NAME¶
gmod_extract_dbxref_from_gff.pl - Extracts Dbxrefs from GFF3 lines that have
Target attributes
SYNOPSIS¶
% gmod_extract_dbxref_from_gff.pl gff_file_name > output_file
DESCRIPTION¶
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.
Rationale¶
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.
COMMAND-LINE OPTIONS¶
None.
AUTHOR¶
Scott Cain <cain@cshl.org>
Copyright (c) 2007
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself.