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type variable_option = [ ` Blanked | ` Non_ignorable | ` Shifted | ` Shift_Trimmed ] |
type precision = [ ` Primary | ` Secondary | ` Tertiary | ` Quaternary ] |
module type Type = sig type text type index val compare : ? locale : string -> ? prec : precision -> ? variable : variable_option -> text -> text -> int val sort_key : ? locale : string -> ? prec : precision -> ? variable : variable_option -> text -> string val compare_with_key : ? locale : s... |
module Make ( Config : ConfigInt . Type ) Type ( Text : UnicodeString . Type ) Type = struct module Unidata = Unidata . Make ( MakeConfig ) MakeConfig module UCharInfo = UCharInfo . Make ( MakeConfig ) MakeConfig let logical_order_exception_tbl = UCharInfo . load_property_tbl ` Logical_... |
type t = ( int32 , int32_elt , c_layout ) c_layout Array1 . t |
let rec validate_aux ( a : t ) t i = if i >= Array1 . dim a then ( ) else match Int32 . to_int ( Int32 . shift_right a { . i } i 31 ) 31 with 0 -> validate_aux a ( i + 1 ) 1 | _ -> raise Malformed_code |
let validate ( a : t ) t = validate_aux a 0 |
let look ( a : t ) t i : UChar . t = UChar . chr_of_uint ( Int32 . to_int a { . i } i ) i |
let length ( a : t ) t = Array1 . dim a |
let next _ i = i + 1 |
let prev _ i = i - 1 |
let move ( _ : t ) t i c = i + c |
let first _ = 0 |
let last ( a : t ) t = Array1 . dim a - 1 |
let out_of_range ( a : t ) t i = i < 0 || i >= Array1 . dim a |
let compare_index _ i j = i - j |
let nth ( _ : t ) t c = c |
let get ( a : t ) t c = look a c |
let rec iter_aux proc ( a : t ) t i = if i >= Array1 . dim a then ( ) else begin proc ( look a i ) i ; iter_aux proc a ( i + 1 ) 1 end |
let iter proc ( a : t ) t = iter_aux proc a 0 |
let init len f = let a = Array1 . create int32 c_layout len in for i = 0 to len - 1 do a { . i } i <- Int32 . of_int ( UChar . uint_code ( f i ) i ) i done ; a |
module Buf = struct type buf = { init_size : int ; mutable pos : index ; mutable contents : t } t let create n = let contents = Array1 . create int32 c_layout n in { init_size = n ; pos = 0 ; contents = contents } contents let clear buf = buf . pos <- 0 let reset buf = buf . contents ... |
let compare ( a : t ) t ( b : t ) t = match Array1 . dim a - Array1 . dim b with 0 -> Pervasives . compare a b | sgn -> sgn |
type genome = [ ` dm3 | ` droSim1 | ` hg18 | ` hg19 | ` hg38 | ` mm8 | ` mm9 | ` mm10 | ` sacCer2 ] |
let string_of_genome = function | ` dm3 -> " dm3 " | ` droSim1 -> " droSim1 " | ` hg18 -> " hg18 " | ` hg19 -> " hg19 " | ` hg38 -> " hg38 " | ` mm8 -> " mm8 " | ` mm9 -> " mm9 " | ` mm10 -> " mm10 " | ` sacCer2 -> " sacCer2 " |
let genome_of_string = function | " dm3 " -> Some ` dm3 | " droSim1 " -> Some ` droSim1 | " hg18 " -> Some ` hg18 | " hg19 " -> Some ` hg19 | " hg38 " -> Some ` hg38 | " mm8 " -> Some ` mm8 | " mm9 " -> Some ` mm9 | " mm10 " -> Some ` mm10 | " sacCer2 ... |
let img = [ docker_image ~ account " : pveber " ~ name " : ucsc - kent " ~ tag " : 330 " ( ) ] |
type chromosome_sequences = [ ` ucsc_chromosome_sequences ] directory |
let chromosome_sequence org chr = let org = string_of_genome org in let url = sprintf " ftp :// hgdownload . cse . ucsc . edu / goldenPath /% s / chromosomes /% s . fa . gz " org chr in let descr = sprintf " ucsc_gb . chromosome_sequence ( % s , % s ) " org chr in Workflow . shell... |
let chromosome_sequences org = let org = string_of_genome org in let url = sprintf " ftp :// hgdownload . cse . ucsc . edu / goldenPath /% s / chromosomes " /* org in Workflow . shell ~ descr ( : sprintf " ucsc_gb . chromosome_sequences ( % s ) " org ) [ mkdir_p dest ; cd dest ;... |
