot" style="overflow-x:scroll;"></div>
121 |             </div>
122 |         </div>
123 | 
124 |         <div class="row pt-2 mb-4">
125 |             <div class="col-md-5 col-lg-7">
126 |                 <h5>Depth per base:
127 |                     <span id="header-selected-gene"></span>
128 |                     <span id="depth-plot-popover" data-toggle="popover"><i class="far fa-question-circle fa-sm"></i></span>
129 |                 </h5>
130 |             </div>
131 |             <div class="col-12"><div id="gene_plot"></div></div>
132 |         </div>
133 |     </main>
134 | </body>
135 | 
136 | SEQCOVER_JAVASCRIPT
137 | 
138 | </html>
139 | 


--------------------------------------------------------------------------------
/src/seqcover.nim:
--------------------------------------------------------------------------------
  1 | import argparse
  2 | import strformat
  3 | import tables
  4 | import sequtils
  5 | import algorithm
  6 | import json
  7 | import hts/fai
  8 | import tables
  9 | import os
 10 | import d4
 11 | import ./seqcoverpkg/utils
 12 | import ./seqcoverpkg/transcript
 13 | import ./seqcoverpkg/background
 14 | import ./seqcoverpkg/seqcover_html
 15 | 
 16 | proc get_pctile(path:string): int =
 17 |   let parts = path.split("_")
 18 |   if parts.len == 0:
 19 |     raise newException(OSError, &"[seqcover] path {path} doesn't have expected naming. use files generated by seqcover background")
 20 |   let last = parts[^1].split(".")[0]
 21 |   if last[0] != 'p':
 22 |     raise newException(OSError, &"[seqcover] path {path} doesn't have expected naming. use files generated by seqcover background")
 23 |   return parseInt(last[1..last.high])
 24 | 
 25 | 
 26 | proc read_backgrounds(dir:string): TableRef[int, D4] =
 27 |   if dir == "": return
 28 |   result = newTable[int, D4]()
 29 |   if not dirExists(dir):
 30 |     raise newException(OSError, "[seqcover] directory {dir} not found")
 31 |   for path in (&"{dir}/seqcover_*.d4").walkFiles:
 32 |     var d:D4
 33 |     if not d.open(path):
 34 |       quit &"error reading {path}"
 35 |     result[get_pctile(path)] = d
 36 | 
 37 |   if result.len == 0:
 38 |     var msg = &"[seqcover] no background d4 files found in {dir}"
 39 |     raise newException(OSError, msg)
 40 |   stderr.write_line &"[seqcover] read {result.len} background percentiles"
 41 | 
 42 | proc report_main() =
 43 |   let p = newParser("seqcover report"):
 44 |     option("--background", default="", help="optional path to d4 file created with seqcover background")
 45 |     option("--genes", default="", help="comma-delimited list of genes for initial report")
 46 |     option("--fasta", default="", help="required path to fai indexed fasta file")
 47 |     option("-r", "--report-path", default="seqcover_report.html", help="path to html report to be written")
 48 |     option("-t", "--transcripts-file", default="", help="path to transcript file for use if no internet connection (can be made with the save-transcripts option)")
 49 |     option("--extend-intron", default="10",help="The number of nucleotides to extend into the intron")
 50 |     flag("--hg19", help="coordinates are in hg19/GRCh37 (default is hg38).")
 51 |     arg("samples", nargs= -1, help="d4 files, bed files or a glob of d4 or bed files")
 52 | 
 53 |   var argv = commandLineParams()
 54 |   if len(argv) > 0 and argv[0] == "report":
 55 |     argv = argv[1..argv.high]
 56 |   if len(argv) == 0:
 57 |     argv.add("--help")
 58 | 
 59 |   var opts = p.parse(argv)
 60 |   if opts.help:
 61 |     quit 0
 62 |   if opts.fasta == "":
 63 |     echo p.help
 64 |     stderr.write_line "[seqcover] --fasta argument is required."
 65 |     quit 1
 66 | 
 67 |   var fa:Fai
 68 |   if not fa.open(opts.fasta):
 69 |     quit "[seqcover] couldn't open fasta file"
 70 | 
 71 |   var extend_intron = parseInt(opts.extend_intron) 
 72 |   if extend_intron < 0:
 73 |     echo p.help
 74 |     stderr.write_line "--extend-intron must be >= 0"
 75 |     quit 1
 76 | 
 77 |   var backgrounds = read_d4s_to_table(@[opts.background])
 78 |   var sample_d4s = read_d4s_to_table(opts.samples)
 79 |   stderr.write_line &"[seqcover] read {sample_d4s.len} sample coverage files"
 80 |   var gpt: seq[GenePlotData]
 81 |   
 82 |   var genes = get_genes(opts.genes.split(","), hg19=opts.hg19, transcript_file=opts.transcripts_file)
 83 |       
 84 |   for gene in genes:
 85 |       var u = gene.transcripts.union
 86 |       echo &"{u.chr}\t{u.txstart - 500}\t{u.txend + 500}"
 87 |       var pd = gene.plot_data(sample_d4s, backgrounds, extend=extend_intron.uint32, fai=fa, max_gap=50)
 88 |       gpt.add(pd)
 89 | 
 90 |   gpt.sort(proc(a, b: GenePlotData): int = cmp(a.symbol, b.symbol))
 91 | 
 92 |   write_html(opts.report_path, gpt)
 93 |   stderr.write_line &"[seqcover] wrote report to:{opts.report_path}"
 94 | 
 95 | proc save_transcripts_main() =
 96 |   let p = newParser("seqcover save-transcripts"):
 97 |     option("--genes", default="", help="comma-delimited list of genes for initial report")
 98 |     option("-o", "--output-path", default="transcripts.json", help="path to transcript file to be written")
 99 |     flag("--hg19", help="coordinates are in hg19/GRCh37 (default is hg38).")
100 |   
101 |   var argv = commandLineParams()
102 |   if len(argv) > 0 and argv[0] == "save-transcripts":
103 |     argv = argv[1..argv.high]
104 |   if len(argv) == 0:
105 |     argv.add("--help")
106 | 
107 |   var opts = p.parse(argv)
108 |   if opts.help:
109 |     quit 0
110 |   
111 |   let g = get_genes(opts.genes.split(","), hg19=opts.hg19)
112 |   writeFile(opts.output_path, $(pretty(%*g)))
113 |   
114 | 
115 | proc main() =
116 |   type pair = object
117 |     fn: proc()
118 |     description: string
119 | 
120 |   var dispatcher = {
121 |     "generate-background": pair(fn:generate_background_main, description: "generate background file(s) from a set of samples"),
122 |     "report": pair(fn:report_main, description: "create an HTML report from a set of sample coverage files"),
123 |     "save-transcripts": pair(fn:save_transcripts_main, description: "create a json-file with transcripts that can be used as input for report if you cannot access mygene.info")
124 |   }.toOrderedTable
125 | 
126 |   var args = commandLineParams()
127 |   if len(args) > 0 and args[0] in dispatcher:
128 |     dispatcher[args[0]].fn()
129 |     return
130 | 
131 |   if len(args) == 0 or args[0] in ["-h", "--help"]:
132 |     stdout.write_line "Commands: "
133 |     for k, v in dispatcher:
134 |       echo &"  {k:<19}:   {v.description}"
135 |   else:
136 |     echo &"unknown program '{args[0]}'"
137 |     quit ""
138 | 
139 | 
140 | when isMainModule:
141 |   main()
142 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/transcript.js:
--------------------------------------------------------------------------------
  1 | "use strict";
  2 | 
  3 | function binary_search(A, v) {
  4 |     var result = 0;
  5 |     var j = A.length
  6 |     while (j != 0) {
  7 |         let step = j >> 1
  8 |         let pos = result + step;
  9 |         if (A[pos] < v) {
 10 |             result = pos + 1
 11 |             j -= step + 1
 12 |         } else {
 13 |             j = step
 14 |         }
 15 | 
 16 |     }
 17 |     return result
 18 | }
 19 | 
 20 | // enum
 21 | const FeatureType = Object.freeze({
 22 |     EXON: "exon",
 23 |     CDS: "CDS",
 24 |     UTR: "UTR",
 25 |     TRANSCRIPT: "transcript"
 26 | })
 27 | 
 28 | const aesthetics = {
 29 |     TRANSCRIPT_COLOR: "rgba(65, 65, 65, 0.6)",
 30 |     TRANSCRIPT_WIDTH: 4,
 31 |     EXON_COLOR: "rgba(105,105,105, 0.6)",
 32 |     EXON_WIDTH: 19,
 33 |     CDS_COLOR: 'rgb(195, 155, 155)',
 34 |     CDS_WIDTH: 12,
 35 | }
 36 | 
 37 | class Feature {
 38 |     constructor(start, stop, type, transcript) {
 39 |         this.start = start
 40 |         this.stop = stop
 41 |         this.type = type
 42 |         this.transcript = transcript
 43 |     }
 44 |     get coding() {
 45 |         return this.type == FeatureType.CDS
 46 |     }
 47 | 
 48 | 
 49 |     hoverinfo(xs, gs) {
 50 |         // xs is plot coordinates, gs is genome coordinates
 51 |         // get genomic coordinate by finding index of plot-coord
 52 |         // and then looking it up in genomic array
 53 |         var start = gs[binary_search(xs, this.start)]
 54 |         var stop = gs[binary_search(xs, this.stop)]
 55 |         return {
 56 |             "transcript": this.transcript.data.transcript,
 57 |             "strand": this.transcript.strand,
 58 |             "start": start,
 59 |             "stop": stop,
 60 |             "type": this.type.toString()
 61 |         }
 62 |     }
 63 | }
 64 | 
 65 | class Transcript {
 66 |     constructor(data) {
 67 |         this.data = data
 68 |     }
 69 |     get cdsstart() {
 70 |         return this.data.cdsstart
 71 |     }
 72 |     get cdsend() {
 73 |         return this.data.cdsend
 74 |     }
 75 |     get chr() {
 76 |         return this.data.chr
 77 |     }
 78 | 
 79 |     get exons() {
 80 |         return this.data.position
 81 |     }
 82 | 
 83 |     get position() {
 84 |         return this.data.position
 85 |     }
 86 |     get strand() {
 87 |         return this.data.strand == -1 ? "-" : "+"
 88 |     }
 89 | 
 90 |     get name() {
 91 |         return this.data.transcript
 92 |     }
 93 | 
 94 |     get txstart() {
 95 |         return this.data.txstart
 96 |     }
 97 |     get txend() {
 98 |         return this.data.txend
 99 |     }
100 | 
101 |     parts() {
102 |         // return CDS,exon,UTR in an array. exon and CDS are potentially
103 |         // (often) duplicated.
