Source file ucsc_genome_browser.ml
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open Printf
type assembly = [ `dm3 | `droSim1 | `hg18 | `hg19 | `hg38 | `mm8 | `mm9 | `mm10 | `sacCer2 ]
let string_of_assembly = function
| `dm3 -> "dm3"
| `droSim1 -> "droSim1"
| `hg18 -> "hg18"
| `hg19 -> "hg19"
| `hg38 -> "hg38"
| `mm8 -> "mm8"
| `mm9 -> "mm9"
| `mm10 -> "mm10"
| `sacCer2 -> "sacCer2"
type track_attribute = [
| `name of string
| `description of string
| `type_ of track_type
| `visibility of [ `hide | `full | `dense | `pack | `squish ]
| `color of color
| `itemRgb of bool
| `colorByStrand of color * color
| `useScore of bool
| `group of string
| `priority of int
| `db of assembly
| `offset of int
| `maxItems of int
| `url of string
| `htmlUrl of string
| `bigDataUrl of string
]
and color = int * int * int
and track_type = [
`bam
| `bedDetail
| `bedGraph
| `bigBed
| `bigWig
| `broadPeak
| `narrowPeak
| `array
| `vcf
| `wig
]
let string_of_track_type = function
| `bam -> "bam"
| `bedDetail -> "bedDetail"
| `bedGraph -> "bedGraph"
| `bigBed -> "bigBed"
| `bigWig -> "bigWig"
| `broadPeak -> "broadPeak"
| `narrowPeak -> "narrowPeak"
| `array -> "array"
| `vcf -> "vcf"
| `wig -> "wig"
let unparse_track_attribute buf = function
| `name n -> bprintf buf " name=\"%s\"" n
| `description d -> bprintf buf " description=\"%s\"" d
| `type_ t -> bprintf buf " type=%s" (string_of_track_type t)
| `visibility v ->
let v = match v with
| `full -> "full"
| `dense -> "dense"
| `hide -> "hide"
| `pack -> "pack"
| `squish -> "squish"
in
bprintf buf " visibility=%s" v
| `color (r,g,b) ->
bprintf buf " color=%d,%d,%d" r g b
| `itemRgb b ->
if b then bprintf buf " itemRgb=On"
| `colorByStrand ((r,g,b), (r',g',b')) ->
bprintf buf " color=%d,%d,%d %d,%d,%d" r g b r' g' b'
| `useScore b -> bprintf buf " useScore=%d" (if b then 1 else 0)
| `group g -> bprintf buf " group=\"%s\"" g
| `priority p -> bprintf buf " priority=%d" p
| `db assembly -> bprintf buf " db=%s" (string_of_assembly assembly)
| `offset o -> bprintf buf " offset=%d" o
| `maxItems m -> bprintf buf " maxItems=%d" m
| `url u -> bprintf buf " url=%s" u
| `htmlUrl u -> bprintf buf " htmlUrl=%s" u
| `bigDataUrl u -> bprintf buf " bigDataUrl=%s" u
let track_line opts =
let buf = Buffer.create 1024 in
bprintf buf "track" ;
List.iter ~f:(unparse_track_attribute buf) opts ;
Buffer.contents buf
type url_param = [
| `pix of int
| `hgt_labelWidth of int
| `textSize of int
]
let main_server = "http://genome.ucsc.edu"
let base db =
main_server ^ "/cgi-bin/hgTracks?db=" ^ (string_of_assembly db)
let string_of_position (chr, maybe_pos) =
chr ^ (
match maybe_pos with
| None -> ""
| Some (a, b) -> sprintf ":%d-%d" a b
)
let encode_url_param = function
| `pix n -> sprintf "pix=%d" n
| `hgt_labelWidth n -> sprintf "hgt.labelWidth=%d" n
| `textSize n -> sprintf "textSize=%d" n
let encode_url_params xs =
List.map ~f:encode_url_param xs
|> String.concat ~sep:"&"
let custom_track_url ?(params = []) ~db ~position ~data_url () =
sprintf
"%s&position=%s&hgt.customText=%s%s"
(base db)
(string_of_position position)
data_url
(encode_url_params params)
let bigData_custom_track_url ?(params = []) ~db ~position ~track () =
let escaped_custom_text =
Uri.pct_encode ~component:`Query (track_line track)
in
sprintf "%s&position=%s&hgct_customText=%s%s"
(base db)
(string_of_position position)
escaped_custom_text
(encode_url_params params)