let genome_sequence org = let chr_seqs = chromosome_sequences org in Workflow . shell ~ descr " : ucsc_gb . genome_sequence " [ cmd " bash " [ opt " - c " string " ' shopt - s nullglob ; cat $ 0 { / chr . ? fa , chr . ?? fa , chr . ??? fa , chr . ???? fa } > $ ... |
let genome_2bit_sequence_dir org = let org = string_of_genome org in let url = sprintf " ftp :// hgdownload . cse . ucsc . edu / goldenPath /% s / bigZips /% s . 2bit " org org in Workflow . shell ~ descr ( : sprintf " ucsc_gb . 2bit_sequence ( % s ) " org ) [ mkdir dest ; c... |
let genome_2bit_sequence org = Workflow . select ( genome_2bit_sequence_dir org ) [ ( string_of_genome org ) ^ " . 2bit " ] |
let twoBitToFa twobits bed = Workflow . shell ~ descr " : ucsc_gb . twoBitToFa " ~ img [ cmd " twoBitToFa " [ opt ' " - bed " dep bed ; dep twobits ; dest ] ] |
let faToTwoBit fa = Workflow . shell ~ descr " : ucsc_gb . faToTwoBit " ~ img [ cmd " faToTwoBit " [ dep fa ; dest ] ] |
let fetchChromSizes org = Workflow . shell ~ descr " : ucsc_gb . fetchChromSizes " ~ img [ cmd " fetchChromSizes " ~ stdout : dest [ string ( string_of_genome org ) ; ] ] |
let bedClip org bed = Workflow . shell ~ descr " : ucsc_gb . bedClip " ~ img [ cmd " bedClip - verbose = 2 " [ dep bed ; dep org ; dest ; ] ] |
let bedGraphToBigWig org bg = let tmp = seq [ tmp ; string " / sorted . bedGraph " ] in Workflow . shell ~ descr " : bedGraphToBigWig " ~ img [ cmd " sort " ~ stdout : tmp [ string " - k1 , 1 " ; string " - k2 , 2n " ; dep bg ; ] ; cmd " bedGraphToBigWig " ... |
let bedToBigBed_command org bed = let tmp = seq [ tmp ; string " / sorted . bed " ] in let sort = cmd " sort " ~ stdout : tmp [ string " - k1 , 1 " ; string " - k2 , 2n " ; dep bed ; ] in let bedToBigBed = cmd " bedToBigBed " [ tmp ; dep ( fetchChromSizes org )... |
let bedToBigBed org = let f bed = Workflow . shell ~ descr " : ucsc_gb . bedToBigBed " ~ img ( bedToBigBed_command org bed ) in function | ` bed3 bed -> f bed | ` bed5 bed -> f bed |
let bedToBigBed_failsafe org = let f bed = let test = cmd " test " [ string " ! - s " ; dep bed ] in let touch = cmd " touch " [ dest ] in let cmd = or_list [ and_list [ test ; touch ] ; and_list ( bedToBigBed_command org bed ) ; ] in Workflow . shell ~ img [ cmd ] ... |
module Lift_over = struct class type chain_file = object inherit regular_file_t method format : [ ` lift_over_chain_file ] end type ' a output = [ ` ucsc_lift_over of ' a ] directory let chain_file ~ org_from ~ org_to = let org_from = string_of_genome org_from and org_to = string_of_genome org_... |
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 s... |
let string_of_track_type = function | ` bam -> " bam " | ` bedDetail -> " bedDetail " | ` bedGraph -> " bedGraph " | ` bigBed -> " bigBed " | ` bigWig -> " bigWig " | ` broadPeak -> " broadPeak " | ` narrowPeak -> " narrowPeak " | ` array -> " array " | ... |
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 ) t | ` visibility v -> let v = match v with | ` full -> " ... |
let track_line opts = let buf = Buffer . create 1024 in bprintf buf " track " ; List . iter ~ f ( : unparse_track_attribute buf ) buf opts ; Buffer . contents buf |
type url_param = [ | ` pix of int | ` hgt_labelWidth of int | ` textSize of int ] |
let base db = main_server ^ " / cgi - bin / hgTracks ? db " = ^ ( string_of_assembly db ) db |
let string_of_position ( chr , maybe_pos ) maybe_pos = chr ^ ( match maybe_pos with | None -> " " | Some ( a , b ) 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 ) db ( string_of_position position ) position data_url ( encode_url_params params ) params |
let bigData_custom_track_url ( ? params = [ ] ) ~ db ~ position ~ track ( ) = let escaped_custom_text = Uri . pct_encode ~ component ` : Query ( track_line track ) track in sprintf " % s & position =% s & hgct_customText =% s % s " ( base db ) db ( string_of_position position ) ... |
