agat_sp_add_start_and_stop.pl.pl#

DESCRIPTION#

The script adds start and stop codons when a CDS feature exists. The script looks at the nucleotide sequence and checks the presence of start and stop codons. The script works even if the start or stop codon are split over several CDS features.

SYNOPSIS#

agat_sp_add_start_and_stop.pl.pl --gff infile.gff --fasta genome.fa --out outfile.gff
agat_sp_add_start_and_stop.pl.pl --help

OPTIONS#

• --gff, -i or -g

  Input GTF/GFF file.

• --fasta, --fa or -f

  Input fasta file. Needed to check that CDS sequences start by start codon and stop by stop codon.

• --ct, --codon or --table

  Codon table to use. [default 1]

• --out, --output or -o

  Output gff file updated

• -e or --extend

  Boolean - When no start/stop codon found, try to extend the CDS to meet the next start/stop codon in the sequence.

• --ni or --na

  Boolean - no iupac / no ambiguous, avoid usage of IUPAC. By default IUPAC is used that means, NNN is seen as start and/or stop codon.

• -v

  Verbose for debugging purpose.

• -c or --config

  String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

• --help or -h

  Display this helpful text.