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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.