type fs = { fs_id : string ; fs_name : string ; fs_supports_unix_owners : bool ; fs_can_mount : bool ; fs_can_create : bool ; fs_max_label_len : int ; fs_supports_label_rename : bool ; fs_supports_online_label_rename : bool ; fs_supports_fsck : bool ; fs_supports_online_fsck : bool ; fs... |
type job = { job_device : UDisks_device . t ; job_in_progress : bool ; job_is_cancellable : bool ; job_id : string ; job_num_tasks : int ; job_cur_task : int ; job_cur_task_id : string ; job_cur_task_percentage : float ; } |
let daemon ( ) = let % lwt bus = OBus_bus . system ( ) in return ( OBus_peer . make bus " org . freedesktop . UDisks " ) |
let proxy daemon = OBus_proxy . make daemon [ " org " ; " freedesktop " ; " UDisks " ] |
let make_device context path = UDisks_device . of_proxy ( OBus_proxy . make ( OBus_context . sender context ) path ) |
let make_adapter context path = UDisks_adapter . of_proxy ( OBus_proxy . make ( OBus_context . sender context ) path ) |
let make_expander context path = UDisks_expander . of_proxy ( OBus_proxy . make ( OBus_context . sender context ) path ) |
let make_port context path = UDisks_port . of_proxy ( OBus_proxy . make ( OBus_context . sender context ) path ) |
let enumerate_adapters daemon = let % lwt ( context , devices ) = OBus_method . call_with_context m_EnumerateAdapters ( proxy daemon ) ( ) in return ( List . map ( make_adapter context ) devices ) |
let enumerate_expanders daemon = let % lwt ( context , devices ) = OBus_method . call_with_context m_EnumerateExpanders ( proxy daemon ) ( ) in return ( List . map ( make_expander context ) devices ) |
let enumerate_ports daemon = let % lwt ( context , devices ) = OBus_method . call_with_context m_EnumeratePorts ( proxy daemon ) ( ) in return ( List . map ( make_port context ) devices ) |
let enumerate_devices daemon = let % lwt ( context , devices ) = OBus_method . call_with_context m_EnumerateDevices ( proxy daemon ) ( ) in return ( List . map ( make_device context ) devices ) |
let enumerate_device_files daemon = OBus_method . call m_EnumerateDeviceFiles ( proxy daemon ) ( ) |
let find_device_by_device_file daemon ~ device_file = let % lwt ( context , device ) = OBus_method . call_with_context m_FindDeviceByDeviceFile ( proxy daemon ) device_file in return ( make_device context device ) |
let find_device_by_major_minor daemon ~ device_major ~ device_minor = let % lwt ( context , device ) = OBus_method . call_with_context m_FindDeviceByMajorMinor ( proxy daemon ) ( device_major , device_minor ) in return ( make_device context device ) |
let drive_inhibit_all_polling daemon ~ options = OBus_method . call m_DriveInhibitAllPolling ( proxy daemon ) options |
let drive_uninhibit_all_polling daemon ~ cookie = OBus_method . call m_DriveUninhibitAllPolling ( proxy daemon ) cookie |
let drive_set_all_spindown_timeouts daemon ~ timeout_seconds ~ options = let timeout_seconds = Int32 . of_int timeout_seconds in OBus_method . call m_DriveSetAllSpindownTimeouts ( proxy daemon ) ( timeout_seconds , options ) |
let drive_unset_all_spindown_timeouts daemon ~ cookie = OBus_method . call m_DriveUnsetAllSpindownTimeouts ( proxy daemon ) cookie |
let linux_lvm2_vgstart daemon ~ uuid ~ options = OBus_method . call m_LinuxLvm2VGStart ( proxy daemon ) ( uuid , options ) |
let linux_lvm2_vgstop daemon ~ uuid ~ options = OBus_method . call m_LinuxLvm2VGStop ( proxy daemon ) ( uuid , options ) |
let linux_lvm2_vgset_name daemon ~ uuid ~ name = OBus_method . call m_LinuxLvm2VGSetName ( proxy daemon ) ( uuid , name ) |
