This directory contains utility scripts for format conversion and validation.

It also contains the legacy TransDecoder.LongOrfs and TransDecoder.Predict compatibility wrappers. The preferred user-facing entrypoint is pyTransdecoder, but these wrappers remain available for phase-specific workflows and older scripts.

These scripts are pure Python with no Perl dependencies:

• fasta_prot_checker.py - Validates protein FASTA files

  • Checks for start codon (M)
  • Checks for stop codon (*)
  • Detects internal stop codons

• gff3_file_to_bed.py - Converts GFF3 to BED format

  • Simple format conversion
  • Preserves strand and score information

These scripts still use Perl but will be ported to Python in future versions:

• cdna_alignment_orf_to_genome_orf.pl - Maps cDNA ORF coordinates to genome
• gtf_to_alignment_gff3.pl - Converts GTF to alignment GFF3 format
• gtf_genome_to_cdna_fasta.pl - Extracts transcript sequences from genome
• gtf_to_bed.pl - Converts GTF to BED format
• gff3_gene_to_gtf_format.pl - Converts GFF3 genes to GTF format

The PerlLib/ directory contains Perl modules required by the Perl scripts:

• Gene_obj.pm - Gene object model
• GTF_utils2.pm - GTF parsing utilities
• GFF3_utils2.pm - GFF3 parsing utilities
• Fasta_reader.pm - FASTA file parsing
• And others...

All scripts can be called directly:

# Preferred full pipeline
../pyTransdecoder -t transcripts.fa

# Legacy phase-specific wrappers
./TransDecoder.LongOrfs -t transcripts.fa
./TransDecoder.Predict -t transcripts.fa

# Python scripts
./fasta_prot_checker.py proteins.fa
./gff3_file_to_bed.py annotations.gff3 > output.bed

# Perl scripts
./gtf_to_bed.pl transcripts.gtf > output.bed
./fasta_prot_checker.pl proteins.fa

The goal is to port all Perl utilities to Python to make PyTransDecoder a completely self-contained Python package with no Perl dependencies.

Priority porting order:

1. gtf_to_bed.py - GTF to BED conversion
2. gtf_to_alignment_gff3.py - GTF to GFF3 conversion
3. gtf_genome_to_cdna_fasta.py - Transcript extraction
4. cdna_alignment_orf_to_genome_orf.py - Coordinate mapping (most complex)