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.