qualfa2fq-pl

name	qualfa2fq-pl
description	Use when merging a legacy FASTA file and matching QUAL file into FASTQ, including `.gz` inputs, before downstream alignment or QC steps.
disable-model-invocation	true
user-invocable	true

qualfa2fq-pl

Quick Start

• Command: qualfa2fq.pl reads.fa reads.qual > reads.fastq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/qualfa2fq.pl
• Inputs: exactly two files, FASTA first and QUAL second; .gz suffixes are supported

When To Use This Tool

• Convert paired FASTA + QUAL inputs into FASTQ.
• Rescue older sequencing datasets that still store bases and qualities in separate files.
• Stay in a tiny shell / Perl workflow instead of writing a custom converter.
• Prepare legacy reads for aligners or QC tools that expect FASTQ.

Common Patterns

# 1) Basic conversion
qualfa2fq.pl reads.fa reads.qual > reads.fastq

# 2) Gzipped inputs are handled automatically by filename suffix
qualfa2fq.pl reads.fa.gz reads.qual.gz > reads.fastq

# 3) Validate the first record after conversion
qualfa2fq.pl reads.fa reads.qual | sed -n '1,8p'

Recommended Workflow

1. Confirm that the FASTA and QUAL files contain the same records in the same order.
2. Run the converter and redirect stdout to a FASTQ file or immediate downstream consumer.
3. Spot-check the first few records to confirm sequence lengths and quality lengths still match.
4. Run a normal FASTQ-aware validator or QC tool before using the output in a larger pipeline.

Guardrails

• The script requires exactly two positional arguments and has no real --help or --version interface beyond the usage error path.
• FASTA and QUAL records are consumed in lockstep, but the script does not verify matching record IDs; mismatched order silently corrupts the output.
• Quality integers are converted with chr(score + 33) and are not range-checked.
• The converter writes to stdout.
• .gz handling is suffix-based; compressed files without a .gz name will not be auto-decompressed.
• Sequence formatting is preserved from the FASTA record, while qualities are wrapped at 60 characters, so pre-wrapped FASTA input can produce non-canonical multi-line FASTQ records.