104 |         var that = this
105 |         var result = []
106 |         result.push(new Feature(this.data.txstart, this.data.cdsstart, FeatureType.UTR, that))
107 |         this.data.position.forEach((exon, i) => {
108 |             result.push(new Feature(exon[0], exon[1], FeatureType.EXON, that))
109 |             if (exon[1] < this.data.cdsstart || exon[0] > this.data.cdsend) {
110 |                 // continue
111 |             } else {
112 |                 result.push(new Feature(Math.max(this.data.cdsstart, exon[0]), Math.min(this.data.cdsend, exon[1]), FeatureType.CDS, that))
113 |             }
114 | 
115 |         })
116 |         result.push(new Feature(this.data.cdsend, this.data.txend, FeatureType.UTR, that))
117 |         return result.filter(f => f.stop - f.start > 0)
118 | 
119 |     }
120 | 
121 |     overlaps(position) {
122 |         // return parts() that overlap with this position
123 |         let that = this
124 |         var result = []
125 |         if (position < this.txstart || position > this.txend) { return result }
126 |         if (position < this.cdsstart) { result.push(new Feature(this.data.txstart, this.data.cdsstart, FeatureType.UTR, that)) }
127 |         this.data.position.forEach((exon, i) => {
128 |             if (exon[0] > position || exon[1] < position) {
129 |                 return
130 |             }
131 |             result.push(new Feature(exon[0], exon[1], FeatureType.EXON, that))
132 |             if (exon[1] < that.data.cdsstart || exon[0] > that.data.cdsend) {
133 |                 // continue
134 |             } else {
135 |                 var f = new Feature(Math.max(this.data.cdsstart, exon[0]), Math.min(this.data.cdsend, exon[1]), FeatureType.CDS, that)
136 |                 if (f.stop - f.start > 0) {
137 |                     result.push(f)
138 |                 }
139 |             }
140 |         })
141 |         if (position >= this.cdsend) {
142 |             result.push(new Feature(this.data.cdsend, this.data.txend, FeatureType.UTR, that))
143 |         }
144 |         return result;
145 |     }
146 | 
147 |     traces(y_offset, xs, gs) {
148 | 
149 |         function get_genomic_coord(x) {
150 |             return isNaN(x) ? NaN : gs[binary_search(xs, x)]
151 |         }
152 | 
153 |         var transcript_trace = {
154 |             name: this.data.transcript, x: [this.data.txstart, this.data.txend], y: [y_offset, y_offset],
155 |             type: "scatter", mode: "lines", showlegend: false,
156 |             hoverinfo: "none",
157 |             line: { color: aesthetics.TRANSCRIPT_COLOR, width: aesthetics.TRANSCRIPT_WIDTH }
158 |         }
159 | 
160 |         let parts = this.parts()
161 | 
162 |         var exon_trace = {
163 |             name: this.data.transcript + " exons", x: [], y: [], text:[],
164 |             type: "scatter", mode: "lines", showlegend: false,
165 |             hoverinfo: "text",
166 |             line: { color: aesthetics.EXON_COLOR, width: aesthetics.EXON_WIDTH }
167 |         }
168 |         let exons = parts.filter(p => p.type == FeatureType.EXON)
169 |         exons.forEach((e, i) => {
170 |             if ((exon_trace.x.length) > 0) {
171 |                 exon_trace.x.push(NaN)
172 |                 exon_trace.y.push(y_offset)
173 |                 exon_trace.text.push(undefined)
174 |             }
175 |             var iex = this.data.strand == -1 ? (exons.length - i) : (i + 1)
176 | 
177 |             let txt = `exon ${iex} / ${exons.length}`;
178 |             exon_trace.text.push(txt, txt)
179 |             exon_trace.x.push(e.start, e.stop)
180 |             exon_trace.y.push(y_offset, y_offset)
181 |         })
182 | 
183 |         var cds_trace = {
184 |             name: this.data.transcript + " CDS", x: [], y: [], text:[],
185 |             type: "scatter", mode: "lines", showlegend: false,
186 |             hoverinfo: "text",
187 |             hovermode:"closest-x",
188 |             line: { color: aesthetics.CDS_COLOR, width: aesthetics.CDS_WIDTH }
189 |         }
190 |         parts.filter(p => p.type == FeatureType.CDS).forEach(c => {
191 |             if ((cds_trace.x.length) > 0) {
192 |                 cds_trace.x.push(NaN)
193 |                 cds_trace.y.push(y_offset)
194 |                 cds_trace.text.push(undefined)
195 |             }
196 |             // index back into exon array even for CDS hover
197 |             var ei = 0
198 |             for(var e of exons) {
199 |                 ei += 1
200 |                 if(e.start <= c.start && e.stop >= c.stop) {
201 |                     break;
202 |                 }
203 |             }
204 | 
205 |             var iex = this.data.strand == -1 ? (exons.length - ei + 1) : (ei + 1)
206 |             let txt = `exon ${iex} / ${exons.length} (CDS)`
207 |             cds_trace.text.push(txt, txt)
208 |             cds_trace.x.push(c.start, c.stop)
209 |             cds_trace.y.push(y_offset, y_offset)
210 |         })
211 | 
212 |         var result = [transcript_trace, exon_trace, cds_trace]
213 |         result.forEach(trace => {
214 |             trace.genome_x = trace.x.map(x => get_genomic_coord(x))
215 |         })
216 |         return result
217 | 
218 |     }
219 | 
220 |     stats(xranges, depths, background_depths, low_depth_cutoff) {
221 |         // NOTE xranges is in reduced, plot coords, not genomic coords and it
222 |         // has form [{start: 23, stop: 44}, ...]
223 |         var result = {}
224 |         var background_low;
225 |         // handle missing or undefined backgrounds
226 |         if (background_depths != undefined && background_depths != {} && background_depths != []) {
227 |             // background depths might hvae string keys like p5, p95. so we sort to
228 |             // get the lowest value.
229 |             var lo_key = Object.keys(background_depths).sort((a, b) => {
230 |                 return parseInt(a.replace(/^\D+/g, "")) - parseInt(b.replace(/^\D+/g, ""))
231 |             })[0]
232 |             background_low = background_depths[lo_key] //.slice(xstart, xstop)
233 |         }
234 |         var H = Array(16384);
235 |         for (var sample in depths) {
236 |             var S = 0; var N = 0; var lo = 0; var bg_lo = 0;
237 |             H.fill(0);
238 |             var dps = depths[sample];
239 | 
240 |             for (var rng of xranges) {
241 |                 for (var i = rng.start; i < rng.stop; i++) {
242 |                     let d = dps[i]
243 |                     if (d < 0 || isNaN(d)) { continue; }
244 |                     lo += (d < low_depth_cutoff);
245 |                     if (background_low != undefined) {
246 |                         bg_lo += d < background_low[i];
247 |                     }
248 |                     H[Math.min(d, H.length - 1)] += 1;
249 |                     S += d;
250 |                     N += 1
251 |                 }
252 |             }
253 |             result[sample] = { "low": lo, "lt-background": bg_lo }
254 |             var mid = N * 0.5; // 50% of data below this number of samples.
255 |             var j = 0
256 |             var nc = H[j]
257 |             while (nc < mid) {
258 |                 j += 1
259 |                 nc += H[j]
260 |             }
261 |             result[sample]["mean"] = S / N
262 |             result[sample]["median"] = j
263 |         }
264 |         return result;
265 |     }
266 | }
267 | 
268 | function z_transform(data) {
269 |     // TODO: use 1-pass for mean, sd
270 |     var s = 0
271 |     for(let d of data) s += d;
272 |     let mean = s / data.length;
273 | 
274 |     var sd = 0;
275 |     for(let d of data) { sd += Math.pow(d - mean, 2); }
276 |     sd = Math.sqrt(sd / data.length);
277 | 
278 |     return data.map(d => (d - mean) / sd)
279 | }
280 | 
281 | try {
282 |     // node.js stuff to allow testing
283 |     exports.Transcript = Transcript
284 |     exports.FeatureType = FeatureType
285 |     exports.z_transform = z_transform
286 | 
287 | 
288 |     if (require.main === module) {
289 |         // xs and gs data for testing.
