Module Biocaml_psl (.ml)

PSL files. Tested only on PSL files generated by BLAT version 34, which output psLayout version 3 files.

module Biocaml_psl:

sig

type item = {

matches : int; (* number of bases that match that aren't repeats *)

mismatches : int; (* number of bases that don't match *)

rep_matches : int; (* number of bases that match but are part of repeats *)

n_count : int; (* number of 'N' bases *)

q_num_insert : int; (* number of inserts in query *)

q_base_insert : int; (* number of bases inserted in query *)

t_num_insert : int; (* number of inserts in target *)

t_base_insert : int; (* number of bases inserted in target *)

q_name : string; (* query sequence name *)

q_strand : char; (* '+' or '-' for query strand *)

q_size : int; (* query sequence size *)

q_start : int; (* alignment start position in query *)

q_end : int; (* alignment end position in query *)

t_name : string; (* target sequence name *)

t_strand : char option; (* target strand for translated alignments *)

t_size : int; (* target sequence size *)

t_start : int; (* alignment start position in target *)

t_end : int; (* alignment end position in target *)

block_count : int; (* number of blocks in the alignment (a block contains no gaps) *)

block_sizes : int list; (* sizes of each block *)

q_starts : int list; (* starting positions of each block in query *)

t_starts : int list; (* starting positions of each block in target *)

}

module Error:

sig

type t = [ `incomplete_input of
 Biocaml_internal_utils.Pos.t * string list * string option
 | `invalid_int of Biocaml_internal_utils.Pos.t * string * string
 | `invalid_number_of_columns of Biocaml_internal_utils.Pos.t * string * int
 | `invalid_strands of Biocaml_internal_utils.Pos.t * string * string ]

end

exception Error of Error.t

val in_channel_to_item_stream  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel ->
 (item, [> Error.t ]) Biocaml_internal_utils.Result.t
 Biocaml_internal_utils.Stream.t

val in_channel_to_item_stream_exn  : ?buffer_size:int ->
 ?filename:string ->
 Pervasives.in_channel -> item Biocaml_internal_utils.Stream.t

module Transform:

sig

val string_to_item  : ?filename:string ->
 unit ->
 (string,
 (Biocaml_psl.item, [> Biocaml_psl.Error.t ]) Biocaml_internal_utils.Result.t)
 Biocaml_transform.t

end

val line_to_item  : Biocaml_internal_utils.Pos.t ->
 Biocaml_internal_utils.Line.t ->
 (item, Error.t) Biocaml_internal_utils.Result.t

S-Expressions

val item_of_sexp  : Sexplib.Sexp.t -> item

val sexp_of_item  : item -> Sexplib.Sexp.t

end