FastQ format |
📂View module documentation |
This module allows to parse FASTQ format data with original 4-lines entries into this record type
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To be able to use this parser you need to define two converter functions, one example for each you can also find in our module, but you also may need to write your own.
We can convert sequence string to predefined option type of Amino Acids, using converter function from our library 'BioFSharp.BioItemsConverter.OptionConverter'
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If you have following possible values for quality sequence: '!""#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[]^_`abcdefghijklmnopqrstuvwxyz{|}~', with Sanger format, that can encode a Phred quality score from 0 to 93 using ASCII 33 to 126, then you can use our converting function:
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And then you can easily use this module to read your FastQ file
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{ Header: string
Sequence: 'a
QualityHeader: string
QualitySequence: 'b }
FastqItem record contains header, sequence, qualityheader, qualitysequence of one entry
val string : value:'T -> string
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type string = String
get characters as sequence units
val string : string
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type string = String
type String =
new : value:char[] -> string + 8 overloads
member Chars : int -> char
member Clone : unit -> obj
member CompareTo : value:obj -> int + 1 overload
member Contains : value:string -> bool + 3 overloads
member CopyTo : sourceIndex:int * destination:char[] * destinationIndex:int * count:int -> unit
member EndsWith : value:string -> bool + 3 overloads
member EnumerateRunes : unit -> StringRuneEnumerator
member Equals : obj:obj -> bool + 2 overloads
member GetEnumerator : unit -> CharEnumerator
...
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String(value: char []) : String
String(value: nativeptr<char>) : String
String(value: nativeptr<sbyte>) : String
String(value: ReadOnlySpan<char>) : String
String(c: char, count: int) : String
String(value: char [], startIndex: int, length: int) : String
String(value: nativeptr<char>, startIndex: int, length: int) : String
String(value: nativeptr<sbyte>, startIndex: int, length: int) : String
String(value: nativeptr<sbyte>, startIndex: int, length: int, enc: Text.Encoding) : String
member Clone : unit -> obj
member CopyTo : array:Array * index:int -> unit + 1 overload
member GetEnumerator : unit -> IEnumerator
member GetLength : dimension:int -> int
member GetLongLength : dimension:int -> int64
member GetLowerBound : dimension:int -> int
member GetUpperBound : dimension:int -> int
member GetValue : [<ParamArray>] indices:int[] -> obj + 7 overloads
member Initialize : unit -> unit
member IsFixedSize : bool
...
from BioFSharp
from BioFSharp.BioItemsConverter
get Phred quality score
from BioFSharp.IO