290 |         let data = require("./test/data.js")
291 |         let tr = new Transcript(data.tr_data)
292 | 
293 |         tr.parts().forEach(p => console.log(p.hoverinfo(data.xs, data.gs)))
294 | 
295 |         console.log(tr.traces(0))
296 | 
297 |     }
298 | } catch (e) {
299 |     // browser
300 | }
301 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/transcript.nim:
--------------------------------------------------------------------------------
  1 | import binaryheap
  2 | import json
  3 | import sequtils
  4 | import strformat
  5 | import strutils
  6 | import d4
  7 | export d4
  8 | import tables
  9 | import ./typeenum
 10 | import hts/fai
 11 | 
 12 | type Transcript* = object
 13 |   cdsstart*: int
 14 |   cdsend*: int
 15 |   `chr`*: string
 16 |   position*: seq[array[2, int]]
 17 |   strand*: int
 18 |   transcript*: string
 19 |   txstart*:int
 20 |   txend*:int
 21 | 
 22 | # see: https://github.com/nim-lang/Nim/issues/15025
 23 | proc `%`*(a:array[2, int]): JsonNode =
 24 |   result = newJArray()
 25 |   result.add(newJint(a[0]))
 26 |   result.add(newJint(a[1]))
 27 | 
 28 | 
 29 | proc `$`*(t:Transcript): string =
 30 |   result = &"Transcript{system.`$`(t)}"
 31 | 
 32 | proc coding*(t:Transcript): bool =
 33 |   result = t.cdsstart != t.cdsend
 34 | 
 35 | type Gene* = object
 36 |   symbol*: string
 37 |   description*: string
 38 |   transcripts*: seq[Transcript]
 39 | 
 40 | proc `$`*(g:Gene): string =
 41 |   result = &"Gene{system.`$`(g)}"
 42 | 
 43 | type plot_coords* = object
 44 |   x*: seq[uint32]
 45 |   depths*: TableRef[string, seq[int32]]
 46 |   background_depths*: TableRef[string, seq[int32]]
 47 |   g*: seq[uint32]
 48 | 
 49 | type GenePlotData* = object
 50 |   plot_coords*: plot_coords
 51 |   symbol*: string
 52 |   description*: string
 53 |   unioned_transcript*: Transcript
 54 |   transcripts*: seq[Transcript]
 55 | 
 56 | proc union*(trs:seq[Transcript]): Transcript =
 57 |   result = trs[0]
 58 |   result.transcript = "union"
 59 |   ## TODO: heap is not needed here. just sort and check i vs i+1
 60 |   var H = newHeap[array[2, int]] do (a, b: array[2, int]) -> int:
 61 |     if a[0] == b[0]: return a[1] - b[1]
 62 |     return a[0] - b[0]
 63 | 
 64 |   for t in trs:
 65 |     if t.`chr` != result.`chr`: continue
 66 |     if t.coding and t.cdsstart < result.cdsstart:
 67 |       result.cdsstart = t.cdsstart
 68 | 
 69 |     if t.coding and t.cdsend > result.cdsend:
 70 |       result.cdsend = t.cdsend
 71 | 
 72 |     if t.txstart < result.txstart:
 73 |       result.txstart = t.txstart
 74 |     if t.txend > result.txend:
 75 |       result.txend = t.txend
 76 |     for ex in t.position:
 77 |       H.push(ex)
 78 | 
 79 |   result.position = newSeqOfCap[array[2, int]](4)
 80 |   if H.size == 0: return
 81 |   var A = H.pop
 82 |   var B: array[2, int]
 83 |   while H.size > 0:
 84 |     B = H.pop
 85 | 
 86 |     if A == B: continue
 87 | 
 88 |     if B[0] > A[1]:
 89 |       result.position.add(A)
 90 |       A = B
 91 |     else:
 92 |       A[1] = max(A[1], B[1])
 93 | 
 94 |   if result.position.len == 0 or result.position[^1] != A:
 95 |     if result.position.len > 0 and result.position[^1][0] <= A[0] and result.position[^1][1] >= A[1]: return
 96 |     # final interval needs to be merged/extended
 97 |     if result.position.len > 0 and result.position[^1][1] >= A[0]:
 98 |       result.position[^1][1] = max(A[1], result.position[^1][1])
 99 |     else:
100 |       result.position.add(A)
101 | 
102 | proc find_offset*(u:Transcript, pos:int, extend:int, max_gap:int): int =
103 |   doAssert pos >= u.txstart and pos <= u.txend, &"error can't translate position {pos} outside of unioned transcript ({u.txstart}, {u.txend})"
104 |   if u.position.len == 0 or pos < u.position[0][0]:
105 |     return pos - u.txstart
106 | 
107 |   result = u.position[0][0] - u.txstart
108 | 
109 |   for i, exon in u.position:
110 |     if exon[0] > pos: break
111 | 
112 |     # add previous intron
113 |     if i > 0:
114 |       let intron = min(2 * extend + max_gap, exon[0] - u.position[i - 1][1])
115 |       result += intron
116 | 
117 |     # add full size of this exon
118 |     if exon[1] <= pos:
119 |       let exon_bases = exon[1] - exon[0]
120 |       result += exon_bases
121 |     else:
122 |       # exon contains current position
123 |       result += (pos - exon[0])
124 |       break
125 | 
126 |   if pos > u.position[^1][1]:
127 |     result += pos - u.position[^1][1]
128 | 
129 | 
130 | proc translate*(u:Transcript, o:Transcript, extend:uint32, max_gap:uint32): Transcript =
131 |   ## given a unioned transcript, translate the positions in u to plot
132 |   ## coordinates and genomic coordinates.
133 | 
134 |   var extend = extend.int
135 |   result.transcript = o.transcript
136 |   result.strand = o.strand
137 |   result.`chr` = o.`chr`
138 | 
139 |   # needs some padding on left to go upstream, and use same param as for
140 |   # introns, but here we limit to 1000 bases.
141 |   let left = min(1000, extend.int)
142 | 
143 |   doAssert o.txstart >= u.txstart, $o
144 |   result.txstart = left + u.find_offset(o.txstart, extend.int, max_gap.int)
145 |   result.cdsstart = left + u.find_offset(o.cdsstart, extend.int, max_gap.int)
146 | 
147 |   # todo: this in n^2 (but n is small. iterate over uexons first and calc offsets once)?
148 |   for i, o_exon in o.position:
149 |     let l_off = left + u.find_offset(o_exon[0], extend.int, max_gap.int)
150 |     let r_off = left + u.find_offset(o_exon[1], extend.int, max_gap.int)
151 |     doAssert r_off - l_off == o_exon[1] - o_exon[0], $(r_off, l_off, o_exon, i)
152 | 
153 |     result.position.add([l_off, r_off])
154 | 
155 |   result.cdsend = left + u.find_offset(o.cdsend, extend.int, max_gap.int)
156 |   result.txend = left + u.find_offset(o.txend, extend.int, max_gap.int)
157 | 
158 | 
159 | proc `%`*[T](table: TableRef[string, T]): JsonNode =
160 |   result = json.`%`(table[])
161 | 
162 | proc get_chrom(chrom:string, dp:var Cover, fai:Fai): string =
163 |   ## add or remove "chr" to match chromosome names.
164 |   const MTs = ["MT", "chrM", "chrMT", "M"]
165 |   var chroms = dp.chromosomes(fai)
166 |   if chrom in chroms: return chrom
167 |   if chrom[0] != 'c' and ("chr" & chrom) in chroms:
168 |     result = "chr" & chrom
169 |   elif chrom[0] == 'c' and chrom.len > 3 and chrom[1] == 'h' and chrom[2] == 'r' and chrom[3..chrom.high] in chroms:
170 |     result = chrom[3..chrom.high]
171 |   elif chrom in MTs: # try all the MT chroms.
172 |     for c in MTs:
173 |       if c in chroms:
174 |         return c
175 |   else:
176 |     raise newException(KeyError, "chromosome not found:" & chrom)
177 | 
178 | proc exon_plot_coords*(tr:Transcript, dps:TableRef[string, Cover], backgrounds:TableRef[string, Cover], extend:uint32, max_gap:uint32, fai:Fai, utrs:bool=true): plot_coords =
179 |   ## extract exonic depths for the transcript, extending into intron and
180 |   ## up/downstream. This handles conversion to plot coordinates by removing
181 |   ## introns. g: is the actual genomic coordinates.
182 |   var chrom = tr.`chr`
183 |   var dp: Cover
184 |   for k, v in dps:
185 |     dp = v
186 |     break
187 |   if dps.len > 0: chrom = chrom.get_chrom(dp, fai)
188 |   let left = max(0, tr.txstart - min(1000, extend.int))
189 | 
190 |   result.depths = newTable[string, seq[int32]]()
191 |   result.background_depths = newTable[string, seq[int32]]()
192 | 
193 |   var right = if tr.position.len > 0: tr.position[0][0].int else: tr.txstart
194 |   var stop = tr.txend + min(1000, extend.int)
195 | 
196 |   if utrs:
197 |     result.g = toSeq(left.uint32 ..< right.uint32)
198 |     result.x = toSeq(0'u32 ..< result.g.len.uint32)
199 |     when defined(debug):
200 |       stderr.write_line &"utr: <adding> {result.g[0]} ..< {result.g[^1]}"
201 |     for sample, dp in dps.mpairs:
202 |       var x = newSeqUninitialized[int32](result.g[^1] - result.g[0])
203 |       dp.values(chrom, result.g[0], x)
204 |       result.depths[sample] = x
205 |     for lvl, dp in backgrounds.mpairs:
206 |       var x = newSeqUninitialized[int32](result.g[^1] - result.g[0])
207 |       dp.values(chrom, result.g[0], x)
208 |       result.background_depths[lvl] = x
209 | 
210 |   var lastx:uint32
211 |   var lastg:uint32
212 | 
213 |   for i, p in tr.position:
214 | 
215 |     lastx = result.x[^1] + 1
216 |     lastg = result.g[^1] + 1
217 |     when defined(debug):
218 |       stderr.write_line "\nbefore i:", $i, &" exon:{p} lastx: {lastx} lastg: {lastg}"
219 | 
220 | 
221 |     # maxes and mins prevent going way past end of gene with huge extend value.
