The script aims to remove from a gff file all the sequence that have a similarity over THRESHOLD with another sequence (will keep only one). This is typically useful when creating a list of mRNA to use to train abinitio gene finder. A reciprocal blast of the sequences need to have been performed prior to the use of this script in order to get the blastp input file.
agat_sp_filter_by_mrnaBlastValue.pl --gff infile.gff --blast blastfile --outfile outFile agat_sp_filter_by_mrnaBlastValue.pl --help
Input GTF/GFF file.
The list of the all-vs-all blast file (outfmt 6, blastp)
The name of the output file. By default the output is the standard output.
-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
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