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ReadFX: A Nim library for bioinformatics sequence file parsing

This module provides efficient parsing and manipulation of FASTA/FASTQ format sequence files commonly used in bioinformatics.

Features:

• Fast FASTA/FASTQ sequence parsing (supports gzipped files)
• Buffered I/O for efficient file reading
• Interval tree implementation for genomic interval operations

Example:

import readfx

# Read a FASTQ file
for record in readFQ("sample.fastq.gz"):
  echo "Sequence name: ", record.name
  echo "Sequence: ", record.sequence
  echo "Quality: ", record.quality

Iterator for reading FASTQ files, returning pointers to record data

Note: The pointers are reused between iterations, so don't store them. For stdin input, use "-" as the path parameter.

Args: path: Path to the FASTQ file (supports gzipped files)

Returns: An iterator yielding FQRecordPtr objects

Example:

for rec in readFQPtr("sample.fastq.gz"):
  echo $rec.name
  echo $rec.sequence

Iterator for reading FASTQ files, returning copies of record data

This iterator creates copies of the strings, unlike readFQPtr which returns pointers to the underlying data.

Args: path: Path to the FASTQ file (supports gzipped files)

Returns: An iterator yielding FQRecord objects with copied data

Example:

for rec in readFQ("sample.fastq.gz"):
  echo rec.name
  echo rec.sequence

Iterator for reading paired-end FASTQ files synchronously

Reads two FASTQ files in parallel, yielding pairs of corresponding records. The files must have the same number of sequences in the same order.

Args: path1: Path to the first FASTQ file (R1, forward reads) path2: Path to the second FASTQ file (R2, reverse reads) checkNames: Whether to verify that read names match (default: false)

Returns: An iterator yielding FQPair objects with synchronized reads

Raises: IOError: If files cannot be opened or have mismatched lengths ValueError: If checkNames is true and read names don't match

Example:

for pair in readFQPair("sample_R1.fastq.gz", "sample_R2.fastq.gz"):
  echo "Forward: ", pair.read1.name
  echo "Reverse: ", pair.read2.name
  processReadPair(pair.read1.sequence, pair.read2.sequence)

Formats a sequence record as a FASTA or FASTQ string

Args: name: Sequence name/identifier comment: Sequence comment (optional) sequence: The sequence string quality: Quality scores (empty for FASTA format)

Returns: Formatted FASTA/FASTQ string

Print FASTA record splitting the sequence into lines of N characters Returns: Formatted FASTA stringPrint FASTA record splitting the sequence into lines of N characters Returns: Formatted FASTA stringReturns: Formatted FASTA/FASTQ string

Convert a FQRecordPtr to a string (FASTA or FASTQ format)

Returns: Formatted FASTA/FASTQ string