222 |     let left = max(lastg, p[0].uint32 - (if i == 0: 0'u32 else: min(p[0].uint32, extend)))
223 |     let right = min(stop.uint32, max(left, p[1].uint32 + (if i == tr.position.high: 0'u32 else: extend)))
224 | 
225 |     let isize = right.int - left.int
226 |     if isize <= 0: continue
227 |     let size = isize.uint32
228 | 
229 |     # insert value for missing data to interrupt plot
230 |     if i > 0:
231 |       let gap = min(max_gap, left - lastg)
232 |       when defined(debug):
233 |         stderr.write_line &"[seqcover] gap: {gap}"
234 |       if gap > 0:
235 |         result.x.add(lastx-1)
236 |         result.g.add(lastg-1)
237 |         lastx += gap
238 |         result.x.add(lastx-1)
239 |         result.g.add(lastg-1)
240 |         for sample, dp in dps.mpairs:
241 |           result.depths[sample].add(@[int32.low, int32.low])
242 |         for lvl, dp in backgrounds.mpairs:
243 |           result.background_depths[lvl].add(@[int32.low, int32.low])
244 | 
245 |       when defined(debug):
246 |         stderr.write_line &"<adding> gap at {lastg} (x:{lastx})"
247 | 
248 |     when defined(debug):
249 |       stderr.write_line "i:", $i, &"exon:{p}", &" <adding> {left} ..< {right}"
250 |     result.g.add(toSeq(left..<right))
251 |     result.x.add(toSeq((lastx..<(lastx + size))))
252 | 
253 |     var x = newSeqUninitialized[int32](right - left)
254 |     for sample, dp in dps.mpairs:
255 |       dp.values(chrom, left, x)
256 |       result.depths[sample].add(x)
257 |     for lvl, dp in backgrounds.mpairs:
258 |       dp.values(chrom, left, x)
259 |       result.background_depths[lvl].add(x)
260 | 
261 |   if utrs:
262 |     lastx = result.x[^1] + 1
263 |     lastg = result.g[^1] + 1
264 |     let left = max(lastg, tr.cdsend.uint32)
265 |     let right = max(left, stop.uint32) # already added extend to stop
266 |     let size = right - left
267 |     if size > 0:
268 |       result.g.add(toSeq(left..<right))
269 |       result.x.add(toSeq((lastx..<(lastx + size))))
270 | 
271 |       var x = newSeqUninitialized[int32](right - left)
272 |       for sample, dp in dps.mpairs:
273 |         dp.values(chrom, left, x)
274 |         result.depths[sample].add(x)
275 |       for lvl, dp in backgrounds.mpairs:
276 |         dp.values(chrom, left, x)
277 |         result.background_depths[lvl].add(x)
278 | 
279 |   doAssert result.x.len == result.g.len
280 | 
281 | 
282 | proc plot_data*(g:Gene, d4s:TableRef[string, Cover], backgrounds:TableRef[string, Cover], extend:uint32, max_gap:uint32, fai:Fai, utrs:bool=true): GenePlotData =
283 |   result.description = g.description
284 |   result.symbol = g.symbol
285 |   result.unioned_transcript = g.transcripts.union
286 | 
287 |   result.plot_coords = result.unioned_transcript.exon_plot_coords(d4s, backgrounds, extend, max_gap, fai, utrs)
288 |   for t in g.transcripts:
289 |     if t.`chr` != result.unioned_transcript.`chr`: continue
290 |     result.transcripts.add(result.unioned_transcript.translate(t, extend=extend, max_gap=max_gap))
291 | 
292 |   result.unioned_transcript = result.unioned_transcript.translate(result.unioned_transcript, extend=extend, max_gap=max_gap)
293 | 
294 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/utils.nim:
--------------------------------------------------------------------------------
  1 | import os
  2 | import d4
  3 | import sets
  4 | import httpclient
  5 | import strformat
  6 | import sequtils
  7 | import hts/fai
  8 | import algorithm
  9 | import json
 10 | import strutils
 11 | import ./typeenum
 12 | import ./transcript
 13 | export transcript
 14 | 
 15 | proc get_gene(gene:string, species:string="human") =
 16 |   var C = newHttpClient()
 17 |   var r = C.getContent(&"http://mygene.info/v3/query?q={gene}&species={species}")
 18 |   let js = parseJson(r)
 19 |   var gene_id = $js["hits"][0]["_id"]
 20 |   gene_id = gene_id.strip(chars={'"'})
 21 | 
 22 |   echo &"http://mygene.info/v3/gene/{gene_id}?fields=name,symbol,exons"
 23 |   var exons = C.getContent(&"http://mygene.info/v3/gene/{gene_id}?fields=name,symbol,exons")
 24 |   echo exons
 25 | 
 26 | proc `$`(j:JsonNode): string =
 27 |   return json.`$`(j).strip(chars={'"'})
 28 | 
 29 | proc cds_max(g:Gene): int =
 30 |   ## find largest cds region across all transcripts in the gene.
 31 |   for tr in g.transcripts:
 32 |     result = max(result,  tr.cdsend - tr.cdsstart)
 33 | 
 34 | proc drop_alt_chroms(g:var Gene) =
 35 |   # prefer, e.g. 22 over 22_KI270879v1_alt
 36 |   var chromset = initHashSet[string]()
 37 |   for t in g.transcripts:
 38 |     chromset.incl($(t.`chr`))
 39 | 
 40 |   if chromset.len <= 1: return
 41 |   var chroms: seq[string] = toSeq(chromset)
 42 |   chroms.sort do (a:string, b:string) -> int:
 43 |     result = len(a) - len(b)
 44 |   var drop: seq[int]
 45 |   for i, t in g.transcripts:
 46 |     if t.`chr` != chroms[0]: drop.add(i)
 47 | 
 48 |   for i in reversed(drop):
 49 |     g.transcripts.delete(i)
 50 | 
 51 | proc drop_dups(genes:var seq[Gene], symbol: string) =
 52 |   # keep gene with highest cound of CDS
 53 | 
 54 |   var idxs = newSeqOfCap[int](4)
 55 |   var sel = newSeq[Gene]() 
 56 | 
 57 |   for i, gene in genes:
 58 |     if gene.symbol == symbol:
 59 |       idxs.add(i)
 60 |     sel.add(gene)
 61 | 
 62 |   idxs.sort do (i, j:int) -> int:
 63 |     var icds = cds_max(sel[i])
 64 |     var jcds = cds_max(sel[j])
 65 |     return icds - jcds
 66 | 
 67 |   # we drop all but the last idx from the genes
 68 |   # so we drop the one we want to keep here.