let linux_lvm2_vgadd_pv daemon ~ uuid ~ physical_volume ~ options = let physical_volume = OBus_proxy . path ( UDisks_device . to_proxy physical_volume ) in OBus_method . call m_LinuxLvm2VGAddPV ( proxy daemon ) ( uuid , physical_volume , options ) |
let linux_lvm2_vgremove_pv daemon ~ vg_uuid ~ pv_uuid ~ options = OBus_method . call m_LinuxLvm2VGRemovePV ( proxy daemon ) ( vg_uuid , pv_uuid , options ) |
let linux_lvm2_lvset_name daemon ~ group_uuid ~ uuid ~ name = OBus_method . call m_LinuxLvm2LVSetName ( proxy daemon ) ( group_uuid , uuid , name ) |
let linux_lvm2_lvstart daemon ~ group_uuid ~ uuid ~ options = OBus_method . call m_LinuxLvm2LVStart ( proxy daemon ) ( group_uuid , uuid , options ) |
let linux_lvm2_lvremove daemon ~ group_uuid ~ uuid ~ options = OBus_method . call m_LinuxLvm2LVRemove ( proxy daemon ) ( group_uuid , uuid , options ) |
let linux_lvm2_lvcreate daemon ~ group_uuid ~ name ~ size ~ num_stripes ~ stripe_size ~ num_mirrors ~ options ~ fstype ~ fsoptions = let num_stripes = Int32 . of_int num_stripes in let num_mirrors = Int32 . of_int num_mirrors in let % lwt ( context , created_device ) = OBus_method . call_with_... |
let linux_md_start daemon ~ components ~ options = let components = List . map ( fun c -> OBus_proxy . path ( UDisks_device . to_proxy c ) ) components in let % lwt ( context , device ) = OBus_method . call_with_context m_LinuxMdStart ( proxy daemon ) ( components , options ) in r... |
let linux_md_create daemon ~ components ~ level ~ stripe_size ~ name ~ options = let components = List . map ( fun c -> OBus_proxy . path ( UDisks_device . to_proxy c ) ) components in let % lwt ( context , device ) = OBus_method . call_with_context m_LinuxMdCreate ( proxy daemon ) (... |
let inhibit daemon = OBus_method . call m_Inhibit ( proxy daemon ) ( ) |
let uninhibit daemon ~ cookie = OBus_method . call m_Uninhibit ( proxy daemon ) cookie |
let device_added daemon = OBus_signal . map_with_context make_device ( OBus_signal . make s_DeviceAdded ( proxy daemon ) ) |
let device_removed daemon = OBus_signal . map_with_context make_device ( OBus_signal . make s_DeviceRemoved ( proxy daemon ) ) |
let device_changed daemon = OBus_signal . map_with_context make_device ( OBus_signal . make s_DeviceChanged ( proxy daemon ) ) |
let device_job_changed daemon = OBus_signal . map_with_context ( fun context ( device , job_in_progress , job_is_cancellable , job_id , job_num_tasks , job_cur_task , job_cur_task_id , job_cur_task_percentage ) -> { job_device = make_device context device ; job_in_progress = job_in_progres... |
let adapter_added daemon = OBus_signal . map_with_context make_adapter ( OBus_signal . make s_AdapterAdded ( proxy daemon ) ) |
let adapter_removed daemon = OBus_signal . map_with_context make_adapter ( OBus_signal . make s_AdapterRemoved ( proxy daemon ) ) |
let adapter_changed daemon = OBus_signal . map_with_context make_adapter ( OBus_signal . make s_AdapterChanged ( proxy daemon ) ) |
let expander_added daemon = OBus_signal . map_with_context make_expander ( OBus_signal . make s_ExpanderAdded ( proxy daemon ) ) |
let expander_removed daemon = OBus_signal . map_with_context make_expander ( OBus_signal . make s_ExpanderRemoved ( proxy daemon ) ) |
let expander_changed daemon = OBus_signal . map_with_context make_expander ( OBus_signal . make s_ExpanderChanged ( proxy daemon ) ) |
let port_added daemon = OBus_signal . map_with_context make_port ( OBus_signal . make s_PortAdded ( proxy daemon ) ) |
let port_removed daemon = OBus_signal . map_with_context make_port ( OBus_signal . make s_PortRemoved ( proxy daemon ) ) |
let port_changed daemon = OBus_signal . map_with_context make_port ( OBus_signal . make s_PortChanged ( proxy daemon ) ) |
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