agat_sp_filter_record_by_coordinates.pl

DESCRIPTION

The script aims to filter the records to keep only those contained within coordinates defined in an input csv file. A record can be a feature or a set of features with part-of relationships. By default we keep records overlapping the coordinates. The --exclude parameter allows to keep only record fully contained within the coordinates.

! With default paramater, an exon out of the coordinates can be kept if the gene it is part of is overlaping the coordinates.

SYNOPSIS

agat_sp_filter_record_by_coordinates.pl --gff infile.gff --tsv coordinates.tsv [ --output outfile ]
agat_sp_filter_record_by_coordinates.pl --help

OPTIONS

• -i, --input, --gtf or --gff

  Input GTF/GFF file

• --coordinates, --tsv, -r or --ranges

  String - tsv file containing the coordinates. Coordinates must be one per line. Each line must contain 3 fields separated by a tabulation. Field1 is the sequence id Field2 is the start coordinate (included) Field3 is the end coordinate (included)

• -e or --exclude

  Select only the features fully containined within the coordinates, exclude the overlapping ones.

• -o or --output

  Output folder.

• -v or --verbose

  Verbosity.

• -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.