 69 |   idxs = idxs[0..<idxs.high]
 70 | 
 71 |   for idx in reversed(idxs):
 72 |     genes.delete(idx)
 73 | 
 74 | proc drop_dups(genes: var seq[Gene]) =
 75 |   var c = initCountTable[string]()
 76 |   for g in genes:
 77 |     c.inc(g.symbol)
 78 | 
 79 |   for symbol, cnt in c:
 80 |     if cnt == 1: continue
 81 |     genes.drop_dups(symbol)
 82 | 
 83 | 
 84 | proc fill(res:JsonNode, key:string): JsonNode =
 85 |     return % @[{"txstart": res[key]["start"],
 86 |                       "txend": res[key]["end"],
 87 |                       "cdsstart": res[key]["end"],
 88 |                       "cdsend": res[key]["end"],
 89 |                       #"position": % @[@[res[key]["start"], res[key]["end"]]],
 90 |                       "position": % newSeq[int](),
 91 |                       "chr": res[key]["chr"],
 92 |                       "transcript": %"NA",
 93 |                       "strand": res[key]["strand"]
 94 |                       }]
 95 | 
 96 | proc get_genes*(genes:seq[string], species:string="human", hg19:bool=false, transcript_file:string=""): seq[Gene] =
 97 |   # If exists a transcripts-file - use instead of mygene.info 
 98 |   if transcript_file != "":
 99 |     var query_genes = genes
100 |     for gene in parseFile(transcript_file):
101 |       if to(gene, Gene).symbol in query_genes:
102 |         result.add(to(gene, Gene))
103 |         query_genes.del(query_genes.find(to(gene, Gene).symbol))
104 |     if len(query_genes) > 0:
105 |       echo "The following genes were not in the transcripts-file: "&query_genes.join(", ")
106 | 
107 |   else:
108 |     var C = newHttpClient()
109 |     var data = newMultipartData()
110 |     data["q"] = genes.join(",")
111 |     data["species"] = species
112 |     data["scopes"] = "symbol,entrezgene,ensemblgene,retired"
113 | 
114 |     var r = C.postContent("http://mygene.info/v3/query", multipart=data)
115 |     var js = parseJson(r)
116 |     var ids = newSeq[string]()
117 |     for res in js:
118 |       if "_id" in res:
119 |         ids.add($res["_id"])
120 |       elif "notfound" in res:
121 |         stderr.write_line &"""[seqcover] {res["query"]} not found, skipping"""
122 | 
123 |     data = newMultipartData()
124 |     data["species"] = species
125 |     data["ids"] = ids.join(",")
126 |     if hg19:
127 |       data["fields"] = "name,symbol,exons_hg19,genomic_pos_hg19"
128 |     else:
129 |       data["fields"] = "name,symbol,exons,genomic_pos"
130 | 
131 | 
132 |     for res in C.postContent("http://mygene.info/v3/gene", multipart=data).parseJson:
133 |       var gene = Gene(symbol: $res["symbol"], description: $res["name"])
134 |       var res = res
135 | 
136 |       if hg19:
137 |         if "exons_hg19" notin res:
138 |           if "genomic_pos_hg19" in res:
139 |             res["exons_hg19"] = fill(res, "genomic_pos_hg19")
140 |           else:
141 |             continue
142 |         gene.transcripts = to(res["exons_hg19"], seq[Transcript])
143 |       else:
144 |         if "exons" notin res:
145 |           if "genomic_pos" in res:
146 |             res["exons"] = fill(res, "genomic_pos")
147 |           else:
148 |             continue
149 |         gene.transcripts = to(res["exons"], seq[Transcript])
150 | 
151 |       gene.drop_alt_chroms
152 |       result.add(gene)
153 |     result.drop_dups
154 | 
155 | 
156 | proc get_glob_samples*(paths: seq[string]): seq[string] =
157 |   result = newSeqOfCap[string](paths.len)
158 |   for i, p in paths:
159 |     var n = 0
160 |     for w in p.walkFiles:
161 |       n.inc
162 |       result.add(w)
163 |     if n == 0:
164 |       raise newException(OSError, "[seqcover]: file:" & p & " not found")
165 | 
166 | 
167 | proc read_dps*(paths: seq[string]): seq[Cover] =
168 |   result = newSeq[Cover](paths.len)
169 |   for i, p in paths:
170 |     result[i] = open_dp(p)
171 | 
172 | proc read_d4s_to_table*(paths: seq[string]): TableRef[string, Cover] =
173 |   result = newTable[string, Cover]()
174 |   for pat in paths:
175 |     for p in walkPattern(pat):
176 |       var name = splitFile(p).name
177 |       if name in result:
178 |         raise newException(OSError, "[seqcover] repeated d4 name:" & p)
179 |       if name.endsWith(".bed"):
180 |         name = name[0..<name.len - 4]
181 |       if name.endsWith(".per-base"):
182 |         name = name[0..<name.len - 9]
183 |       var d:Cover = p.open_dp
184 |       result[name] = d
185 | 
186 | proc check_same_lengths*(dps: var seq[Cover], chrom: string, length: uint32, fai:Fai) =
187 |   var lens = dps[0].chromosomes(fai)
188 |   for d in dps.mitems:
189 |     var clens = d.chromosomes(fai)
190 | 
191 |     doAssert lens[chrom] == clens[chrom], "[seqcover] differing chromosome lengths among samples"
192 | 
193 | when isMainModule:
194 |   import json
195 |   import algorithm
196 |   import sequtils
197 | 
198 |   when true:
199 |      #var ge = Gene(symbol: "MUC5B", description: "mucin 5B, oligomeric mucus/gel-forming", transcripts: @[Transcript(cdsstart: 1223123, cdsend: 1261608, chr: "11", position: @[[1223065, 1223193], [1225680, 1225737], [1226204, 1226276], [1226614, 1226876], [1227030, 1227145], [1227307, 1227398], [1227674, 1227781], [1228563, 1228765], [1229169, 1229295], [1229689, 1229807], [1230004, 1230143], [1230489, 1230600], [1230935, 1231005], [1231422, 1231560], [1231995, 1232160], [1232449, 1232544], [1232643, 1232770], [1233012, 1233268], [1233792, 1233848], [1234204, 1234305], [1234528, 1234680], [1235084, 1235223], [1235302, 1235413], [1236385, 1236562], [1236924, 1237164], [1238870, 1239027], [1239437, 1239566], [1239798, 1239943], [1240044, 1240088], [1240177, 1240375], [1240850, 1251743], [1252342, 1252524], [1252808, 1252980], [1254091, 1254351], [1254693, 1254880], [1255040, 1255266], [1255382, 1255558], [1256155, 1256225], [1256670, 1256771], [1257239, 1257271], [1257529, 1257710], [1258098, 1258203], [1258329, 1258367], [1258941, 1259061], [1259755, 1259842], [1259962, 1260085], [1260350, 1260393], [1260625, 1260728], [1261388, 1262172]], strand: 1, transcript: "NM_002458", txstart: 1223065, txend: 1262172)])
200 |     var d4s = read_d4s_to_table(toSeq(walkPattern("d4s/*.d4")))
201 |     var fa:Fai
202 | 
203 |     doAssert fa.open("/data/human/Homo_sapiens_assembly38.fasta")
204 | 
205 |     var backgrounds = read_d4s_to_table(toSeq(walkPattern("seqcover-backgrounds/*.d4")))
206 |     var gpt: seq[GenePlotData]
207 |     for gene in get_genes(@["PIGA", "KCNQ2", "MUC5B", "ARX", "DNM1", "SLC25A22", "CDKL5", "GABRA1", "ITPA", "GABRB1", "FRRS1L", "SLC12A5", "SIK1", "GRIN2D", "FGF12", "CAD", "DENND5A", "MDH2", "SCN1B", "AP3B2", "DENND5A", "MDH2", "GUF1", "YWHAG", "CNPY3", "CPLX1", "RHOBTB2"]):
208 |     #for gene in get_genes(@["PIGA"]):
209 |       echo gene
210 | 
211 |       #[
212 |       let u = gene.transcripts.union
213 |       stderr.write_line ">>> u:", u
214 |       #for t in gene.transcripts:
215 |       #  if t.transcript == "NM_001324238":
216 |       #    stderr.write_line ">>> t:", $t
217 |       stderr.write_line "######################"
218 | 
219 |       #var t = gene.transcripts[1]
220 |       #var u = gene.transcripts.union
221 | 
222 |       #var last = t.position[^1]
223 |       #t.position = @[last]
224 |       #stderr.write_line "after:", $t
225 | 
226 |       #stderr.write_line u.translate(t, extend=10)
227 |       #stderr.write_line "################"
228 | 
229 |       var pd = gene.plot_data(d4s, backgrounds, extend=10, fai=fa, max_gap=50)
230 |       gpt.add(pd)
231 | 
232 |       for i, x in pd.plot_coords.x:
233 |         if i == 0: continue
234 |         doAssert x >= pd.plot_coords.x[i-1]
235 |         doAssert pd.plot_coords.g[i] >= pd.plot_coords.g[i-1]
236 | 
237 | 
238 |       var dlen:int
239 |       for s, d in pd.plot_coords.depths.mpairs:
240 |         dlen = d.len
241 |         break
242 |       for s, d in pd.plot_coords.background_depths.mpairs:
243 |         doAssert d.len == dlen
244 | 
245 |       for i, p in pd.unioned_transcript.position:
246 |         var idx = pd.plot_coords.x.lowerBound(p[0].uint32)
247 |         if u.position[i][0].int != pd.plot_coords.g[idx].int:
248 |           stderr.write_line &"i[{i}][0]:"
249 |           stderr.write_line &"ERR LEFT : idx:{idx}, pd.plot_coords.g[idx]: {pd.plot_coords.g[idx]}, u.position[i][0]: {u.position[i][0]} l..r: {pd.plot_coords.g[idx-1..idx+1]} diff: {u.position[i][0].int - pd.plot_coords.g[idx].int}"
250 | 
251 |         idx = pd.plot_coords.x.lowerBound(p[1].uint32)
252 |         if u.position[i][1].int != pd.plot_coords.g[idx].int:
253 |           stderr.write_line &"i[{i}][1]:"
254 |           stderr.write_line &"ERR RIGHT idx:{idx}, pd.plot_coords.g[idx]: {pd.plot_coords.g[idx]}, u.position[i][1]: {u.position[i][1]} l..r: {pd.plot_coords.g[idx-1..idx+1]} diff {u.position[i][1].int - pd.plot_coords.g[idx].int}"
255 |           stderr.write_line "OK"
256 | 
257 | 
258 |       #for t in pd.transcripts:
259 |       #  if t.transcript == "NM_001324238":
260 |       #    stderr.write_line ">>> t:", $t
261 | 
262 |       stderr.write_line " unioned:", pd.unioned_transcript
263 | 
264 |     gpt.sort(proc(a, b: GenePlotData): int = cmp(a.symbol, b.symbol))
265 |     echo "plot_data = ", (%(gpt))
266 |     ]#
267 | 
268 | 
269 | 
270 | 


--------------------------------------------------------------------------------
/src/seqcoverpkg/seqcover.js:
--------------------------------------------------------------------------------
  1 | var nan = NaN; // hack to support json dumped with NaN values.
