agat_sp_alignment_output_style.pl

DESCRIPTION

The script takes a normal gtf/gff annotation format file and convert it to gff3 alignment format. It means it add a structure of match / match_part as relationship between the different features.

SYNOPSIS

agat_sp_alignment_output_style.pl -g infile.gff [ -o outfile ]
agat_sp_alignment_output_style.pl --help

OPTIONS

• -g, --gff or -ref

  Input GTF/GFF file.

• -c or --ct

  When the gff file provided is not correcly formated and features are linked to each other by a comon tag (by default locus_tag), this tag can be provided to parse the file correctly.

• -v

  Verbose option to see the warning messages when parsing the gff file.

• -o or --output

  Output GFF file. If no output file is specified, the output will be written to STDOUT.

• -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).

• -h or --help

  Display this helpful text.