agat_sq_add_attributes_from_tsv.pl
DESCRIPTION
The purpose of the script is to add information from a tsv/csv file to the attributes of a gff file (9th column). e.g. an attribute looks like this in a GFF3 file: tag=value1,value2 The first line of the tsv/csv file must contain the headers (corresponding to an attribute tag in the GFF/GTF file), while the other lines contain the values (corresponding to an attribute value in the GFF/GTF file). The first column is used to synchronize information between the tsv file and the GFF/GTF file. In other words, it's used to determine which feature we're going to add attributes to. The other columns will be added as attribute in the GFF/GTF file. The header becomes the tag for the new attribute, and the value is that defined for the corresponding feature line. (If the tag already exists, we append the value only if the value doesn't already exist).
--- example ---
input.tsv:
ID annot_type1
gene1 annot_x
cds1 annot_y
input.gff:
chr1 irgsp gene 1000 2000 . + . ID=gene1
chr1 irgsp CDS 2983 3268 . + . ID=cds1
output.gff:
chr1 irgsp gene 1000 2000 . + . ID=gene1;annot_type1=annot_x
chr1 irgsp CDS 2983 3268 . + . ID=cds1;annot_type1=annot_y
--- example2 ---
input.tsv:
gene_id annot_type1
gene1 anot_x
cds1 anot_y
input gtf:
chr1 irgsp gene 1000 2000 . + . gene_id gene1;
chr1 irgsp CDS 2983 3268 . + . gene_id cds1;
output.gtf:
chr1 irgsp gene 1000 2000 . + . gene_id gene1; annot_type1 anot_x
chr1 irgsp CDS 2983 3268 . + . gene_id cds1; annot_type1 anot_y
SYNOPSIS
agat_sq_add_attributes_from_tsv.pl --gff input.gff --tsv input.tsv [ -o output.gff3 ]
agat_sq_add_attributes_from_tsv.pl --help
OPTIONS
--gff
STRING: Input GTF/GFF file.
--tsv
STRING: Input tsv file
--csv
BOLEAN: Inform the script that the tsv input file is actually a csv (coma-separated).
-v or --verbose
BOLEAN: Add verbosity
-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.