  2 | const gene_plot_height = 500
  3 | const color_list = [
  4 |     "#1f77b4", "#ff7f0e", "#2ca02c", "#d62728", "#9467bd", "#8c564b",
  5 |     "#e377c2", "#7f7f7f", "#bcbd22", "#17becf", "#7CB5EC", "#434348",
  6 |     "#90ED7D", "#F7A35C", "#8085E9", "#F15C80", "#E4D354", "#2B908F",
  7 |     "#F45B5B", "#91E8E1", "#4E79A7", "#F28E2C", "#E15759", "#76B7B2",
  8 |     "#59A14F", "#EDC949", "#AF7AA1", "#FF9DA7", "#9C755F", "#BAB0AB",
  9 | ]
 10 | const HOVER_TEMPLATE = '<b>position</b>:%{text}<br><b>depth</b>:%{y}<br>(debug) x: %{x}';
 11 | 
 12 | 
 13 | // https://stackoverflow.com/a/4198132
 14 | function getHashParams(h=false) {
 15 | 
 16 |     var hashParams = {};
 17 |     var e,
 18 |         a = /\+/g,  // Regex for replacing addition symbol with a space
 19 |         r = /([^&;=]+)=?([^&;]*)/g,
 20 |         d = function (s) { return decodeURIComponent(s.replace(a, " ")); },
 21 |         q = h ? h : window.location.hash.substring(1)
 22 | 
 23 |     while (e = r.exec(q))
 24 |        hashParams[d(e[1])] = d(e[2]);
 25 | 
 26 |     return hashParams;
 27 | }
 28 | 
 29 | function setHashParams(obj) {
 30 |     var old = getHashParams();
 31 |     for(var k in obj){
 32 |         if(obj[k] == null){
 33 |             delete old[k];
 34 |         } else {
 35 |           old[k] = obj[k]
 36 |         }
 37 |     }
 38 |     var str = "#";
 39 |     for(var k in old){
 40 |         str += `${k}=${old[k]}&`
 41 |     }
 42 | 
 43 |     window.location.hash = str.slice(0, -1); // drop final '&'
 44 |     return old;
 45 | 
 46 | }
 47 | 
 48 | window.onhashchange = function(event) {
 49 |     let old_hp = getHashParams(new URL(event.oldURL).hash.substring(1))
 50 |     let new_hp = getHashParams()
 51 | }
 52 | 
 53 | function update_selected_gene_header(gene) {
 54 |     let g = plot_data.filter(g => g.symbol == gene)[0]
 55 |     if(g == undefined) g = plot_data[0];
 56 |     let chrom = g.transcripts[0].chr
 57 |     let start = g.plot_coords.g[0]
 58 |     let stop = g.plot_coords.g[g.plot_coords.g.length - 1]
 59 |     document.getElementById("header-selected-gene").innerHTML = `${gene} <i>${chrom}:${start}-${stop}</i>`
 60 | }
 61 | 
 62 | function update_header_metadata(n_samples, n_genes) {
 63 |     document.getElementById("sample-count").innerHTML = n_samples
 64 |     document.getElementById("gene-count").innerHTML = n_genes
 65 | }
 66 | 
 67 | // https://stackoverflow.com/questions/8069315/create-array-of-all-integers-between-two-numbers-inclusive-in-javascript-jquer/8069367
 68 | function range(start, end, step = 1) {
 69 |     const len = Math.floor((end - start) / step) + 1
 70 |     return Array(len).fill().map((_, idx) => start + (idx * step))
 71 | }
 72 | 
 73 | function get_gene_plot_layout(gene) {
 74 |     let step = Math.round(gene.plot_coords.x.length / 10)
 75 |     let layout = {
 76 |         grid: { rows: 3, columns: 1, },
 77 |         autosize: true,
 78 |         height: gene_plot_height,
 79 |         margin: { t: 10, r: 0, b: 30 },
 80 |         hovermode: 'x',
 81 |         xaxis: {
 82 |             tickvals: range(gene.plot_coords.x[0], gene.plot_coords.x[gene.plot_coords.x.length - 10], step),
 83 |             ticktext: range(gene.plot_coords.g[0], gene.plot_coords.g[gene.plot_coords.x.length - 10], step),
 84 |             showgrid: false,
 85 |             ticklen: 5,
 86 |         },
 87 |         yaxis: { title: "Depth", domain: [0.28, 1]},
 88 |         yaxis2: {
 89 |             range: [0.5, -0.5],
 90 |             showlegend: false,
 91 |             zeroline: false,
 92 |             tickvals: [0],
 93 |             ticktext: ["Merged<br>Transcript"],
 94 |             tickangle: 40,
 95 |             domain: [0.25, 0.28],
 96 |         },
 97 |         yaxis3: {
 98 |             range: [0, 2],
 99 |             zeroline: false,
100 |             showlegend: false,
101 |             domain: [0.0, 0.25],
102 |             tickangle: 40,
103 |             ticktext: gene.transcripts.map(t => t.data.transcript),
104 |         },
105 |         hoverdistance: 100000,
106 |         hoverinfo: "none",
107 |         showlegend: false,
108 |     }
109 | 
110 |     return (layout)
111 | }
112 | 
113 | //Get a by position trace per sample of depth
114 | function get_depth_trace(gene) {
115 | 
116 |     var traces = [];
117 |     var low_lvl = 10000;
118 |     var low_dp;
119 |     for (var slvl in gene.plot_coords.background_depths) {
120 |         let lvl = slvl.replace(/^\D+/g, "")
121 | 
122 |         let dp = gene.plot_coords.background_depths[slvl].map(function (v) { return v < -1000 ? NaN : v })
123 |         if (lvl < low_lvl) { low_dp = dp; low_lvl = lvl }
124 | 
125 |         var trace = {
126 |             x: gene.plot_coords.x,
127 |             text: gene.plot_coords.g,
128 |             y: dp,
129 |             type: "scatter",
130 |             mode: "lines",
131 |             name: `Percentile: ${lvl}`,
132 |             tracktype: "background",
133 |             line: { width: 1, /* dash: "dot", */ color: 'rgb(200, 200, 200)' },
134 |             yaxis: "y",
135 |             hoverinfo: "skip",
136 |         }
137 |         traces.push(trace)
138 |     }
139 | 
140 |     var i = -1;
141 |     var samples_ = []
142 | 
143 |     for (var sample in gene.plot_coords.depths) {
144 |         samples_.push(sample)
145 |     }
146 |     for (var sample of samples_.sort()) {
147 | 
148 | 
149 |         i += 1
150 |         var dp = gene.plot_coords.depths[sample]
151 |         dp = dp.map(function (v) { return v < -1000 ? NaN : v })
152 |         var color = color_list[i % color_list.length];
153 |         var trace = {
154 |             x: gene.plot_coords.x, text: gene.plot_coords.g, y: dp,
155 |             type: 'scattergl', mode: 'lines', name: sample, line: { width: 0.36, color: color_list[i % color_list.length] },
156 |             hovertemplate: HOVER_TEMPLATE,
157 |             hoverdistance: 1000,
158 |             hoverinfo: "none",
159 |             yaxis: "y",
160 |             tracktype: "sample",
161 |         };
162 | 
163 |         traces.push(trace);
164 | 
165 |         // extract parts of this sample that are below the threshold and plot
166 |         // in a similar trace with wider line.
167 |         if (low_dp) {
168 |             var low_trace = {
169 |                 x: [], y: [], text: [], type: 'scatter', mode: "lines", name: sample, line: { width: 3.0, color: color_list[i % color_list.length] },
170 |                 hoverinfo: "none",
171 |                 connectgaps: false,
172 |                 yaxis: "y",
173 |             };
174 | 
175 |             dp.forEach((d, i) => {
176 |                 if (d < low_dp[i]) {
177 |                     low_trace.x.push(gene.plot_coords.x[i])
178 |                     low_trace.y.push(d)
179 |                 } else {
180 |                     if (low_trace.x.length > 0 && !isNaN(low_trace.x[low_trace.x.length - 1])) {
181 |                         low_trace.x.push(gene.plot_coords.x[i])
182 |                         low_trace.y.push(null)
183 |                     }
184 |                 }
185 | 
186 |             })
187 |             traces.push(low_trace)
188 | 
189 |         }
190 |     };
191 | 
192 |     return (traces)
193 | 
194 | };
195 | 
196 | //Get the transcript shapes for the current region
197 | function get_transcript_traces(gene, transcripts, plotRef) {
198 |     var traces = []
199 |     // use negative values for y_offset so we can tell from y-value if we
200 |     // are in depth plot (which must be positive) or in transcript plot
201 | 
202 |     transcripts.forEach((transcript, y_offset) => {
203 |         var trs = transcript.traces(-(y_offset), gene.plot_coords.x, gene.plot_coords.g)
204 |         trs.forEach(t => {
205 |             t.yaxis = plotRef
206 |             traces.push(t)
207 |         })
208 |     })
209 |     return traces
210 | };
211 | 
212 | 
213 | function plot_per_base_depth(gene) {
214 |     setHashParams({'gene': gene.symbol})
215 |     update_selected_gene_header(gene.symbol)
216 |     let gene_layout = get_gene_plot_layout(gene)
217 |     let depth_traces = get_depth_trace(gene)
218 |     let unioned_transcript_traces = get_transcript_traces(gene, [gene.unioned_transcript], "y2")
219 |     unioned_transcript_traces.forEach(t => depth_traces.push(t))
220 | 
221 |     let transcript_traces = get_transcript_traces(gene, gene.transcripts, "y3")
222 |     transcript_traces.forEach(t => depth_traces.push(t))
223 |     // each transcript is centered on the negative integers.
