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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