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Library
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package bio_io
Module Fasta.RecordSource
A record type for FASTA files.
Overview
Example 1
If you have a fasta file something like this:
>s1 apple pie
ACTG
actgThen you would get a record something like this:
Fasta.Record.id record (* "s1" *) Fasta.Record.desc record
(* Some "apple pie" *) Fasta.Record.seq record
(* "ACTGactg" *)Example 2
If you have a fasta file something like this:
>s1
ACTG
actgThen you would get a record something like this:
Fasta.Record.id record (* "s1" *) Fasta.Record.desc record (* None *)
Fasta.Record.seq record
(* "ACTGactg" *)Example 3
To change a part of the Fasta.Record use the with_* functions. E.g.,
Fasta.Record.with_id "apple" recordwould change give you a t with the id set to "apple".
API
create ~id ~desc ~seq creates a new t. Shouldn't raise as literally any values of the correct type are accepted.
of_header_exn header returns a t from a FASTA header. May raise exceptions. Used internally for parsing FASTA files, but the code consuming the bio_io module probably won't need to use this function.
of_header header is like of_header_exn header except that it returns Or_error.t rather than raising exceptions.
to_string t returns a string representation of t ready to print to a FASTA output file.
to_string_nl t ~nl returns a string representation of t ready to print to a FASTA output file, including a trailing newline (nl) string. nl defaults to "\n".
serialize t returns the Sexp of t as a string.
equal this other returns true if all fields of two ts are the same.
id t returns the id of the t.
desc t returns the desc (description) of the t.
seq t returns the seq of the t.
seq_length t returns the length of the seq of t.
If you construct a record by hand (e.g., with create), and there are spaces or other weird characters in the sequences, they will be counted in the length. E.g.,
let r = Fasta.Record.create ~id:"apple" ~desc:None ~seq:"a a" in
assert (Int.(3 = Fasta.Record.seq_length r))with_id new_id t returns a t with new_id instead of the original id.
with_seq new_seq t returns a t with new_seq instead of the original seq.
with_desc new_desc t returns a t with new_desc instead of the original desc.