224 |     gene_layout.yaxis3.range = [0.5, -(1 + transcript_traces.length / 3)]
225 |     gene_layout.yaxis3.tickvals = [...Array(gene.transcripts.length).keys()].map(f => -f)
226 |     gene_layout.yaxis3.ticktext = gene.transcripts.map(t => t.data.transcript)
227 | 
228 |     let d = document.getElementById("gene_plot")
229 |     let p = Plotly.newPlot(d, depth_traces, gene_layout, {responsive: true})
230 |     d.on("plotly_hover", data => {
231 |         // handle_hover(data, depth_traces, gene, gene_layout)
232 |         Plotly.react("gene_plot", depth_traces, gene_layout)
233 |         data.event.stopPropagation()
234 |     }).on("plotly_unhover", data => {
235 |         if (gene_layout.shapes != undefined && gene_layout.shapes.length > 0) {
236 |             gene_layout.shapes.pop()
237 |         }
238 |         Plotly.react("gene_plot", depth_traces, gene_layout)
239 |         data.event.stopPropagation()
240 |     })
241 |     return p
242 | }
243 | 
244 | function mean(data) {
245 |     var result = 0
246 |     var n = 0
247 |     for (var i = 0; i < data.length; i++) {
248 |         let d = data[i]
249 |         if (d >= 0) {
250 |             n += 1
251 |             result += d
252 |         }
253 |     }
254 |     return result / n
255 | }
256 | 
257 | function handle_hover(data, depth_traces, gene, gene_layout) {
258 |     //  this function handles hover events in the transcript plots. it
259 |     //  finds the correct transcript and feature (exon/transcript/UTR, etc)
260 |     //  and calculates stats, and updates the gene_layout to draw the
261 |     //  region shape.
262 |     //
263 |     let ax = data.yaxes[0]._attr;
264 |     // don't handle hover in depth plot
265 |     if (ax == "yaxis") { return false; }
266 |     // this is the x in plot coordinates.
267 |     var x = Math.round(data.xvals[0])
268 |     var y = Math.round(Math.abs(data.yvals[0])) // can now use this as an index to get the transcript.
269 |     var transcript = ax == "yaxis2" ? gene.unioned_transcript : gene.transcripts[y]
270 | 
271 | 
272 |     if (transcript == undefined) { return false }
273 | 
274 |     let overlaps = transcript.overlaps(x)
275 |     if (overlaps.length > 1) {
276 |         if (overlaps.some(p => p.type == FeatureType.CDS)) {
277 |             overlaps = overlaps.filter(p => p.type == FeatureType.CDS)
278 |         } else if (overlaps.some(p => p.type == FeatureType.EXON)) {
279 |             overlaps = overlaps.filter(p => p.type == FeatureType.EXON)
280 |         }
281 |     }
282 |     if (overlaps.length == 0) {
283 |         overlaps.push(new Feature(transcript.txstart, transcript.txend, FeatureType.TRANSCRIPT))
284 |     }
285 |     if (gene_layout.shapes == undefined) { gene_layout.shapes = [] }
286 |     gene_layout.shapes.push({
287 |         type: "rect",
288 |         xref: "x",
289 |         yref: "paper",
290 |         y0: 0,
291 |         y1: 1,
292 |         fillcolor: "#cccccc",
293 |         opacity: 0.2,
294 |         x0: overlaps[0].start,
295 |         x1: overlaps[0].stop,
296 |     })
297 | 
298 |     var start_idx = binary_search(gene.plot_coords.x, overlaps[0].start)
299 |     var stop_idx = binary_search(gene.plot_coords.x, overlaps[0].stop)
300 | 
301 |     let low_depth_cutoff = 7; // TODO: get this from user-form input.
302 |     var selection_stats = transcript.stats([{ start: start_idx, stop: stop_idx }], gene.plot_coords.depths, gene.plot_coords.background_depths, low_depth_cutoff)
303 | 
304 |     var tx_stats = transcript.stats([{ start: 0, stop: gene.plot_coords.x.length }], gene.plot_coords.depths, gene.plot_coords.background_depths, low_depth_cutoff)
305 | 
306 |     // example of how to get stats for all CDSs. NOTE: this should only be done
307 |     // once per gene and result cached.
308 |     var cds = transcript.parts().filter(p => p.type == FeatureType.CDS)
309 |     var cds_stats = transcript.stats(cds, gene.plot_coords.depths, gene.plot_coords.background_depths, low_depth_cutoff)
310 | 
311 |     var gstart = gene.plot_coords.g[start_idx]
312 |     var gstop = gene.plot_coords.g[stop_idx]
313 | 
314 |     var columns = [{ title: "sample" }, { title: "transcript mean" }, { title: "CDS mean" }, { title: "selection mean" },
315 |     { title: "transcript bases < lower" }, { title: "CDS bases < lower" }, { title: "selection bases < lower" }];
316 |     var table = []
317 |     var samples_ = [];
318 | 
319 |     //var means = {}
320 |     //hoverInfo.innerHTML = `${gene.unioned_transcript.chr}:${gstart}-${gstop}<br><ul>`
321 |     for (var sample in gene.plot_coords.depths) { samples_.push(sample) }
322 |     for (var sample of samples_.sort()) {
323 | 
324 |         var row = [sample, tx_stats[sample].mean.toFixed(2), cds_stats[sample].mean.toFixed(2), selection_stats[sample].mean.toFixed(2), tx_stats[sample].low, cds_stats[sample].low, selection_stats[sample].low]
325 |         table.push(row)
326 |         //let depths = gene.plot_coords.depths[sample];
327 |         //means[sample] = mean(depths.slice(start_idx, stop_idx)).toPrecision(4)
328 |     }
329 |     if (datatable) {
330 |         datatable.clear()
331 |         datatable.rows.add(table)
332 |         datatable.draw()
333 |     } else {
334 |         datatable = jQuery('table#stats_table').DataTable({ data: table, columns: columns })
335 |     }
336 | }
337 | 
338 | function highlight_sample(sample) {
339 |     setHashParams({'sample': sample})
340 |     let d = document.getElementById("gene_plot")
341 |     let vals = d.data.map((t, i) => {
342 |         if (t.tracktype == "background") {
343 |             return [1, 1.5]
344 |         }
345 |         if (t.tracktype != 'sample') {
346 |             return [undefined, undefined]
347 |         } else {
348 |             if (t.name == sample) {
349 |                 return [1, 1.8]
350 |             } else {
351 |                 return [0.15, 0.36]
352 |             }
353 |         }
354 |     })
355 | 
356 |     Plotly.restyle(d, {'opacity': vals.map(i => i[0]), 'line.width': vals.map(i => i[1]), 'hovertemplate': vals.map(i => i[1] > 0.8 ? HOVER_TEMPLATE: null)})
357 | }
358 | 
359 | function tie_heatmap_to_line_plot() {
360 |     // clicks on heatmap x-axis labels highlights sample in line plot
361 |     // https://issue.life/questions/44297012
362 |     var xticks = jQuery("#heatmap_plot .xaxislayer-above > .xtick > text")
363 |     xticks.css({ "cursor": "pointer" })
364 |     xticks.attr('class', 'unselected_label')
365 |     var d = document.getElementById("gene_plot")
366 | 
367 |     xticks.each(function (i) {
368 |         var item = jQuery(this);
369 |         item.css({ "fill": color_list[i % color_list.length] })
370 |         item.attr('pointer-events', 'all')
371 |         item.on("click", function (e) {
372 |             var n = jQuery(this)
373 |             var undo = n.css("font-weight") == "800";
374 |             xticks.attr('class', 'unselected_label')
375 |             var sample = n.text()
376 |             var vals = null
377 |             if (undo) {
378 |                 vals = d.data.map((t, i) => [1, (t.tracktype == 'sample' || t.tracktype == 'background') ? 0.36 : undefined])
379 |                 Plotly.restyle(d, {'opacity': vals.map(i => i[0]), 'line.width': vals.map(i => i[1]), 'hovertemplate': d.data.map((t) => t.tracktype == "sample" ? HOVER_TEMPLATE: null)})
380 |                 setHashParams({'sample': null})
381 |             } else {
382 |                 n.attr('class', 'selected_label')
383 |                 highlight_sample(sample)
384 |             }
385 |             // see: https://codepen.io/etpinard/pen/RQQqzq?editors=0010
386 |         }).on("unhover", function (e) {
387 |         })
388 |     })
389 | }
390 | 
391 | function draw_heatmap() {
392 | 
393 |     let sample_z_scale = jQuery('#z_scale_samples').is(":checked")
394 |     let gene_z_scale = jQuery('#z_scale_genes').is(":checked")
395 | 
396 |     let stat_metric = jQuery("#metric_select").val()
397 | 
398 |     var low_depth_cutoff = 7;
399 |     var z = []
400 |     var x = [] // samples
401 |     var y = [] // genes
402 | 
403 |     var is_cds = stat_metric.startsWith("cds")
404 |     var metric = stat_metric.split("_")[1]
405 |     for (var i = 0; i < plot_data.length; i++) {
406 |         var g = plot_data[i]
407 |         y.push(g.symbol)
408 | 
409 |         var transcript = g.unioned_transcript
410 |         var stats = null
411 |         if (is_cds) {
412 |             var cds = transcript.parts().filter(p => p.type == FeatureType.CDS)
413 |             stats = transcript.stats(cds, g.plot_coords.depths, g.plot_coords.background_depths, low_depth_cutoff)
414 |         } else {
415 |             stats = transcript.stats([{ start: 0, stop: g.plot_coords.x.length }], g.plot_coords.depths, g.plot_coords.background_depths, low_depth_cutoff)
416 |         }
417 | 
418 |         var row = []
419 | 
420 |         // get samples in alphabetical order
421 |         if (i == 0) {
422 |             for(var s in stats) { x.push(s) }
423 |             x = x.sort()
424 |         }
425 | 
426 |         for(var s of x) {
427 |             row.push(stats[s][metric])
428 |         }
429 |         // row is a set of samples for a given metric
430 |         if(gene_z_scale) {
431 |             row = z_transform(row)
432 |         }
433 | 
434 |         z.push(row)
435 |     }
436 | 
437 |     if(sample_z_scale) {
438 |         z = z_transform_columns(z)
439 |     }
440 | 
441 |     // heatmap draws from bottom up by default
442 |     z = z.reverse()
443 |     y = y.reverse()
444 | 
445 |     let hlayout = {
446 |         title: "",
447 |         margin: { t: 10 },
448 |         height: 20 * y.length + 60,
449 |         width: 20 * x.length + 30,
450 |         paper_bgcolor: '#f8f9fa',
451 |         uniformtext: { mode: 'show', minsize: 2 },
452 |         xaxis: { tickfont: { size: 12 }, fixedrange: true, automargin: true, type: "category"},
453 |         yaxis: { fixedrange: true, automargin: true, },
454 |         font: { size: 14 },
455 |     }
456 |     // TODO: this should be based on window width.
