package biocaml
Install
Dune Dependency
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doc/biocaml.unix/Biocaml_unix/Bed/index.html
Module Biocaml_unix.Bed
BED data files.
A BED file is in the format shown below, where columns must be separated by a tab character.
chrA lo1 hi1 chrA lo2 hi2 . . . . . . . . . chrB lo1 hi1 chrB lo2 hi2 . . . . . . . . .
The definition is that intervals are zero based and half-open. So by default the line "chrA lo hi" is parsed to the interval [lo + 1, hi] on chromosome chrA. Similarly, when printing, the default is to print [lo - 1, hi]. The optional argument increment_lo_hi allows changing this behavior for non-conformant files. In addition, the optional argument chr_map is a string -> string function that allows changing of the chromosome name to a specified format, and defaults to identity.
Some tools require that the set of intervals do not overlap within each chromosome. This is not enforced, but you can use any_overlap to verify this property when needed.
Item Types
type item = string * int * int * Table.Row.tThe type of BED data stream items.
Tags: Describe The Format: TODO
The specification of how to parse the remaining columns.
Error Types
module Error : sig ... endDefinitions of error types (with sexp)
In_channel Functions
exception Error of Error.tThe exception raised by the *_exn functions.
val in_channel_to_item_stream :
?buffer_size:int ->
?more_columns:parsing_spec ->
Core_kernel.In_channel.t ->
(item, [> Error.parsing ]) Core_kernel.result Stream.tParse an input-channel into item values.
val in_channel_to_item_stream_exn :
?buffer_size:int ->
?more_columns:parsing_spec ->
Core_kernel.In_channel.t ->
item Stream.tLike in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).
Conversions to/from Line.t
See also Line.t.
val item_of_line :
how:parsing_spec ->
Lines.item ->
(item, [> Error.parsing ]) Core_kernel.resultBasic parsing of a single line.
val item_to_line : item -> Lines.itemBasic “printing” of one single item.
Transforms
module Transform : sig ... endLower-level transforms of BED data-streams.
S-Expressions
val item_of_sexp : Sexplib.Sexp.t -> itemval sexp_of_item : item -> Sexplib.Sexp.tval parsing_spec_of_sexp : Sexplib.Sexp.t -> parsing_specval sexp_of_parsing_spec : parsing_spec -> Sexplib.Sexp.t