readfx

ReadFX Methods

This page is incomplete and a placeholder for the methods reference. It will be updated with more details and examples.

Parsing Methods

readFQ

iterator readFQ*(path: string): FQRecord

High-level iterator for FASTA/FASTQ parsing.

• Parameters:
  • path: string - File path (use “-“ for stdin)
• Returns: FQRecord objects with string fields
• Usage: For clean, easy-to-use code with string manipulation

readFQPtr

iterator readFQPtr*(path: string): FQRecordPtr

High-performance iterator with pointer-based records.

• Parameters:
  • path: string - File path (use “-“ for stdin)
• Returns: FQRecordPtr objects with C-like pointers
• Usage: For maximum performance and low memory usage
• Note: Pointers are reused on each iteration!

readFastx

proc readFastx*[T](f: var Bufio[T], r: var FQRecord): bool

Low-level procedure for custom parsing workflows.

• Parameters:
  • f: var Bufio[T] - Buffered input stream
  • r: var FQRecord - Record to populate
• Returns: Boolean indicating success
• Usage: For integration with custom I/O workflows

File Handling Utilities

xopen

proc xopen*[T](fn: string, mode: FileMode = fmRead, sz: int = 0x10000): Bufio[T]

Opens a file with buffered I/O.

• Parameters:
  • fn: string - File path
  • mode: FileMode - File mode (default: fmRead)
  • sz: int - Buffer size (default: 0x10000)
• Returns: Bufio object

open

proc open*[T](f: var Bufio[T], fn: string, mode: FileMode = fmRead, sz: int = 0x10000): int

Opens a file for buffered I/O.

• Parameters: Same as xopen
• Returns: Status code (0 for success)

close

proc close*[T](f: var Bufio[T]): int

Closes a buffered I/O handle.

• Parameters:
  • f: var Bufio[T] - File handle to close
• Returns: Status code

Sequence Manipulation Functions

reverseComplement

proc reverseComplement*(sequence: string): string

Reverse complements a DNA sequence.

• Parameters:
  • sequence: string - Input DNA sequence
• Returns: Reverse complemented sequence
• Example: reverseComplement("ATGC") returns “GCAT”

reverseComplementRecord (in-place)

proc reverseComplementRecord*(record: var FQRecord)

Reverse complements a sequence record in place.

• Parameters:
  • record: var FQRecord - Record to modify
• Note: Modifies the record in place, also reversing quality if present

reverseComplementRecord (copy)

proc reverseComplementRecord*(record: FQRecord): FQRecord

Creates a new record with reverse-complemented sequence.

• Parameters:
  • record: FQRecord - Input record
• Returns: New FQRecord with reverse-complemented sequence

gcContent

proc gcContent*(sequence: string): float

Calculates GC content of a DNA sequence.

• Parameters:
  • sequence: string - DNA sequence
• Returns: GC content as a fraction between 0.0 and 1.0

Quality-Based Operations

trimQuality

proc trimQuality*(quality: string, minQual: int, offset: int = 33): string

Trims a quality string based on minimum quality threshold.

• Parameters:
  • quality: string - Quality string
  • minQual: int - Minimum quality value (0-40)
  • offset: int - Quality score offset (default: 33)
• Returns: Trimmed quality string

qualityTrim

proc qualityTrim*(record: var FQRecord, minQual: int, offset: int = 33)

Trims a record based on quality scores.

• Parameters:
  • record: var FQRecord - Record to modify
  • minQual: int - Minimum quality value
  • offset: int - Quality score offset (default: 33)
• Note: Modifies both sequence and quality in place

maskLowQuality

proc maskLowQuality*(record: var FQRecord, minQual: int, offset: int = 33, maskChar: char = 'N')

Masks sequence positions with low quality scores.

• Parameters:
  • record: var FQRecord - Record to modify
  • minQual: int - Minimum quality value
  • offset: int - Quality score offset (default: 33)
  • maskChar: char - Character to use for masking (default: ‘N’)

Record Manipulation

subSequence

proc subSequence*(record: FQRecord, start: int, length: int = -1): FQRecord

Extracts a subsequence from a record.

• Parameters:
  • record: FQRecord - Input record
  • start: int - Start position (0-based)
  • length: int - Length to extract (-1 for end of sequence)
• Returns: New FQRecord with extracted subsequence

$ (string representation)

proc `$`*(rec: FQRecord): string
proc `$`*(rec: FQRecordPtr): string 

Converts records to string representation in FASTA/FASTQ format.

• Parameters:
  • rec: FQRecord/FQRecordPtr - Record to convert
• Returns: String in FASTA or FASTQ format based on record content

Other Utilities

Interval Operations

type Interval*[S,T] = tuple[st, en: S, data: T, max: S]
proc sort*[S,T](a: var seq[Interval[S,T]])
proc index*[S,T](a: var seq[Interval[S,T]]): int
iterator overlap*[S,T](a: seq[Interval[S,T]], st: S, en: S): Interval[S,T]

Interval tree implementation for genomic intervals.

• Usage: For interval overlap queries in genomic data

Usage Examples

Basic Parsing

import readfx

# Using readFQ (string-based)
for record in readFQ("sample.fastq.gz"):
  echo record.name, " has length ", record.sequence.len
  
# Using readFQPtr (pointer-based)
for record in readFQPtr("sample.fastq.gz"):
  echo $record.name, " has length ", len($record.sequence)

# Using readFastx (low-level)
var record: FQRecord
var f = xopen[GzFile]("sample.fastq.gz")
defer: f.close()
while f.readFastx(record):
  echo record.name, " has length ", record.sequence.len

Record Manipulation

# GC content calculation
let gc = gcContent(record.sequence)

# Reverse complement
let rcSeq = reverseComplement(record.sequence)
let rcRecord = reverseComplementRecord(record)

# Quality trimming
qualityTrim(record, 20)  # Trim bases with quality < 20

# Masking low quality bases
maskLowQuality(record, 20)  # Mask bases with quality < 20 as 'N'

# Extract subsequence
let firstTenBases = subSequence(record, 0, 10)

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