457 |     if(hlayout.width < jQuery('#heatmap_plot').width()) {
458 |         hlayout.width = jQuery('#heatmap_plot').width();
459 |     }
460 |     if(hlayout.height < 300) {
461 |         hlayout.height = 300;
462 |     }
463 |     let heatmap_config = {
464 |         displaylogo: false,
465 |         toImageButtonOptions: {
466 |             format: 'svg', // one of png, svg, jpeg, webp
467 |             filename: 'seqcover_summary',
468 |             height: 18 * y.length + 60,
469 |             width: 1200,
470 |             scale: 1 // Multiply title/legend/axis/canvas sizes by this factor
471 |         },
472 |         // responsive: true,
473 |     }
474 |     let trace = [{ x: x, y: y, z: z, type: 'heatmap', hoverongaps: false, colorscale: "Cividis" }]
475 | 
476 |     //https://plotly.com/javascript/reference/heatmap/
477 |     let p = document.getElementById('heatmap_plot')
478 | 
479 |     let yticks = jQuery("#heatmap_plot .yaxislayer-above > .ytick > text")
480 |     let selected = false
481 |     yticks.each(function (i) {
482 |         let elem = jQuery(this)
483 |         if (elem.css("font-weight") == "800") {
484 |             selected = i
485 |         }
486 |     })
487 | 
488 |     Plotly.newPlot(p, trace, hlayout, heatmap_config)
489 |     p.removeAllListeners("plotly_click")
490 |     p.on('plotly_click', function (click_data) {
491 |         let selected_gene_idx = click_data.points[0].pointIndex[0]
492 |         let gene_idx = plot_data.length - selected_gene_idx - 1
493 |         let selected_sample_idx = click_data.points[0].pointIndex[1]
494 |         let sample = click_data.points[0].x
495 |         let gene = click_data.points[0].y
496 | 
497 |         // y-axis ticks
498 |         let yticks = jQuery("#heatmap_plot .yaxislayer-above > .ytick > text")
499 |         yticks.attr('class', 'unselected_label')
500 |         yticks.each(function (i) {
501 |             if (i == selected_gene_idx) {
502 |                 jQuery(this).attr('class', 'selected_label')
503 |             }
504 |         })
505 |         // x-axis ticks
506 |         let xticks = jQuery("#heatmap_plot .xaxislayer-above > .xtick > text")
507 |         xticks.attr("class", "unselected_label")
508 |         xticks.each(function (i) {
509 |             if (i == selected_sample_idx) {
510 |                 jQuery(this).attr("class", "selected_label")
511 |             }
512 |         })
513 | 
514 |         if(selected_gene_idx != selected) {
515 |             // only redraw if it's a new gene
516 |             plot_per_base_depth(plot_data[gene_idx]).then(highlight_sample(sample))
517 |             selected = selected_gene_idx;
518 |             setHashParams({'gene': gene, 'sample': sample});
519 |         } else {
520 |             highlight_sample(sample)
521 |         }
522 | 
523 |     })
524 |     p.on('plotly_afterplot', function () {
525 |         // initialize first gene as selected; or re-use selected (when changing metric)
526 |         let yticks = jQuery("#heatmap_plot .yaxislayer-above > .ytick > text")
527 |         yticks.attr('class', 'unselected_label')
528 |         if (!selected) {
529 |             jQuery(yticks[plot_data.length - 1]).attr("class", "selected_label")
530 |         } else {
531 |             jQuery(yticks[selected]).attr("class", "selected_label")
532 |         }
533 | 
534 |         // x-axis ticks
535 |         tie_heatmap_to_line_plot()
536 |         // y-axis ticks
537 |         Plotly.d3.selectAll(".yaxislayer-above").selectAll('text')
538 |             .on("click", function (d) {
539 |                 yticks.attr("class", "unselected_label")
540 |                 jQuery(this).attr('class', 'selected_label')
541 |                 var hash = setHashParams({'gene': d.text})
542 |                 plot_per_base_depth(plot_data[plot_data.length - d.x - 1])
543 |                 if("sample" in hash){ highlight_sample(hash.sample) }
544 |             })
545 |     })
546 | }
547 | 
548 | function update_popovers() {
549 |     $('[data-toggle="tooltip"]').tooltip()
550 | 
551 |     $("#navigation-popover").popover({
552 |         container: "body",
553 |         html: true,
554 |         title: "Navigating the report",
555 |         content: `
556 |             <ul class="m-0 ml-1 p-2">
557 |                 <li>X and Y axes labels are clickable</li>
558 |                 <li>Clicking gene names (y-axis labels) updates 'Depth per base' plot</li>
559 |                 <li>Clicking sample names (x-axis labels) highlights the sample trace</li>
560 |                 <li>Clicking heatmap values updates the selected gene and highlights the sample</li>
561 |             </ul>
562 |         `,
563 |     })
564 |     $("#depth-plot-popover").popover({
565 |         container: "body",
566 |         html: true,
567 |         title: "Depths by position across gene",
568 |         content: `
569 |             <ul class="m-0 ml-1 p-2">
570 |                 <li>Depths per base per sample are displayed over gene length</li>
571 |                 <li>Individual transcripts are merged into the Merged transcript</li>
572 |                 <li>CDS segments are colored light red</li>
573 |                 <li>UTR segments are light gray</li>
574 |             </ul>
575 |         `,
576 |     })
577 | }
578 | 
579 | jQuery(document).ready(function () {
580 |     update_header_metadata(Object.keys(plot_data[0].plot_coords.depths).length, plot_data.length)
581 |     update_popovers()
582 | 
583 |     if (Object.keys(plot_data[0].plot_coords.background_depths).length == 0) {
584 |         jQuery('#cds_lt_bg').remove()
585 |     }
586 | 
587 |     for(var g of plot_data) {
588 |         if (g.unioned_transcript.constructor.name == "Object") {
589 |             g.unioned_transcript = new Transcript(g.unioned_transcript)
590 |             g.transcripts = g.transcripts.map(t => new Transcript(t))
591 |             for(var s in g.plot_coords.depths) {
592 |                 g.plot_coords.depths[s] = Float32Array.from(g.plot_coords.depths[s])
593 |             }
594 | 
595 |             g.plot_coords.x = Int32Array.from(g.plot_coords.x)
596 |             g.plot_coords.g = Int32Array.from(g.plot_coords.g)
597 |         }
598 |     }
599 | 
600 |     jQuery('#metric_select,.z_scale').on('change', function() { draw_heatmap() })
601 |     jQuery('#metric_select').trigger('change')
602 |     var p = getHashParams();
603 |     var i = 0; // TODO: rename `i`
604 |     if ("gene" in p) {
605 |         var gene = p.gene;
606 |         for(var j = 0; j < plot_data.length; j++){
607 |             if(plot_data[j].symbol == gene){
608 |                 i = j
609 |                 break
610 |             }
611 |         }
612 | 
613 |     }
614 |     plot_per_base_depth(plot_data[i]).then(function() {
615 |         // NOTE we should put these events directly in the plot fn so we don't
616 |         // have code duplication, but here for now...
617 |         let yticks = jQuery("#heatmap_plot .yaxislayer-above > .ytick > text")
618 |         yticks.attr('class', 'unselected_label')
619 |         yticks.each(function (k) {
620 |             if (i == plot_data.length - k - 1) {
621 |                 jQuery(this).attr('class', 'selected_label')
622 |             }
623 |         })
624 |         if("sample" in p) {
625 |             highlight_sample(p.sample)
626 |             jQuery("#heatmap_plot .xaxislayer-above > .xtick > text").each(function(i, v) {
627 |                 if(v.innerHTML == p.sample){
628 |                     jQuery(v).attr('class', 'selected_label')
629 |                 }
630 |             })
631 | 
632 |         }
633 |     })
634 | })
635 | 
636 | function z_transform_columns(z) {
637 |     var ztr = new Array(z.length);
638 |     for(var rowi=0; rowi < z.length; rowi++){
639 |         ztr[rowi] = new Array(z[0].length)
640 |     }
641 | 
642 |     for(var coli=0; coli < z[0].length; coli++){
643 |         var col = []
644 |         for(var rowi=0; rowi < z.length; rowi++) {
645 |             col.push(z[rowi][coli])
646 |         }
647 |         var tr = z_transform(col)
648 |         for(var rowi=0; rowi < z.length; rowi++) {
649 |             ztr[rowi][coli] = tr[rowi];
650 |         }
651 | 
652 |     }
653 |     return ztr
654 | }
655 | 


--------------------------------------------------------------------------------
/test/data.js:
--------------------------------------------------------------------------------
1 | exports.tr_data = {"cdsstart":2065,"cdsend":3986,"chr":"X","position":[[10,2332],[2402,2609],[2679,2812],[2882,3015],[3085,3862],[3932,3986]],"strand":-1,"transcript":"union","txstart":10,"txend":3986}
2 | 
3 | 
4 | exports.xs = 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5 | exports.gs = 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6 | 


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