The script aims to add info from a tsv/csv file to the attributes of a gff file. An attribute looks like that: tag=value1,value2 The first line of the tsv/csv must contains the headers, the other lines contain the values. The header becomes the tag of the new attribute. If the tag already exists, the value will be added only if the value does not already exists. The first column does not become an attribute, indeed it must contain the feature ID that will be used to know to which feature we will add the attributes.
--- 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
agat_sq_add_attributes_from_tsv.pl --gff input.gff --tsv input.tsv [ -o output.gff3 ]
agat_sq_add_attributes_from_tsv.pl --help
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--gff
STRING: Input GTF/GFF file.
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--tsv
STRING: Input tsv file
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--csv
BOLEAN: Inform the script that the tsv input file is actually a csv (coma-separated).
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-v or --verbose
BOLEAN: Add verbosity
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-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.
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--help or -h
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