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agat_sq_rfam_analyzer.pl#

DESCRIPTION#

The script allows to generate a tabulated format report of rfam-id annotated from a gff file containing rfam results (type of the 3rd column must be ncRNA or nc_RNA - not case sensitive. And the 9th column must contain the rfam-id attribute). e.g: ScG6Pog_82 Rfam ncRNA 737595 737663 20.7 + 0 ID=RF00134_ScG6Pog_82_737595;Name=RF00134_ScG6Pog_82_737595;evalue=0.45;gc-content=0.28;model_end=1;model_start=1;rfam-acc=RF00134;rfam-id=snoZ196 ScG6Pog_82 Rfam ncRNA 305023 305103 20.8 + 0 ID=RF00227_ScG6Pog_82_305023;Name=RF00227_ScG6Pog_82_305023;evalue=0.35;gc-content=0.31;model_end=1;model_start=1;rfam-acc=RF00227;rfam-id=FIE3

SYNOPSIS#

agat_sq_rfam_analyzer.pl -i <input file> [-g <integer or fasta> -o <output file>]
agat_sq_rfam_analyzer.pl --help

OPTIONS#

  • -i, --gff, --file or --input

    STRING: Input GTF/GFF file(s). Several files can be processed at once: -i file1 -i file2

  • -g, --genome

    That input is design to know the genome size in order to calculate the percentage of the genome represented by each kind of rfam-id. You can provide an INTEGER or the genome in fasta format. If you provide the fasta, the genome size will be calculated on the fly.

  • -o or --output

    STRING: Output file. If no output file is specified, the output will be written to STDOUT. The result is in tabulate format.

  • -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.