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gmod_extract_dbxref_from_gff.pl - Extracts Dbxrefs from GFF3 lines that have Target


% gmod_extract_dbxref_from_gff.pl gff_file_name > output_file


For GFF3 lines of the form:

chr1 CDNA cDNA_match 69388 69593 0 - . Dbxref=Sorghum_CDNA:Contig_448;Target=Contig_448 75 295 +

that is, that have both Target and Dbxref attributes, this script extracts the Dbxref
value and prints out a list of the database and accession parts of the Dbxref value. This
functionality depends on a standard format for the Dbxref value, one where the name of the
database preceeds the accession and are separated by a colon.

Another script, gmod_make_gff_from_dbxref.pl, takes a list of databases and accessions
(like this script provides) and a directory of FASTA files and builds a GFF3 file that
corresponds to those targets. The use for these files is to load them into Chado before
that compuational analysis results are loaded to ensure that the database has a complete
picture of the analysis performed.



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